Palmer 1985

ANNUAL
REVIEWS
Further
Quick links to online content

1985. 19:325-354
1985 by Annual Reviews Inc.
Ann. Rev. Genet.

Copyright
All rights reserved
COMPARATIVE ORGANIZATION OF
Annu. Rev. Genet. 1985.19:325-354. Downloaded from www.annualreviews.org
Access provided by Laurentian University on 12/09/14. For personal use only.
CHLOROPLAST GENOMES
Jeffrey D. Palmer
Division of Biological Sciences, University of Michigan, Ann Arbor, Michigan 48109
CONTENTS
INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
325
DIVERSITY OF CHLOROPLAST DNA ARRANGEMENTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
326
326
329
332
335
335
341
343
343
343
345
345
346
Genome Size and Conformation . . . . . . . . . . . . . .. . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Repeated Sequences . . . . ... . . . . . . . . . . ... . . . . . . . . . .. . . . . . . . . . . . ... . . . . . . . . . . .... . . . . . . . . . . . ... . . . . .
Gene Content. Order. and Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
EVOLUTIONARY TRENDS IN CHLOROPLAST GENOME ORGANIZATION . . . . . . .

Land Plants . . . ...... . . . . . . . . .... . . . . . . . . . ......... . . . . . . . . ... . . . . . . .. . . . . . . . . . . . . . . .. . . . . . . . . . . . . . .
Chlamydomonas.. . . . . . . . . . .. . ... . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . ... . . . . . . . . . . .... . . . . . . . . . . . . .. . .
Euglena gracilis ...................................................................................
INDUCED ALTERATIONS IN CHLOROPLAST GENOME STRUCTURE . . . . . . . . . . . . .

Chlamydomonas reinhardtii . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Euglena gracilis . . . . . . . . . . . . . .. ... . . . . . . . .. ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . .
Angiosperms .. ... . . . . . . . . . . . ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
CONCLUDING REMARKS . . . . . . . . . . . . .
.............
.............
INTRODUCTION
The recognition , just over 20 years ago , that chloroplasts contain their own
unique DNA species has led to intensive study of the structure and organization
of chloroplast genomes, and of the identity, sequence properties, and modes of
expression of their constituent genes. This article is concerned with how
chloroplast DNA (cpDNA) molecules are structured and organized among
different land plants and algae, and what the mutational processes are that lead
to evolutionary changes in chloroplast genome architecture . I consider specific
chloroplast genes only from a structural standpoint, in terms of their arrange
ment on the chloroplast chromosome and transcriptional organization . Readers
325
0066-4197/85 /1215 -0325 $02. 00
326
PALMER

interested in the sequence and expression of chloroplast genes are referred to

several recent reviews (6, 8, 14, 14a, 15, 32, 7 3, 130).
The first part of this review is a broad survey of chloroplast genome organiza
tion among major p hyletic lines of eukaryotic algae and land plants . I then
present an in-depth description of the types of structural variation , and of the
underlying mutational processes responsible for this variation , found among
the only three intensively studied groups of chloroplast genomes . Finally , I
describe briefly the alterations in cpDNA structure that have been induced by
mutagenic treatment and cultural manipulation.
DIVERSITY OF CHLOROPLAST DNA ARRANGEMENTS

The structural variation described in this and the following section is, in all
cases, the result of evolutionary change rather than alterations that occur during
plastid development and differentiation. Among multicellular land plants,
w here the greatest diversity of plastid types is found, no differences have been
found in the size and structure of DNA isolated from mesophyll and bundle
sheath chloroplasts of the C4 plant Pan icum maximum (125), from chromo
plasts and chloroplasts of daffodil ( 117 ) and nasturtium ( 118), and from
amyloplasts and c hloroplasts of potato ( 102).
Genome Size and Conformation

Almost all cpDNAs examined fall into a rather restricted s ize range of between
120 kilobase pairs (kb) and 160 kb (Table 1). This is true for all but three (see
section on land plants , below) of well over 200 species of angiosperms ex
amined, seve ral diverse nonangiospermous land plants, and repres entatives of
several major l ineages of algae. Only among green algae does one encounter a
wide range of cpDNA sizes. Greater than three-fold s ize variation , from 85 kb
to 292 kb, is found among those green algal cpDNAs whose c ircularity has been
establis hed by electron microscopy and restriction mapping (Table 1 ). More
over, the cpDNAs of two species in the green algal genus Aceta bularia have
been estimated to have a kinetic complexity of roughly 2000 kb ( 38, 7 1 ).
Consistent with these estimates are the ability to isolate Ace ta bularia cpDNA in
the form of extremely large (up to 600 kb) l inear molecules as determined by
electron microscopy ( 36, 62), and the highly complex patterns revealed by
restriction fragment analysis ( 121).
The above findings promote several speculations . The highly uniform s ize of
cpDNAs from almost all major l ineages of plants and algae suggests the
possibility that selection maintains a fairly restricted chloroplast genome size,
especially w hen viewed against the fairly random and large-scale s ize variation
found among both mitochondrial (7 3, 104, 126) and nuclear ( 26) genomes.
That almost all cpDNAs are about the same size, at least 20-30 times smaller
CHLOROPLAST DNA ORGANIZATION
Table 1
327
Size and structure of chloroplast DNAs

Reference
Conformation
Repeat
size (kb)a
Unicircular
1 0-76
Footnote b
Unicircular
17
Footnote c
144
ISO
ISO
Unicircular
Unicircular
U nicircular
10
nd
nd
81
45
45
121
125
Unicircular
Unicircular
11
nd
69
45
85
174
1 95
199
243
292
ca. 200
ca. 2000
ca. 2000
Unicircular
U nicircular
Unicircular
Unicircular
Unicircular
Unieireular
nd
nd
nd
nd
23
22
23
20
41
nd
10
nd
41
1 36
92
74
59
58e
108
38, 121
36, 7 1
1 23
1 25
1 27
1 3CJ-. 152
140
150
1 54
Unicircular
Unicircular
U nicircular
U nicircular
Multicircular
Multicircular
Unicircular
nd
nd
10
6
nd
nd
22
57a
45
5
5 3 , 1 33
16
16
I, Footnote d
Genome
size (kb)
Taxa
1 20-2 1 7
Angiosperms
(230 species, 90 genera, 33 families)
Gymnosperms
158
Ginkgo biloba
Ferns

Osmunda cinnamomea
Asplenium nidus
Pteris vittata
Bryophytes
Marchantia polymorpha
Sphaerocarpus donnellii
Green Algae
Codium fragile
Chlorella ellipsoidea
Chlamydomonas reinhardtii
Chlamydomonas smithii
Chlamydomonas eugametos
Chlamydomonas moewusii
Polytoma obtusum
Acetabularia mediterranea
Acetabularia cliftonia
Other Algae
Dictyota dichotoma
Vaucheria sessilis
Cyanophora paradoxa
Euglena gracilis
Plylaiella littorali
Sphacelaria sp.
Olisthodiscus lute us
'Only those repeats larger than I kb are cited. All repeats are inverted except for tandem repeats in Euglena and
Ace/abularia.
bData summarized from tables in
(6,
14a,
32, 73,
data).
13(1) and from J. Palmer and
W.
Thompson (unpublished
'J. Palmer, D. Stein (unpublished data).
dM. Reith, R. Cattolico (unpublished data).
than the genomes of their prokaryotic ancestors (e. g. cyanobacteria and Pro
chloron), sugg ests that most of the e volutionary reduction in chloroplast
genome size took place during a relatively short period soon after their
34,35 , 73). If this inference is true, then the

in
size [as is the case for the similarly large mitochondrial genomes found in
certain cucurbit species (126)] rather than the retention of a primordially large
genome. Consistent with this speculation is the observation that chloroplasts
endosymbiotic origin (reviewed in
larger genome size in Acetabularia is likely the result of secondary increases

328
PALMER
from Acetabularia and angiosperms synthesize much the same pattern of

proteins (37). Finally, the reduced genome size ( 85 kb) in Codiumfragile (41)
may indicate a reduced gene content. Alternatively, it may reflect a more tightly
packed gene arrangement, with fewer and smaller s pacers , introns, and un
translated flanking sequen ces .
Almost all cpDNAs that have been carefully examined by electron micros
copy and restriction mapping exist as a single, more or less homogeneous, size
class of circular molecules (Figure 1 ; Table 1 ) . A small proportion of these
molecules exist as circular dimers (57; see next section) . A more complex
situation appears to pertain for cpDNA from two species of brown algae,
psaA 1 psaA2
\ I psbC
t E
atPSP
' -psbD
,bel -
tuf A
petA
psbE
psbB
petS
petD
rps 19'p12-
psbA
'pl2
o,,
psbA
23S
168
CHLAMYDOMONAS
___
psbA
REINHARDTII
195 kb
23S
168
psbC
OLiSTHODI8CUS
lUTEUS
rRNA
154 kb
rRNA

329
Plylaiella littorali and Sphacelaria sp. This DNA is visualized in the electron
microscope as a collection of different-sized circles, none of which alone can
accommodate the entire array of fragments produced upon restriction endonu
clease digestion (Table 1; 16). These findings , which clearly need confirmation
by restriction mapping, suggest that these two brown algal chloroplast genomes
may exist as a heterogeneous population of different-sized circles, perhaps in a
fashion similar to the multicircular genomes found in plant mitochondria (60,
78). Note , however, that the only brown algal genome , from Dictyota di
chotoma, for which a complete restriction map has been established, exists as a
single, homogeneous s ize class of circular molecules (S7a).
Repeated Sequences
Chloroplast genomes generally have few repeated sequences. However, those
they do possess often dominate the landscape of the genome and are associated
with interesting recombinational and evolutionary properties . Aside from short
repeated sequences of less than 100 bp, which have been described in a number
of sequencing s tudies, only five repeat families have been found in chloroplast
genomes. One of these is organized as a two-copy inve rted repeat, two as
tandem repeats , and two as dispersed repeats. The most widespread of these is a
Figure 1
Physical and gene maps of cpDNAs representing six major lines of chloroplast
evolution. Heavy lines centered on the circles indicate the extent of major repeat elements in the
genomes. Only one of two genome orientations is shown for the four cpDNAs that contain a large
inverted repeat (see text). Filled boxes indicate the location of exon sequences and open boxes the
location of introns for all mapped genes encoding ribosomal RNAs and proteins. Transfer RNA
genes are not shown. Arrows indicate direction of transcription. Asterisks indicate genes whose
positions have been imprecisely or ambiguously assigned by heterologous filter hybridizations.
Filled triangles indicate the positions of replication origins (designated either ori or oriA and oriB) .
Gene designations: rbcL and rbcS-genes for the large and small subunits, respectively, of RuBP
carboxylase; atpA , atpB, atpE, atpF, mpH-genes for the alpha, beta, epsilon, CFo-I, and
proton-translocating subunits, respectively, of coupling factor; psaAl and psaA2-genes for the
two P700 chlorophyll a apoproteins of photosystem I; psbA, psbB, psbC, psbD, andpsbE-genes
for the Q-beta ("32 kd", "herbicide-binding"), 51-kd chlorophyll a-binding, 44-kd chlorophyll
a-binding,"D2",and cytochrome b-559 components,respectively, of photo system II;petA, petB,
petD-genes for the cytochrome f,cytochrome b6. and subunit 4 components,respectively,of the
cytochrome b6-f complex; tufA -gene for elongation factor EF-Tu; rpl 2, rps7, rpsl2, and
rps 19-genes for putative chloroplast ribosomal proteins homologous to E. coli ribosomal proteins
L2, S7, S12, and S19, respectively; ppcA and ppcB-genes for the alpha and beta subunits,
respectively,of phycocyanin; papA andpa pB-genes for the alpha and beta subunits,respectively,
of allophycocyanin. Spinach (Spinacia oleracea) data are from (3, 127, 128, 137); pea (Pisum
sativum) data are from (85,89,127; J. Gray,T. A. Dyer,D. L. Willey,G. R. M. Courtice,T. M .

Bowman, et ai,unpublished data; J . Palmer, W. Thompson, unpublished data); Chlamydomonas
reinhardtii data are from (92, 94, 100, 132; J. D. Rochaux, M. Spierer-Herz,C. Kovacic, M .
Schneider,M . Dron, U . Kiick, unpublished data); Euglena gracilis data are from (39); Cyanophora
paradoxa data are from (5, Ila, 58, 58a, 110; H. Bohnert, unpublished data); and Olisthodiscus
luteus data are from (M. Reith, R. Cattolico, unpublished data).
330
PALMER

large ( 10-76 kb) inverted duplication found in cpDNAs from almost all land
plants and from several major lineages of al gae (Figures 1 and 2; Table 1 ) .
Large tandem repeats have been described in two algal species. Acetabularia
mediterranea contains at least five copies of a l O-kb tandem repeat that does not
encode the rRNA genes (121) , and Euglena gra cilis contains between one and
five tandemly arrayed copies of a 6. 2-kb repeat encoding a complete set of
rRNA genes (Figure 1 ; 53, 5 6 , 9 1 , 133). Families of dispersed repeats have
been found in Chlamydomonas reinhardtii (29 , 9 2, 95) and C. smith ii (74) ,
which contain 25 -40 short ( 100-300 bp) inverted repeats dispersed throughout
SPINACH
c,165235 235165
LETTUCE
165 235
235 165 ...Q-""

q
23
L..-....---J
kb inversion
'< QO
WHEAT
'f}'f}
165 235 235 163 q QQ
Figure 2
25 kb
inversion
Inversions in angiosperm cpDNAs. Note that the mung bean inversion is shared by all 1 2
genera examined i n the Fabaceae (75, 80, 83; J . Palmer, W. Thompson, unpublished data), the
lettuce inversion by 34 of 35 genera examined in the Asteraceae (B . Jansen, J. Palmer, unpublished
data), and at least one, if not both, of the wheat inversions by 3 genera examined in the Poaceae (83,
88). As indicated, an inversion in the same approximate lucatiun as the mung bean change is also
found in Oenothera (46), but these are clearly two independent mutations since other genera
(Epilobium: U . Schmitz, R. Herrmann , unpublished data; Clarkia: K. Sytsma, L. Gottlieb,
unpublished data; Fuchsia: J. Palmer, W. Thompson, unpublished data) in the same family
(Onagraceae) as Oenothera have the primitive gene order found in spinach. Spinach (Spinacia
oleracea) data are from (3, 1 27 , 128, 1 37); mung bean (Vigna radiata) data are from (75 , 1 27; J .
Palmer, W . Thompson, unpublished data); lettuce (Lactuca sativa) data are from (57; B . Jansen, J .
Palmer, unpublished data); and wheat (Triticum aestivum) data are from ( 3 a , 1 3 1 ; J . Gray, T. Dyer,
G. Courtice, S. Hind, P. Nixon, ct ai, unpublished data).

331
the genome, and in subclover (Trifolium subterra neum), w hich contains at least
five copies of a 200-1000-bp repeat dispersed throughout at least a quarter of
the genome (J. Palmer, W . Thompson, unpublished data). Structural rear
rangements associated with these last three families (from Eugle na , Chlamydo
monas, and subclover) are discussed in later sections dealing specifically with
these and related organisms .
Although the large inverted repeats in the cpDNAs of land plants and algae
all contain a complete set of rRNA genes (Figures I and 2; see references to
Table 1) , this fact should not be taken to imply a single common origin for this
repeat in these very diverse phyletic lines. However, several other features are
common to the inverted repeat of land plants . These include its asymmetric
position (dividing the genome into small and large single-copy regions of
average size 20 kb and 80 kb) , location relative to such flankin g genes as psbA,
and rRNA gene transcriptional orientation [always towards the small single
copy region; see Figure 4 for one exception (geranium) to this rule] (Figure 2 ;
see references in Table 1) . This constellation of shared c haracters suggests that
the inverted repeat was present in the common ancestor of land plants.
In contrast, aside from the presence of the rRNA genes, there are no features
common to the inverted repeats of land plants and various groups of algae
(Fi gure 1; 58b, 58c, 5 9, 136) . Large differences are apparent in the positioning
of the repeat segments (almost 1800 apart in Chlamydomonas. much closer
together in land plants and Cya noph ora, and an intermediate distance apart in
Olisthodiscus; Figure 1; 5 9) and in the gene content of the repeat (cfrpI2, psbA ,
rbcL, and rbcS locations in Figure 1). Given the overall differences in organiza
tion of these genomes (Figure 1; see next section) and the ability of the inverted
repeat to spread and shrink in size (see the section below on land plants) , it is
certainly possible that these repeats are of a single common origin but are highly
altered in present structure owing to subsequent rearrangement. On the other
hand, there is good reason to think that certain of these inverted repeat
containing cpDNAs originated via separate endosymbiotic events ( 30, 35 , 7 3,
129). Also, note that rRNA genes clearly have been dupli cated on multiple
independent occasions in other organelle lineages [at least once in Eu glena
cpDNA (see above) and several times in mitochondrial DNAs (reviewed in
73)] . These two observations, together with the observed differences in in
verted repeat organization, certainly lend plausibility to the idea that the repeats
may have originated independently on several occasions . Regardless of how
many times they originated , that all large cpDNA inverted repeats contain a
complete rRNA operon and that multiple rRNA genes are also found in Eugle na
cpDNA and in several mitochondrial genomes (73) raise the possibility that
there is a selective advantage to having multiple, at least duplicate, rRNA gene
sets in organelle genomes.
Three distinct recombinational properties are associated with the presence of

332
PALMER
the large inverted repeat in chloroplast genomes. First, some sort of gene
conversion/copy-correction mechanism maintains sequence identity between
the two repeat elements present within a given genome (e. g . 27 , 3 3 , 57, 66, 98 ,
109, 115, 137). Second, head-to-head circular dimers, presumably the result of
intermolecular recombination within the inverted repeat, are found only in su ch
inverted repeat-containing species as spinach and lettuce, but are absent in pea,
which lacks the repeat and which contains only head-to-tail dimers (57). Third,
a high frequency of intramolecular recombination between repeats is inferred
from the fact that all inverted repeat-containing cpDNAs that have been careful
ly examined in this regard exi st as a 50 : 50 mixture of two inversion i somers that
differ only in the relative orientation of their single-copy regions ( 2, 5 , 65 , 7 2,
74, 77; J. Palmer, D . Stein, W. Thompson, unpubli shed data). Deletion
analy si s indicates that in Chla mydomo nas reinhardtii thi s "flipping"
recombination reaction occurs at multiple places within the inverted repeat,
either at multiple specific sites (perhaps the short dispersed repeats described
above) or throughout the repeat (74). In contrast, in the structurally analogous
yeast 2 j.Lm circle, "flipping" is confined to a single specific site embedded
within its inverted repeat (10).
Gene Content, Order, and Structure

Chloroplast genes identified thus far include a complete set of rRNA (Figure 3 )
and tRNA genes and some 2 5 protein-encoding genes (Figure 1) . Another 20
polypeptides (primarily ribosomal proteins) are known to be synthesized within
chloroplasts and are presumably encoded by cpDNA (reviewed in 8, 3 2, 7 3 ,
130). With three groups o f exceptions, the same spectrum o f genes i s encoded
by all chloroplast genomes studied to date . Two of the differences involve
genes whose products almost certainly function in all chloroplasts. In all
chlorophyll b-containing eukaryotes (land plants, green algae. and Euglena
gracilis) rbcS is encoded by the nucleus (8), while in several non-chlorophyll
b-containing algae [Cyanophora paradoxa (43 , 110), Olisthodiscus lu teu s (M.
Reith , R. Cattolico, unpublished data), and, tentatively, two red algae ( 111)]
rbcS is a chloroplast gene. A less certain difference involves elongation factor
G, which is thought to be a chloroplast gene product in spinach and Chlorella
but is encoded by nuclear DNA in Euglena and perhaps in Chlamydomona s
(reviewed i n 8 , 3 2, 7 3 ) . The third difference i n gene content involves a set of
genes whose products-the polypeptide components of the light-harvesting
phycobilisomes-are found only in certain non-chlorophyll b-containing
algae. At least four of the phycobilisome polypeptides are encoded by cpDNA
in CyanojJhora (Figure 1; lla, 5 8 , 58a), and several are synthesized within the
chloroplast in three red algal species (23) .
That chloroplast genomes encode for the most part the same set of genes
suggests that most of the transfer of genes from chloroplast to nucleus occurred

333
relatively soon after endosymbiosis (3 4,35,73) and that most plants and algae
are now settled into a set compartmentalization of genes between chloroplast
and nucleus. In addition, given the likelihood of multiple independent en
dosymbioses (30, 3 5, 7 3, 129), it appears that different chloroplast lineages
have followed much the same pattern of gene transfers, with the aforemen
tioned exceptions of rbcS and the gene for elongation factor G. Factors-such
as "lock-in" requirements for components of multi-subunit complexes, the
intrinsic untransportability of certain polypeptides, the evolution of barriers to
transgenomic expression, and selection operating to "fix" a gene within the
asexual, slowly evolving environment of the chloroplast genome-that might
have played a role in determining the present,rather constant and fixed patterns
of gene dispersal, have been discussed at some length already (4, 73).
Chloroplast gene order is almost completely different in each of the six
genomes shown in Figure 1. Clearly, extensive rearrangements of common
sequence elements have occurred during the evolution of the chloroplast
genomes of these two angiosperms and four diverse algae. The extent of
sequence scrambling in these genomes and the lack of intermediate and an
cestral genome types preclude any conclusions about the specific nature,
frequency, and evolutionary direction of these rearrangement events. As will be
discussed in some detail in the next section, it is only in the case of land plants,
angiosperms in particular, that we can describe genome rearrangement as a
process.
Closer examination of Figure 1 does reveal several sets of two or three genes
that are closely linked in two or more chloroplast genomes. Often,the gene sets
are known to be cotranscribed in at least one of the chloroplast genomes,as well
as in the putative cyanobacterial ancestors of chloroplasts. The foremost ex
ample of this type of cotranscriptional linkage is the ribosomal RNA operon,
which has the same basic structure and transcriptional order (16S-tRNAIletRNAA1a-23 S-5S) in all examined chloroplast genomes and in the cyanobacteri
um Anacystis nidulans (Figure 3). Note that this transcriptional linkage re
mains unaffected by the variable presence of large introns in the spacer tRNA
genes and 23S gene, by the splitting off of small RNA species from the 5' (7S
and 3 S rRNA in Chlamydomo nas) and 3' (4.5S rRNA in angiosperms) ends of
the 23S rRNA gene, and by the duplicational insertion of part of the middle of
the operon into the 16S leader region in Euglena (Figure 3; see the section
below on Euglena gracilis for more details). Other cases of conserved trans
criptional linkage in chloroplasts and cyanobacteria include the following: (a )
rbcL and rbcS are cotranscribed in Cyanophora cpDNA (Figure 1; 110) and in
two cyanobacterial genomes (67, 107), and are closely spaced and possibly
cotranscribed in O listhodiscus cpDNA (Figure 1; M. Reith, R. Cattolico,
unpublished data). (b) ppcB and ppcA are cotranscribed in Cyanophora
cpDNA (Figure 1; 58a) and in the cyanobacterium Agmenellum quad-
PALMER
334
Val
tRNA
16S
lie
Ala
tRNA tRNA
23S
4.5S 5S
MAI Z E
58
CHLAMYDOMONAS
--=LoI2 0 REINHARDT II
888 100"
EUGLENA
GRACILIS
869 15
1487
7476
16133201
2869
120
70
ANACYSTIS
NIDULANS
Figure 3
Ribosomal RNA transcription units of chloroplasts and cyanobacteria. Filled boxes

indicate exons and open boxes introns (I). Numbers immediately below the maps indicate sizes of
coding regions. while numbers next below indicate sizes of spacers and introns. Asterisks indicate
approximate sizes where complete sequence data are not available. Maize (Zea mays) data are from
(114); Chlamydomonas data are from (93); Ruglena data are from (24); and Anacystis data are from
( 1 20).
ruplicatum ( 20 , 8 6). (c) atpB and atpE are cotranscribed in several angiosperms
(Figure 1 ; reviewed in 14, 73, 130) and in the cyanobacterium Anabaena (S.
Curtis, unpublished data). In addition , comparisons with E. coli operons
suggest e ven more primitive transcriptional linkages, involving atpH, atpF,
and a tpA in spinach ( 128) and in w heat ( 3a) , rpl2 and rps19 in spinach and
tobacco ( 1 37), and rps7 and rp112 in Euglena (64). Finally, that petB and petD,
and also psaA l and psaA2, are adjacent in spinach, pea, and Cyanophora
(Figure 1 ), and also are known to be cotranscribed in spinach (3, 42), predicts
that these genes are cotranscribed in cyanobacteria. In summary, what little
conservation of overall gene order exists among the diverse algae and land
plants whose cpDNAs are shown in Figure 1 appears to be the consequence of
highly conserved transcriptional linkages that can be traced back to the putative
eubacterial ancestors of chloroplasts.
It should be pointed out, however, that not all cotranscriptional arrangements
present in one c hloroplast genome are found conserved in others. In particular,
all but one of the chloroplast tRNAs of Euglena gracilis are encoded by tight
clusters of two to six genes that are probably polycistronically transcribed (40).
In contrast, with two sets of e xceptions (Figure 3; 68), chloroplast tRNA genes
in angiosperms are not clustered and are transcribed singly (e. g. 21, 22; see 14 ,
14a, 73 , and 130 for additional references).

CHLOROPLAST DNA ORGANIZAnON
335
The most prominent structural differences found among individual chloro

plast genes involve introns . Global analysis by electron microscopy indicates
the presence of at least 50 introns (accounting for over 20% of the genome) in
Euglena gracilis. but perhaps as few as 6 introns in broad bean (55) . Sequenc
ing studies confirm these observations and lead to the following generalizations
( reviewed in 39 , 73): (a) Most Euglena protein genes contain multiple introns
(Figure 1 ) , while with only three known exceptions (3a, 39, 1 37) protein genes
in angiosperms lack introns. (b) Conversely, tRNA genes lack introns in
Euglena but contain (in several cases) large introns (45 1-949 bp) in an
giosperms (e . g. Figure 3). (c) Chlam ydomonas reinhardtii is somewhat in
termediate in intron content, containing the only chloroplast rRNA intron yet
identified (Figure 3) and four large introns in a single one (psbA) of several
protein genes examined (Fi gure 1 ; 25). Intron differences ("optional introns")
have also been found among more closely related taxa. Spinach rpl2 lacks a
large intron found in the tobacco gene (137) , while the l. l -kb intron 3 of psbA
from C. reinhardtii (25) is completely absent from psbA of the interfertile
species C. smithii (74) . As in the case of nuclear and mitochondrial genes,
mechanisms responsible for the evolutionary integration and excision of introns
from chloroplast genes are more or less unknown. Possible mechanisms for the
splicing of chloroplast introns have been discussed elsewhere (7 , 39, 63) .
EVOLUTIONARY TRENDS IN CHLOROPLAST GENOME

ORGANIZAnON
Land Plants
Aspects of chloroplast genome structure have been investigated in well over
200 species of angiosperms. Such an extensive comparative data base allows a
fairly precise description of the tempo and mode of structural evolution in
angiosperm cpDNA. CpDNAs from nonangiospermous land plants are also
considered in this discussion. Although only six of these genomes have been
investigated, their structural conformity to the angiosperm norm greatly ex
tends the phylogenetic scope of the conclusions that can be made regarding the
evolution of cpDNA structure.
With three known exceptions, all
angiosperm and land plant cpDNAs are between 120 kb and 160 kb in size
(Table 1) . The three exceptions, all angiosperms , are Nicotiana accum inata
(genome size 1 7 1 kb) (106) , duckweed (Spirodela oligorhiza; genome size 1 80
kb; 122) and geranium (Pelargonium hortorum; genome size 217 kb; J. Palmer,
J. Nugent, L. Herbon, unpublished data) . Almost two thirds of the 97-kb size
variation found among angiosperm cpDNAs can be accounted for by changes in
the size of the large , rRNA-encoding inverted repeat (i.e. by spreading or
shrinkage of the repeat) , unaccompanied by any overall change in genome
SIZE VARIATION AND REPEAT CONTENT
336
PALMER
, atpH
alpA

pelA I
23S
I pelA
t h 3S
16S.
.16S
rpl2 I
I rpl2
pelD
pelB +
peID
+ pelS
psbS t
t psbS
alpS alpE
rbcL ............
pelA'
psbE 1
psbBI
_
psbA
+ 'pl2
16S +
23S
+ 16S
l l 23S
Figure 4 Variation in inverted repeat size among angiosperm cpDNAs. CpDNAs from geranium
(Pelargonium hortorum: 1. Palmer, 1. Nugent, L. Herbon, unpublished data), spinach (Spinacia
oleracea: 3 , 1 27 , 1 28 , 1 37), and coriander (Coriandrum sativum: 1. Palmer, L. Herbon, 1. Nugent,
unpuhlished data) are shown with their inverted repeats paired .
complexity . At one extreme , the 2 17-kb geranium cpDNA chromosome

possesses a greatly enlarged inverted repeat of 76 kb (Figure 4; J. Palmer, J.
Nugent, L. Herbon , unpublished data) , almost three times the size of any other
angiosperm inverted repeat (6, 14a) . This increase is the result of spreading of
the inverted repeat into both the small and large single-copy regions, producing
duplicate genes for rbcL, petA, psbB, petB, and petD, genes which are single
copy in all other angiosperms (Figure 4). Note that s imple spreading of the
inverted repeat cannot account for the differences in gene order and orientation
present in geranium (Figure 4); several inversions must also be postulated (see
next section) . At the other extreme, the inverted repeat is absent, by virtue of
the deletion of one entire segment of the repeat, in a s ingle group of legumes ,
including pea and broad bean (Figure 1 ; 1 2 , 1 3, 5 1 , 5 2 , 5 7 , 82, 8 3) . This is the
only recorded loss of the inverted repeat among over 200 species and 33
families of angiosperms examined. Associated with this loss is a reduction in
genome size to 1 20 kb , approximately 15 kb smaller than the smallest inverted
repeat-containing angiosperm genomes. In summary, most angiosperm

CHLOROPLAST DNA ORGANIZAnON
337
cpDNAs range in size from only 135 kb to 160 kb,while the range of sequence
complexities found among all angiosperms is only 115-150 kb.
It is striking that although the inverted repeat can vary from 10 to 76 kb
among angiosperms,in the great majority of species it is a rather constant 22-26
kb in size (6). Even more striking is the observation that the junction between
the inverted repeat and the large single-copy region is located in a more or less
fixed position within the 276-bp rps 19 gene in four diverse dicots and monocots
(Figure 1; 87; 109, 137),while in maize the repeat terminates just beyond rps 19
(137). Perhaps this reflects some measure of selection operating to constrain the
boundaries of the inverted repeat. It is clear,however,that the boundaries can
occasionally shift by intermediate amounts compared to the entire deletion of
the repeat in certain legumes or to its tripling in size in geranium. In coriander,
the inverted repeat has shrunk to no more than half the normal size, so that rpi2,
which is normally located within the terminus of the repeat (Figure 2; 87, 137),
is a single-copy gene over 10 kb from the end of the repeat,whereas pshA is
located much closer to the rRNA genes than normal (Figure 4; J. Palmer,L.
Herbon,J . Nugent, unpublished data). The inverted repeat of Nicotiana accu
m inata is about 3.5 kb larger at its large single-copy end than the repeats of 3 0
other species i n Nicotiana (106). Interestingly,this spreading has taken place in
a 3. 5-kb region of "patchy" homology (featuring interspersed repeated and
unique sequence elements) in the genomes with the shorter inverted repeat
(106). This suggests a possible general mechanism for "growth" of the inverted
repeat, via the concomitant pairing of short inverted repeats located outside the
inverted repeat proper and also pairing of the large inverted repeat itself,
followed by the copy-correctional duplication of intervening unique elements.
Deletions and additions (length mutations) of various kinds must be responsi
ble for that component of cpDNA size variation (i.e. changes in sequence
complexity) that occurs independently of spreading and shrinkage of the in
verted repeat. The widespread presence of homologous sequences in chI oro
plast DNA and either nuclear DNA (101,119) or mitochondrial DNA (61, 112,
113) in angiosperms suggests one mechanism for the growth of chloroplast
genomes, i.e. by the stable integration of foreign DNA sequences from outside
the chloroplast. However, where such inferences have been made in the above
studies, it has always been inferred that the direction of sequence transfer has
been from the chloroplast to one of the other two genomes. On the whole this is
not surprising, given the highly variable sizes of plant mitochondrial (73, 104,
126) and nuclear (26) genomes relative to that of the chloroplast. Of the many
length mutations found among angiosperm cpDNAs, only one stands out as
possibly having resulted from the insertion of a large foreign DNA sequence.
This is the recent insertion (see 73) of a 7-9-kb sequence in N. accuminata
cpO NA relative to other species of Nico tiana (106). The origin of this sequence
has not yet been determined.

338
PALMER
Much of the variation in sequence complexity of angiosperm cpDNA appears

to be the result of rather small length mutations. Sequencing studies reveal that
by far the most common of these events are small deletions and insertions 1-10
bp in size (e . g. 116, 138; for more references see 14, 15,73, 130). These occur
predominantly in noncoding regions and are often flanked by or close to very
short direct repeats , suggesting that they might occur mainly by slippage and
mispairing during DNA replication and repair. Larger length mutations, 5 0-1200 bp in size, occur at a significantly lower frequency. Such events are,
however, commonly detected in studies of cpDNA restriction fragment varia
tion (9, 27, 33, 76, 79, 80, 98) and are likely to provide an important
component of cpDNA size and sequence complexity variation . Often, these
mutations have been found to cluster in relative "hotspots" (76). usually at the
two ends of the large single-copy region (9, 33, 80, 98). Sequence studies have
not yet been performed to determine the structural basis of this clustering.
In summary, much of the observed size change in angiosperm cpDNAs can
be accounted for by rare deletions and duplications leading to massive changes
in the size of the prominent rRNA-encoding inve rted repeat sequence. Those
size changes that result in sequence complexity differences are harder to
rationalize. Although both small and moderate-sized length mutations are
common, it is d ifficult to imagine these mutations accumulating by simple
stochastic processes in such a way as to provide the level of variation (from 115
kb to 150 kb) documented thus far. Some additional, undocumented process
e . g. the rare integration of a large sequence element from some foreign
genome-may account for the extra size of the genome in species such as
Sp irodela oligorhiza (122) and Nicotiana accumina ta (106).
INVERSIONS AND GENE ORDER
Inversions and other mutations that change
the relative order of genes are extremely rare in land plant cpDNAs . In fact, the
spinach gene order and arrangement (Figu re 1) appears to be the ancestral one
among angiosperms , vascular plants, and perhaps even all land p lants .
CpDNAs o f spinach, the gymnosperm Ginkgo biloba, and the fern Osmunda
cinnamomea are essentially colinear throughout. This conclusion is based on
two types of hybridization experiments (81; J. Palmer, D. Stein, unpublished
data): (a) "global" c ross hybridizations using cloned fragments representing an
entire angiosperm chloroplast genome to localize regions of homology in the
fern and gymnosperm genomes, and (b) comparative gene mapping of 17
protein genes and the rRNA genes. Thus, it is likely that the spinach arrange
ment is close to that of the common ancestor of vascular plants. In only a single
nonvascular land plant, the liverwort Marchan tia polymorpha. have even a few
genes been localized; their positions are similar to those in the land plants (69),
although more data are clearly needed.
Most angiosperm cpDNAs have the highly conserved gene order typified by

339
spinach. Only a s ingle inversion has been found in a large number of studies (9,
27 , 3 3 , 76, 7 9 , 80, 84, 98) in which the genomes of closely related spec ies have
been compared by restriction mapping and restriction fragment analysis. This is
a small inversion , 2-5 kb in s ize, in the wild ancestor, Pisum humiie, of the
garden pea, P. sativum (Figure 5; 76). "Global" cross-hybridization studies (as
described above) and gene mapping studies have been performed to assay the
extent of positional conservation among more distantly related cpDNAs, from
different families , orders, and subclasses of flowering plants. Of the 30 families
of angiosperms examined in this manner, 24 appear to have the same gene
order, i . e. that of spinach (19, 27,46 , 75, 79, 80, 8 3; 1. Palmer, W. Thompson,
unpublished data) . Gene order differences in the altered genomes can, in
several cases, be explained in terms of one or two large inversions (Figure 2). In
addition, tRNA gene mapping studies have revealed several cases of small
s equence rearrangements of undetermined nature and origin (64a, 64b, 65) .
It is intriguing that all five (see legend) of the inversions shown in Figure 2
have one endpoint just downstream from atpA . Unfortunately, this region has
not been s equenc ed in any of these species . Nor have any of the other inversion
endpoints been sequenced . However, in tobacco, which is essentially colinear
with spinach (27), a 3.5 -kb region immediately downstream from atpA has
been s equenced and found to contain several large (up to 1000 bp) intergenic
spacers that separate four tRNA genes and two short (52 and 98 codons) open
reading frames (21 , 22) . Thus, in tobacco at least, this region contains ample
spacer s equenc es that should be able to accommodate disruption by inversion.
More extensive rearrangement, probably occurring primarily by inversion ,
has taken place in three groups of angiosperms. Geranium cpDNA appears to
have sustained two inversions within its greatly reduc ed large single-copy
region and at l east two inversions w ithin its greatly expanded inverted repeat
(Figure 4; 1. Palmer, 1. Nugent, L. Herbon , unpublished data) . Several rear
rangements, of undetermined size and location , are found in two species of the
Campanulaceae (J. Palmer, W. Thompson , unpublished data) . The most com
plex s ituation exists for several of those legume cpDNAs that share the derived
loss of the inverted repeat. At l east three independent lineages of rearrange
ment, each the result of changes occurring since the loss of the inverted repeat,
can be recognized among these genomes: Broad bean cpDNA has sustained at
l east two large s equence inversions , pea cpDNA approximately a dozen in
versions, and subclover cpDNA an undetermined number of complex rear
rangements (77, 82, 8 3; 1. Palmer, W. Thompson, unpublished data) . Detailed
comparison of the genomes of pea and mung b ean has allowed resolution of the
pea genome into 12 blocks of s equences that occupy different positions and
orientations in pea relative to the conserved mung bean genome (Figure 5; also
see Figure 2). The extent of rearrangement in pea is too great to permit
definitive assignment of these positional differences to discrete mutational
340
PALMER
43
9 8 1 5
12
11
10
r!,

- ._----------------'--'--
---
fir;;
3 456
rv
i-iQJ
S. -QSs
"Cl7Cl7
Q
.:c;;"
"'t""'t".().():s'
::l!.QQ
10
:Ei-
s.s
Cl7Cl7
:r
<b
Q
--
11 12
is
!1 {fge.l2-
Figure 5 Comparative organization of the pea (Pisum sativum; top map) and mung bean (Vigna
radiata; bottom map) chloroplast genomes. Numbers and large arrows indicate the position and
relative orientation of blocks of sequences whose arrangement has been conserved between the two
genomes. Vertical lines, and angled lines connecting groups of vertical lines, shown between the
two genomes indicate cross-hybridizing regions (compiled from 77, 82, 83; J. Palmer, W.
Thompson, unpublished data). The asterisked area at the far right in the pea map indicates the
location of a 2-5 kb inversion in cpDNA of P. humile relative to that of P. sativum (76). Mung bean
mapping data are from (75, 127; J. Palmer, W. Thompson, unpublished data) and pea mapping data
are from (85, 89, 127;J. Gray, T. A. Dyer, D. L. Willey, G. R. M. Courtice, G. M. Bowman, et al,
unpublished data; J. Palmer, W. Thompson, unpublished data).
events; however, modeling efforts suggest that a minimum of about 12 in

versions may have occurred (J. Palmer, W. Thompson, unpublished data) .
Overall, then, most angiosperms have the same conserved gene arrangement
present in o ther land plants. Occasionally, this arrangement is disrupted by
single inversions (Figure 2). Only rarely, as in the case of geranium and pea
(Figures 4 and 5), does one encounter genomes that are extensively rearranged.
It is unclear why most angiosperm genomes, particularly those that retain a
large inverted repeat of normal size, are so conserved in arrangement, whereas
a few genomes, with either greatly enlarged inverted repeats or no inve rted
repeat at all , are so highly rearranged. Rearrangements require three primary
preconditions: the presence of an acti ve recombination system in the chloro
plast, of suitable spacer sequences between genes that can accept inversions
without disruption of gene function, and of repeated sequence elements within
these spacers that can serve as substrates for recombination . Chloroplasts,
particularly those with the inve rted repeat, clearly are proficient in certain kinds
of recombination (see the section above on repeated sequences). Angiosperm
cpDNAs are , however, fairly tightly packed with genes (e. g. 88; reviewed in 6,
14, 73, 130), many of which are coordinately transcribed into large polycistron
ic RNAs (Figu re 1 and references in legend) . On the other hand, that

34 1
certain genomes can tolerate extensi ve rearrangement at all and that abundant
spacer sequences are found in certain portions of unrearranged genomes (e. g.
2 1 , 22) suggest that this is by no means an absolute constraint, as it is,
apparently, for the h ighly constrained and virtually spacerless genome of
vertebrate mitochondria ( 1 1 ) . An i mportant constraint may be the relative
absence of short dispersed repeated sequences , as assayed by filter hybridiza
tion, in most cpDNAs (see the section above on repeated sequences; 7 3) .
Consistent with this idea is the observation that subclover cpDNA, which is
h ighly rearranged, also possesses the only known family of dispersed repeats in
angiosperms (J. Palmer, W . Thompson, unpublished data) . On the other hand,
d ispersed repeats are not found in two other rearranged legume cpDNAs, from
pea and broad bean (5 1 , 82, 8 3) . Furthermore, very short repeats that could be
important as recombination sites might still be present in various cpDNAs, but
be undetectable at the level of filter hybridization.
The mystery of why most angiosperm and l and plant genomes are so stable in
gene order is compounded by the further mystery of why a few are so rear
ranged. Does this indicate a general and consistent enhancement in the overall
rate of rearrangement in these genomes, or does it reflect a few brief episodes of
catastrophic repatteming of the genome? In the case of geranium (Figu re 4)
could such repaUeming be concomitant with the tripling in size of its inverted
repeat? In the case of the rearranged legume genomes, all of which lack the
inverted repeat (e. g. Figure 5), such a direct relationship, at least in temporal
terms, between massive change affecting the inverted repeat and a more general
reorganization of the genome as a whole is untenable , given the fact that two
legume cpDNAs (from alfalfa and wisteria) that lack the inverted repeat are
otherwise unrearranged (J. Palmer, J. Aldrich, W. Thompson, unpublished
data) . More complex speculations about how the loss of the inverted repeat
might nonetheless have led to a "destabilization" of the genome in certain
legume l ineages, and conversely how it might "stabilize" those genome that
retain the repeat, h ave been presented elsewhere ( 1 8, 7 3, 77).
Chlamydomonas
As much variation in genome size and arrangement is found among the four
species of Chlamydomonas whose cpDNAs have been studied as among all of
the more than 200 species of land plants examined. The four Chlamydomonas
species consist of two distantly related pairs (C. reinhardtii and C. smithii; C.
eugametos and C. moewusii) of closely related, interfe rtile species. Except for
deletion/insertion mutations , the chloroplast genomes are colinear within each
species pair but differ by an extensive series of rearrangements between the two
pairs. The s mall , 4-kb difference in overall size (Table 1 ) between cpDNAs of
the interfertile species C. reinhardtii and C. smithii actually represents the
accumulation of a large number of small deletions and insertions (74). For

342
PALMER
example, although their 22-23-kb rRNA-encoding inverted repeats differ by

only 1 kb in size, this represents the accretion of a minimum of 11 different
length mutations of between 20 and 1 600 bp, which sum, independently of
evolutionary direction, to a total of almost 6 kb (74) . Overall it appears that
length mutations are more frequent relative to base substitutions in these two
Chlamydomonas cpDNAs than in angiosperm cpDNA (74) . Many of these
length mutations map close to one or more of the 25-40 short ( 100-300 bp)
inverted repeat sequences dispersed throughout the two chloroplast genomes
(29 , 74 , 92, 95) , suggesting that recombination within and between repeat
elements may be one factor contributing to the enhanced frequency of these
events (74) .
The colinear (in gene order) (58d) genomes of the other interfertile species
pair, C. eugametos and C. moewusii, differ by 49 kb in size (Table 1).
However, 42 kb of this size difference is the result of a single length mutation,
the symmetric insertion in both inverted repeat segments of C. moewusii of a
2 1 -kb sequence relative to the C. eugametos repeats (5Sc) . The presence of
small repeated sequences within and immediately surrounding this extra 2 1 -kb
sequence has led to the speculation (S8c) that the sequence may have entered or
exited the genome via repeat-mediated recombination.
Cross-hybridization s tudies indicate that the cpDNAs of C. reinhardtii and
C. eugametos differ in gene and sequence order by an extensive series of
rearrangements (58b). The degree of sequence scrambling is so extreme that the
rearrangements could not be analyzed as individual events. Rearrangements
were found both within and between the two nearly equal-sized (Figure 1 )
single-copy regions-i . e . sequences present i n different single-copy regions in
one species are present in the same region in the other (58c) . Furthermore , the
large inverted repeats differ in gene content. R bcL is a single-copy gene in C.
reinhardtii (Figure 1 ) but is located within the inverted repeat in C. eugametos
(59) .
Do these extensive rearrangements reflect a more rapid rate of sequence
rearrangement in Chlamydomonas, and perhaps in other green algae, than
among angiosperms and land plants? Obviously a firm answer is impossible
since so few of the algae have been examined . The presence of numerous short,
apparently recombinogenic repeats in the Chlamydomonas genomes is certain
ly one precondition consistent with an enhanced rate of rearrangements. On the
other hand, as pointed out by Lemieux & Lemieux (58b), Chlamydomonas is
large and diverse; it may well be older as a genus than all of angiosperms,
perhaps as old as the land plant lineage . Thus , they argue that the degree of
rearrangement in the two Chlamydomonas genomes may simply reflect a long
period of evolutionary separation. Consistent with this speculation is their
observation (58b) that the C. reinhardtii and C. eugametos genomes are
extremely divergent in nucleotide sequence.
343

Euglena gracilis
A surprising amount of structural variation has been found in cpDNAs from
Euglena gracilis, considering that only laboratory strains of this alga have been
studied . Two cases of rearrangement by unequal crossover have been postu
lated. First, different strains possess one, two, three or five complete rDNA
operons and either one or two partial operons (see Figure 1 for an example of a
" 3 + " genome; 5 3 , 56, 9 1 , 133). As noted by these authors , such copy-number
variation is likely to result from unequal crossover within the tandemly arrayed
operons . Individual repeat units within a strain differ significantly both in
structure and in sequence (24 , 4 8 , 97) , suggesting that intragenomic
homogenization (by unequal crossover or gene conversion) must occur seldom
if at all . Second , highly variable numbers, again presumably resulting from
unequal crossover, of a tandcmly repcated 54-bp sequence are found in differ
ent cpDNA molecules from single cultures of E. gracilis (99) . Two instances of
duplicative transposition have also been inferred, based on the presence of a
pseudogene cluster (consisting of the 3 end of the 1 6S rRNA gene, the adjacent
spacer, and two tRNA-like sequences) in the leader region of the rDNA operon
(Figure 2; 24, 70, 96) . EI-Gewely et al (24) have proposed that this region arose
by the insertion of segments from the middle of the rDNA operon (3 - 1 6S ,
spacer, and tRNA lie) and from a tRNAMet_tRNATrp cluster located elsewhere in
the genome , with the second event occurring by homologous recombination
between the tRNAlle and tRNAMet genes. Stutz and coworkers (96, 97 , 99)
have found a variety of disjunct pieces of the rRNA operon , including an entire
1 6S rRNA gene (Figure 1 ) , an extra 5S rRNA gene, and part of the rDNA
leader, scattered in several positions between the origin of replication and the 5 '
end of the first complete rRNA operon . The complex present-day disposition of
these elements makes it impossible to derive a definitive evolutionary history
for this region .
I
INDUCED ALTERATIONS IN CHLOROPLAST GENOME

STRUCTURE
Chlamydomonas reinhardtii
Procedures for inducing discrete physical alterations in the chloroplast genome
are best developed for Chlam ydomonas reinhardtii, the premier organism for
chloroplast genetic analysis. Growth of Chlam ydomonas in media containing
the thymidine analog 5 -fluorodeoxyuridine (FdUrd) leads to a drastic reduction
in the number of cpDNA molecules per cell ( 1 34) and results in an increase in
the frequency of chloroplast, but not nuclear, mutations ( 1 35 ) . CpDNAs from a
large proportion of the nonphotosynthetic (acetate-requiring) mutants produced
by either FdUrd treatment alone or FdUrd plus X rays contain large deletions,

344
PALMER
all of which extend at least partially into the 22-kb rRNA-encoding inverted
repeat (66; Figure 1 ). These deletion mutants fall into four classes (74): A high
proportion of the mutants (classes 1 and 2) have symmetric 8 . 5-9 .0-kb de
letions of the entire psbA gene . Class 2 mutants also feature symmetric
inversions of the entire rDNA operon. Two mutants (class 3) contain large
asymmetric deletions in both inverted repeat segments, a larger deletion of 1 7
kb extending through psbA and the rDNA operon in one repeat, and a smaller
deletion of 9 kb extending through psbA only. Class 4 mutants have single
deletions affecting the a tpB gene (1 32) and extending various distances into one
inverted repeat segment.
The endpoints of the deletions and inversions present in the first three mutant
classes all map close to one or more of the dozen or so short (1 00-300 bp) repeat
elements that are scattered throughout the 22-kb C. reinhardtii inverted repeat
(74, 95 ). This has led to the speculation that these rearrangements are the result
of homologous recombination between repeat elements located at different
positions (74). This hypothesis needs to be tested by sequencing the endpoints
of these mutations.
No Chlamydomonas mutants have been found lacking both sets of rRNA
genes. This is in spite of the fact that mutants containing symmetric deletions of
the psbA locus (located immediately adjacent to the rDNA operon) , mutants
with symmetric inversions of the entire rDNA operon, and mutants with
asymmetric deletions of just one of the two rDNA operons have all been
recovered. These findings suggest that the plastid genome may provide certain
indispensable functions to the cell in addition to its role in specifying
polypeptides involved in photosynthesis. Consistent with this speculation is the
observation that plastid DNA and ribosomes are present in the permanently
nonphotosynthetic alga Polytoma obtusum (1 08).
A fifth class of FdUrd-induced nonphotosynthetic mutants have enlarged
chloroplast genomes in which the inverted repeat has spread through an adja
cent segment of the genome that is single copy in wild type C. reinhardtii (74).
In three of these mutants the inverted repeat has almost tripled its normal size
(63 kb vs 22 kb) by spreading through the left half of the bottom single-copy
region shown in Figure 1 . Thus, these mutants have not only duplicated such
structural genes as rpl2 and tufA , but also possess duplicated sets of replication
origins (74). It is interesting that the range of inverted repeat sizes (4-65 kb; 7 4)
found in the entire set of Chlamydomonas mutants nearly parallels the naturally
occurring range (1 0-76 kb; Figure 4) found among angiosperm cpDNAs.
All of the alterations in these nonphotosynthetic mutants specifically affect
the inverted repeat (66, 7 4), in spite of the fact that photosynthetic loci are
located at various distances away from the repeat (Figure 1 ). To explain this , it
has been hypothesized (66 ) that intramolecular pairing of the repeat segments
greatly enhances the recovery of mutations in this region by holding damaged,
345
double-stranded ends close together, facilitating their joining and repair. Un

fortunately, the practical consequence of the enhanced mutability of the in
verted repeat, whatever its cause might be , is to severely limit the utility of this
mutational approach for producing a wide spectrum of useful photosynthetic
mutants.

Euglena gracilis
It has long been known that treatment of Euglena gracilis with heat, UV
irradiation, or a wide variety of inhibitors of either DNA replication (e . g .
nalidixic acid) or protein synthesis (e . g . streptomycin) causes permanent
bleaching and loss of chloroplast function , in many cases accompanied by the
apparent complete loss of all cpDNA (reviewed in 3 1 ) . However, more sensi
tive assays have shown recently that all of these mutants contain some cpDNA,
although often in amounts 1 00-- 1 000 times lower than in wild type cells (47).
Moreover, these mutants almost invariably contain nonstoichiometric pro
portions of different regions of the chloroplast genome ( 44, 47) . Certain
portions of the genome, e . g . the rbeL gene (28), appear to be absent in some
mutants (47). Although the structures of these mutant cpDNAs have not been
worked out completely, it is clear that the rRNA genes are often rearranged and
highly amplified relative to the rest of the genome (44, 47). These findings may
be related to the fact that the rRNA genes are located close to the cpDNA
replication origin in Euglena (Figure I ; 5 4, 90).
Angiosperms
Compared to Chlamydomonas and Euglena, rather limited information is
available about induced structural mutations of angiosperm cpDNAs, although
this situation is likely to change with the present interest in genetically engineer
ing the chloroplast genome of crop plants . A potentially useful source of
structural mutations in cpDNA may be the nuclear-encoded cpDNA mutator
genes found in various flowering plants (50). The high frequency of occurrence
and also reversion of cpDNA mutations under the control of these mutator
genes has led to the hypothesis that in at least certain cases these may involve
the activation of a resident chloroplast transposable element ( 103). There is
preliminary evidence that a structural alteration, of uncharacterized nature, has
indeed occurred in cpDNA from a mutant of Oenothera johansen induced by a
mutator gene ( 1 03).
In contrast to the instability of plant mitochondrial genomes, angiosperm
chloroplast genomes are generally stable in culture and during whole-plant
regeneration from culture or from protoplast (e. g . 49 , 105; reviewed in 73) .
Recently, however, i t has been shown that grossly altered chloroplast genomes
are present in albino wheat, barley, and rye plants regenerated from pollen by
anther culture ( 1 7 , 1 8) . Most of the albino plants contained a heterogeneous

346
PALMER
population of cpDNA molecules carrying various large deletions. In one albino

wheat plant, over 80% of the genome, including both sets of rRNA genes, was
deleted in the major cpDNA molecule present ( 1 8) . Assuming that this plant did
not contain a minor but fixed subpopulation of larger cpDNA molecules
containing ribosomal RNA (and ribosomal protein) genes, this result suggests
that the absence of chloroplast gene expression may not necessarily be lethal, at
least to plants grown on a synthetic medium. Circular linkage maps , 39-78 kb
in size, were derived by restriction mapping for several of the deleted cpDNA
molecules from albino wheat plants ( 1 8) . In certain cases the deleted molecules
also appear to exist as linear genomes ( 1 7 ) . All of the deleted molecules contain
a single common region of the genome, which presumably carries at least one
functional origin of replication ( 1 8; in wheat this region is just 3 ' to the psbC
gene shown in Figure 2). The occurrence of deleted cpDNA molecules in albino
pollen plants appears to support the Chloroplast alteration theory for the mater
nal inheritance of cpDNA ( 1 8 , 1 23).
CONCLUDING REMARKS
By now it should be apparent that our present understanding of the comparative
organization and structural evolution of cpDNA is decidedly biased in favor of
flowering plants . Most of the over 200 angiosperm chloroplast genomes ex
amined are overwhelmingly similar in size, conformation , repeat structure,
gene content, and gene order and arrangement. In terms of frequency, the
predominant mode of structural evolution in these genomes takes the form of
small deletions and insertions occurring in intergenic spacers , 5 ' and 3 '
untranslated regions , and i n the few introns found i n their genes. The ancestral
gene order among angiosperms (and quite possibly all land plants) is retained
unchanged in most species . Where gene order differences are found they can
often be accounted for by single large inversional switches. In only a few
angiosperm genomes are major differences in size (primarily of the large
near-universal inverted repeat) or gene arrangement found. It is interesting that
both kinds of these large-scale alterations are found in the same genomes, such
as those of pea and geranium.
Angiosperm cpDNA is highly conserved not only in structure , as reviewed in
this article , but also in the sequence of its constituent genes (reviewed in 1 5 , 73,
1 30). In contrast, animal mitochondrial DNA is also highly constrained in size
and arrangement but evolves rapidly in primary sequence ( 1 1 ) . Plant
mitochondrial DNA evolves still differently-rapidly in structure and organiza
tion but slowly in sequence (73 , 1 04). Overall, then, angiosperm cpDNA is the
most slowly evolving organelle genome known .
Although we know more about the structure and evolution of cpDNA in
angiosperms than in any other plant group, many questions remain concerning
the mechanism and tempo of rearrangement in angiosperm cpDNA . Does the
347
extensive rearrangement of the genome in such species as pea and geranium

reflect an increase in the steady-state frequency of inversions and other rear
rangements, or does it simply bear witness to one or two brief episodes of
catastrophic repatterning of the genome? Are there a few preferred sites of
genomic rearrangement and inversion , and what arc the sequence properties
that determine such sites? So far, there are no clear-cut examples of the
transposition of cpDNA sequences in an angiosperm. Is transposition not a
factor in any of these genomes, or do we simply have to look harder to find a

genome containing active (perhaps under nuclear gene control) transposable

elements? Do chloroplast genomes grow in size by the rare uptake of foreign
DNA sequences , or arc there mechanistic barriers to such events? Finally, we
can do little but ponder the question of whether any form of selection maintains
a genome so highly constrained in size and arrangement.
Grecn algae exhibit the total range of cpDNA structural variation described
among all examined plants and algae. This raises a number of important
questions about these green algal genomes. Does the exceptionally small
genome in
Codium contain fewer genes than the average chloroplast genome?

Acetabularia encode
Conversely, does the extraordinarily large genome in
significantly more genes? If it does not comprise genes, then what is all the
Acetabularia? Do green algal genomes, particularly those in

Chlamydomonas. rearrange more often than their angiosperm counterparts ? Do
the short dispersed repeats found in several Chlamydomonas genomes generate
extra DNA in
an extra component of structural diversity, both in terms of length mutation and

changes in gene order? What do the genomes of other major groups of green
algae look like? In particular, can we trace the highly conserved chloroplast
gene arrangement of land plants back to a specific group of green algae , one that
may therefore have given rise to land plants?
In conclusion , we now know enough about the comparative organization of
cpDNA in angiosperms and land plants to derive certain general rules about
how these genomes are evolving and to ask specific questions about mech
anisms responsible for the observed pattern of evolutionary change . In the case
of green algae , a tantalizing amount of structural diversity is apparent in the few
genomes yet examined , generating a number of intriguing questions. In
vestigators have o n l y begun to examine chloroplast genomes from
nonchlorophytic algae . Based on the known differences in gene content and
possible differences in genome conformation in certain of these algae relative to
chlorophytes, we can only wonder at the diversity of structural arrangements
that will ultimately be uncovered in their genomes.
ACKNOWLEDGMENTS
I am grateful to L. Herbon for preparing the figure s , R . Helling, R . Jansen, and
M. Zolan for critical reading of the manuscript, and numerous colleagues for
kindly providing copies of manuscripts before publication .
348
PALMER

Literature Citations
I . Aldrich, J. , Cattolico, R. A . 1 98 1 . Isola
tion and characterization of chloroplast
DNA from the marine chromophyte ,
Olisthodiscus luteus: Electron micro
scopic visualization of isomeric molecu
lar forms . Plant Physiol . 68:641-47
2. Aldrich, J., Cherny, B . , Merlin, E . , Wil
liams, C . , Mets, L . 1 985. Recombina
tion within the inverted repeat sequences
of the Chlamydomonas reinhardtii chlo
roplast genome produces two orientation
isomers. Curro Genet. 9:233-38
3. AIt, J. , Morris, J. , Westhoff, P . , Herr
mann, R. G. 1 984. Nucleotide sequence
of the clustered genes for the 44 kd chlo
rophyll a apoprotein and the "32 kd"-like
protein of the photosystem II reaction
center in the spinach plastid chromo
some. Curr o Genet. 8:597-606
3a. Bird, C. R . , Koller, B . , Auffret, A. D . ,
Huttley , A . K . , Howe, C . J. , et a1 1 985.
The wheat chloroplast gene for CFo sub
unit I of ATP synthase contains a large
intron. EMBO 1. 4 : 1 38 1-88
4. Bogorad, L. 1 975. Evolution of organ
elles and eukaryotic genomes. Science
1 88:89 1-98
5 . Bohnert, H. J . , Loffelhardt, W. 1 982.
Cyanelle DNA from Cyanophora para
doxa exists in two forms due to in
tramolecular recombination. FEBS Lett.
1 50:403-6
6. Bohnert, H. J. , Crouse, E. J. , Schmitt, J.
M . 1 982. Chloroplast genome organiza
tion and RNA synthesis. Encycl. Plant
Physiol. 14B :475-530
7. Bonnard, G . , Michel, F . , Weil, J. H . ,
Steinmetz, A . 1 984. Nucleotide se
quence of the split tRNALeu-UAA gene
from Vicia faba chloroplasts: evidence
for structural homologies of the chloro
plast tRNALeu intron with the intron from
the autosplicable Tetrahymena ribosomal
RNA precursor. Malec. Gen. Genet.
1 94:330-36
8. Bottomley, W . , Bohnert, H. J. 1 982.
The biosynthesis of chloroplast proteins.
Encycl. Plant Physiol. 14B:531-96
9. Bowman, C. M . , Bonnard, G . , Dyer, T.
A . 1 983. Chloroplast DNA variation be
tween species of Triticum and Aegilops.
Location of the variation on the chloro
plast genome and its relevance to the in
heritance and classification of the cyto
plasm. Theor. Appl. Genet. 65:24762
1 0 . Broach, J. R . , Guarascio, V. R . ,
Jayaram, M . 1 982. Recombination with
in the yeast plasmid 2 micron circle is
site-specific. Cell 29:227-34
1 1 . Brown, W. M. 1983. Evolution of an

imal mitochondrial DNA. In Evolution of
Genes and Proteins, ed. M . Nei, R . K .
Koehn, pp. 62-88. Sunderland, Mass:
Sinauer
l I a. B ryant, D. A . , De Lorimer, R . , Lam
bert, D. H . , Dubbs, 1. M . , Stirewalt, V .
L . , e t a l 1 985. Molecular cloning and
nucleotide sequence of the ex and 13 sub
units of allophycocyanin from the cyanel
Ie genome of Cyanophora paradoxa .
Proc. Natl. Acad. Sci. USA 82:3242-46
1 2 . Chu , N. M . , Oishi, K . K . , Tewari, K . K .
1 98 1 . Physical mapping o f the pea chlo
roplast DNA and localization of the ribo
somal RNA genes. Plasmid 6:279-92
1 3 . Chu, N. M . , Tewari, K. K . 1 982.
Arrangement of the ribosomal RNA
genes in chloroplast DNA of Legumino
sae. Malec. Gen. Genet. 1 86:23-32
14. Crouse, E. J. , Bohnert, H. J . , Schmitt, J.
M. 1 984. Chloroplast RNA synthesis. In
Chloroplast Biogenesis, Seminar Series
of the Society for Experimental Biology,
cd. R. J. Ellis, Vol. 2 1 . pp. 83-136 New

York: Cambridge Univ. Press
1 4a. Crouse, E. J . , Schmitt, 1. M . , Bohnert,
H. J. 1 985 . Chloroplast and cyailObacte
rial genomes, genes and RNAs: a com
pilation. Plant Mol. Bioi. Reporter 3:43-89
1 5 . Curtis, S . E . , Clegg, M . T. 1 984.
Molecular evolution of chloroplast DNA
sequences. Mol. Bioi. Evol. 1 :291-301
16. Dalmon, J. , Loiseaux, S . , B azetoux, S.
1 983. Heterogeneity of plastid DNA of
two species of brown algae. Plant Sci.
Lett. 29:243-53
1 7 . Day, A. 1 985. The chloroplast genome in
albinoplantsproduced by anther culture.
PhD thesis. Univ. East Anglia, U K

1 8 . Day, A. , Ellis, T. H . N . 1 984. Chloro
plast DNA deletions associated with
wheat plants regenerated from pollen:
Possible basis for maternal inheritance of
chloroplasts. Cell 39:359--68
1 9 . De Heij , H . T . , Lustig, H . , Moeskops,
D. J. M . , Bovcnbcrg, W. A . , B isanz, c . ,
Groot, G. S . P . 1 983. Chloroplast DNAs
of Spinacia, Petunia and Spirodela have
a similar gene organization. Curro Genet.
7: 1-6
20. De Lorimer, R . , Bryant, D. A . , Porter,
R. D . , Liu, W. Y . , Jav, E . , Stevens, S .
E . Jr. 1 984. Genes for the ex and 13 sub
units of phycocyanin . Proc. Nat!. Acad.
Sci. USA 8 1 :7946--5 0
2 1 . Deno, H . , Sugiura, M . 1 983. The nucle
otide sequences of tRNASe'(GCU) and
tRNAGln(UUG) genes from tobacco

chloroplasts. Nucleic Acids Res. 1 1 :

8407-1 4
22. Deno, H . , Sugiura, M . 1 984. Chloro
plast tRNAG1y contains a long intron in
the D stem: Nucleotide sequences of
tobacco chloroplast genes for tRNAGly
(DCC) and tRNAA,g(DCD). Proc. Nat/.
A cad. Sci. USA 8 1 :405-8
23. Egelhoff, T . , Grossman, A. 1 983.
Cytoplasmic and chloroplast synthesis of
phycobilisome polypeptides. Proc. Natl.
Acad. Sci. USA 80:3339-43
24. El-Gewely, M. R . , Hclling, R. B . , Dib
bits, J. G. T. 1 984. Sequence and evolu
tion of the regions between the rrn op
erons in the chloroplast genome of Eu
glena gracilis bacillaris . Mol.
Genet. 1 94:432-43
Gen.
Euglena
Lett.
25. Erickson, J. M . , Rahire, M . , Rochaix, J.

D. 1984. Chlamydomonas reinhardii
gene for the 32,000 mol. wt. protein of
photosystem II contains four large introns
and is located entirely within the chloro
plast inverted repeat. EMBO J. 3 : 275362
26. Flavell, R.
1980. The molecular
characterization and organization of plant
chromosomal DNA sequences. Ann.
Rev. Plant Physio/. 31 : 569-96
27. Fluhr, R . , Edel man, M . 1 98 1 . Conserva
tion of sequence arrangement among
higher plant chloroplast DNAs: Mole
cular cross hybridization among the
Solanaceae and between Nicotiana and
Spinacia. Nucleic Acids Res. 9:684153
28. Freyssinct. G . , Freyssinet, M . , Lebrun,
M. 1 985. Occurrence of the gene for the
large subunit of ribulose- 1 ,5-bisphos
phate carboxylase in several mutants of
29.
30.
31.
32.
gracilis.
Plant
Sci.
37:245-49
Gelvin, S. B . , Howell, S . H . 1979. S mall
repeated sequences in the chloroplast
genome of Chlamydomonas reinhardi.
Mol. Gen. Genet. 1 73 : 3 1 5-22
Gibbs, S. P. 1 98 1 . The chloroplast
endoplasmic reticulum: Structure, func
tion, evolutionary significance. Int. Rev.
Cytol. 72:49-99
Gillham, N. W. 1 978. Organelle Hered
ity. New York: Raven Press
Gillham, N. W . , Boynton, J. E . , Harris,
E. H. 1 985 . Evolution of plastid DNA. In
DNA and Evolution: Natural Selection
and Genome Size, ed. T. Cavalier-Smith.
pp . 299-35 1 . New York: Wiley

3 3 . Gordon, K. H. J . , Crouse, E. J . ,
Bohnert, H . 1 . , Herrmann, R . G . 1982.
Physical mapping of differences in chlo
roplast DNA of the five wild-type plas
tomes in Oenothera subsection Eu-
349
oenothera . Theor. Appl. Genet. 6 1 :373-
84
34. Gray, M . W. 1 98 3 . The bacterial an
cestry of plastids and mitochondria.
Bioscience 33:693-99
35. Gray, M. W . , Doolittle, W. F. 1 982. Has
the endosymbiont hypothesis been prov
en? Micro . Rev. 46:1--42
36. Green, B. R . 1 976. Covalently closed
minicircular DNA associated with Ace
tabularia chloroplasts. Biochim. Bio
phys . Acta 447 : 1 56--66
37. Green , B . R. 1 980. Protein synthesis by
isolated Acetahularia chloroplasts. In vi
tro synthesis of the apoprotein of the P700-chlorophyll
a-protein
complex
(CPI). Biochim. Biophys. Acta 609 : 1 0720
3R. Green, B . R . , Muir, B . L . , Padma
nabhan, D. 1 977. The Acetabularia
chloroplast genome: S mall circles and
large kinetic cumplexity. In Progress in
Acetabularia Research, ed. C. F. L.
Woodcock, pp. 1 07-22. New York: Aca
demic
39. Hallick, R. B . , Gingrich, J. c . , Johan
ningmeier, D . , Passavant, C. W. 1 985.
Introns in Euglena and Nicotiana chloro
plast protein genes. In Molecular Form
and Function ofthe Plant Genome, ed. L.
van Vloten-Doting, G. S. P. Groot, T. C.
Hall, pp. 2 1 1-20. New York: Plenum.
40. Hallick, R. B . , Hollingsworth , M. J . ,
Nickoloff, J . A. 1 984. Transfer RNA
genes of Euglena gracilis chloroplast
DNA. Plant Mol. Bioi. 3 : 1 69-75
4 1 . Hedberg, M. F . , Huang, Y . S . , Hom
mersand, M. H. 1 98 1 . Size of the chloro
plast genome in Codiumfragile. Science
2 1 3 :445-47
42. Heinemeyer, W . , Alt, J . , Herrmann, R.
G . 1 984. Nucleotide sequence of the
clustered genes for apocytochrome b6
and subunit 4 of the cytochrome blf com
plex in the spinach plastid chromosome.
Curro Genet. 8:543-49
43 . Heinhorst, S . , Shively, J. M. 1 98 3 .
Encoding o f both subunits o f ribulose1 ,5-bisphosphate carboxylase by orga
nelle genome of Cyanophora paradoxa.
Nature 304:373-74
44. Heizmann, P . , Hussein, Y . , Nicolas, P . ,
Nigon, V . 1982. Modifications of chlo
roplast DNA during streptomycin in
duced mutagenesis in Euglena gracilis.
Curro Genet. 5:9- 1 5
4 5 . Herrmann, R . G . , Paita, H . K . , Kowal
lik, K. V. 1 980. Chloroplast DNA from
three archegoniates. Planta 148: 3 1 9-27
46. Herrmann, R. G . , Westhoff, P . , Alt, J . ,
Winter, P. , Tittgen, J . , Bisanz, C . ,
Sears, B . B . , Nelson, N . , Hurt, E . ,
350
47.

48.
49.
50.
PALMER
Hauska, G . , Viebrock, A . , Sebald, W .
1 983. Identification and characterization
of genes for polypeptides of the thylakoid
membrane. In Structure and Function of
Plant Genomes, ed. O. Ciferri, L. Dure
III, pp. 143- 1 5 3 . New York: Plenum
Hussein, Y . , Heizmann, P . , Nicolas, P . ,
Nigon, V. 1 982. Quantitative estimates
of chloroplast DNA in bleached mutants
of Euglena gracilis. Curro Genet. 6: 1 1 117
Karabin, G. D . , Narita, J. 0 . , Dodd, J .
R . , HaUick, R . B . 1 983. Euglena gracilis
chloroplast ribosomal RNA transcription
units. Nucleotide sequence polymor
phism in 5S rRNAs. J. Bioi. Chem.
258: 1 4790-96
K e mbl e , R. J . , Shep ard , J. F. 1 984.
Cytoplasmic DNA variation in a potato
protoclonal population. Theor. Appl.
Genet. 69:2 1 1- 1 6
Kirk, J . T. 0 . , Tilney-Bassett, R . A. E .
1 978. The Plastid.. Their Chemistry,
Structure, Growth, Inheritance. Amster
dam: Elsevier. 2nd ed.

5 1 . Ko, K . , Straus, N. A . , Williams, J. P.
1 983. Mapping the chloroplast DNA of
Vicia faba. Curro Genet. 7:255-63
52. Koller, B . , Delius, H. 1 980. Vida faba
chloroplast DNA has only one set of
ribosomal RNA genes as shown by
partial denaturation mapping and R-loop
analysis. Mol. Gen. Genet. 1 78:26169
5 3 . Koller, B., Delius, H . 1 982. A chloro
plast DNA of Euglena gracilis with five
complete rRNA operons and two extra
16S rRNA genes. Mol. Gen. Genet.
1 88:305-R
54. Koller, B . , Delius, H. 1 982. Origin of
replication in chloroplast DNA of Eu
glena gracilis located close to the region
of variable size. EMBO J. 1 :995-98
5 5 . Koller, B . , Delius, 1 984. Intervening

sequences in chloroplast genomes. Cell
36:6 1 3-22
56. Koller, B . , Delius, H . , Helling, R. B .
1 984. Structure and rearrangement of
rRNA genes in chloroplast DNA in two
strains of Euglena gracilis . Plant Mol.
Bioi. 3 : 1 27-36
57. Kolodner, R . , Tewari, K. K. 1 979 . In
verted repeats in chloroplast DNA from
higher plants. Proc. Nat!. Acad. Sci.
USA 76:41-45
57a . Kuhsel , M . , Kowallik, K . V. 1985. The
plastome of a brown alga, Dictyota di
chotoma. I. Physical properties and the
Bam HiiSal IIBgl II cleavage site map.
Plant Mol. Bioi. 4:365-76
58. Lemaux, P. G . , Grossman, A . 1 984 .
Isolation and characterization of a
gene for a major light-harvesting

polypeptide from Cyanophora paradoxa.
Proc. Natl. Acad. Sci. USA 8 1 :4100-4
58a. Lemaux , P. G . , Grossman, A . R. 1 985.
Major light-harvesting polypeptides en
coded in polycistronic transcripts in a eu
karyotic alga. EMBO J. 4 : 1 9 1 1 - 1 9
58b. Lemieux, B . , Lemieux, C . 1 985. Ex
tensive sequence rearrangements in the
chloroplast genomes of the green al

gae Chlamydomonas eugametos and
Chlamydomonas reinhardtii. Curro Ge
net. I n press
58c. Lemieux, c . , Turmel, M . , Lee, R. W . ,
Bellemare, G . 1 985. A 21 kilobase-pair

deletion/addition difference in the in
verted repeat sequence of chloroplast
DNA from Chlamydomonas eugametos
and C. moewusii. Plant Mol. Bioi. In
press
58d. Lemieux , B . , Turrnel, M . , Lemieux , C .
1 9 8 5 . Chloroplast DNA variation i n
Chlamydomonas
and its potential
application to the systematics of this
genus. Biosystems In press
59. Lemieux, c . , Turmel, M . , Seligy, V. L . ,
Lee, R. W . 1 98 5 . The large subunit of
ribulose- 1 ,5-bisphosphate carboxylase
oxygenase is encoded in the inverted re
peat sequence of the Chlamydomonas eu
gametos chloroplast genome. Curro
Genet. 9: 1 39-45
60. Lonsdale, D. M . , Hodge, T. P. , Fauron,
C. M. R. 1 984. The physical map and
organization of the mitochondrial
genome from the fertile cytoplasm of
maize. Nucleic Acids Res. 1 2:924961
6 1 . Lonsdale, D. M . , Hodge, T . P., Howe,
C. J . , Stem, D. B. 1 98 3 . Maize
mitochondrial DNA contains a sequence
homologous to the ribulose- I ,5-bisphos
phate carboxylase large subunit gene of
chloroplast DNA. Cell 34: 1 007- 1 4
6 2 . Luttke, A . , Bonotto, S . 1 982. Chloro
plasts and chloroplast DNA of Acetabu
laria mediterranea: facts and hypoth
eses. Int. Rev. Cytol. 77:205-42
63. Michel, F. , Dujon, B . 1983. Conserva
tion of RNA secondary structures in two
intron families including mitochondrial-,
chloroplast- and nuclear-encoded mem
bers. EMBO J. 2: 33-38
64. Montandon, P. E . . Stutz, E. 1 984. The
genes for the ribosomal proteins S 1 2 and
S7 are clustered with the gene for the
EF-Tu protein on the chloroplast genome
of Euglena gracilis. Nucleic Acids Res.
1 2:2851-59
64a. Mubumbila, M . , Bowman, C . M . ,
Droog, F . , Dyer, T . , Kuntz, M . , Weil, J .
H . 1 985. Chloroplast transfer RNAs and

tRNA genes o f wheat. Plant Mol. Bioi.
4:3 1 5-20
64b. Mubumbila, M . , Crouse, E. J . , Weil, J .

H . 1 984. Transfer RNAs and tRNA
genes of Vicia faba chloroplasts. Curro

Genet. 8:379-85
65 . Mubumbila, M . , Gordon, K. H. J . ,
Crouse, E . J . , Burkard, G . , Weil, J . H .
1 983. Construction o f the physical map
of the chloroplast DNA of Phaseolus vul
garis and localization of ribosomal and
transfer RNA genes. Gene 2 1 :257-66
66. Myers, A. M . , Grant, D. M . , Rabert, D .
K . , Harris , E . H . , Boynton, J . E. , Gill
ham, N . W. 1982. Mutants of Chiamydo
monas reinhardtii with physical altera
tions in their chloroplast DNA. Plasmid
7 : 1 33-5 1
67. Nierzwicki-Bauer, S . A . , Curtis, S. E. ,
Haselkorn. R. 1 984. Cotranscription of
genes encoding the small and large sub

units of ribulose- I ,5-bisphosphate car
boxylase in the cyanobacterium An
abaena 7 1 20. Proc. Nat!. Acad. Sci.
USA 8 1 :5961-65
68 . Ohme, M . , Kamogashira, T . , Shinozaki,

K . , Sugiura, M. 1 985. Structure and
cotranscription of tobacco chloroplast

genes for tRNAG1U(VVC), tRNATy,
(GVA) and tRNAA'P(GVC) . Nucleic
Acids Res. 1 3 : 1 045-56

69. Ohyama, K . , Yamano, Y . , Fukuzawa,
H . , Komano, T. , Yamagishi, H . , Fu
jimoto, S . , Sugiura, M. 1 983. Physical
mappings of chloroplast DNA from liver
wort Marchantia polymorpha L. cell sus
pension cultures. Mol. Gen. Genet.
1 89: 1-9
70. Orozco, E. M . Jr. , Rushlow, K . E . ,
Dodd, J . R. , Hallick, R. B . 1 980. Eu
glena gracilis chloroplast ribosomal
RNA transcription units. II . Nucleotide

sequence homology between the 1 6S23S ribosomal RNA spacer and the 1 6S
ribosomal RNA leader regions. 1. Bioi.
Chem . 255 : 1 0997- 1 1 003

7 1 . Padmanabhan, V . , Green, B . R. 1 978.
The kinetic complexity of Acetabularia
chloroplast DNA. Biochim. Biophys .
Acta 52 1 :67-73
72. Palmer, J. D. 1 983. Chloroplast DNA
exists in two orientations. Nature
30 1 :92-93
73. Palmer, J. D. 1 985. Evolution of chloro
plast and mitochondrial DNA in plants
and algae. In Monographs in Evolution

ary Biology: Molecular Evolutionary Ge
netics, ed. R. J. MacIntyre, pp. 1 3 1-240.
New York: Plenum.
74. Palmer, J. D . , Boynton, J. E . , Gillham,

N. W . , Harris , E. H. 1 985. Evolution
and recombination of the large inverted
351
repeat in Chlamydomonas chloroplast

DNA. In Molecular Biology of the
Photosynthetic Apparatus, ed. K. Stein
back, S. Bonitz, C. Arntzen , L. Bogor
ad. New York: Cold Spring Harbor. In
press
75. Palmer, J. D . , Edwards, H . , Jorgensen,
R. A . , Thompson, W . F. 1 982. Novel
evolutionary variation in transcription
and location of two chloroplast genes.
Nucleic Acids Res. 1 0:68 1 9-32
76. Palmer, J. D . , Jorgensen, R. A . , Thomp

son, W. F. 1 985. Chloroplast DNA vari
ation and evolution in Pisum: patterns of
change and phylogenetic analysis. Ge
netics 1 09: 1 95-2 1 3
77 . Palmer , 1 . D . , Osorio, B . , Watson , J . C . ,
Edwards, H . , Dodd, J . , Thompson, W .

F . 1 984. Evolutionary aspects o f chloro
plast genome expression and organiza
tion. In Biosynthesis of the Photosynthet
ic Apparatus: Molecular Biology, De
velopment and Regulation, ed. J . P.
Thornber, L . A . Staehelin, R. B. Hal

lick. VCLA Molec. Symp. Cell. BioI . ,
New Ser. 14:273-83. New York: Alan R .
Liss
78. Palmer, J . D . , Shields, C . R. 1 984. Tri
partite structure of the Brassica campes
tris mitochondrial genome. Nature
307:437-40
79. Palmer, J . D . , Shields, C . R. , Cohen, D.
B . , Orton, T. J . 1 983. Chloroplast DNA
evolution and the origin of amphidiploid
Brassica . Theor. Appl. Genet. 65 : 1 8 189

80. Palmer, 1 . D . , Singh, G. P . , Pillay, D. T.
N . 1 983. Structure and sequence evolu
tion of three legume chloroplast DNAs.
Mol. Gen. Genet. 1 90: \ 3- 1 9

8 1 . Palmer, J . D . . Stein, D . B . 1 982. Chloro
plast DNA from the fern Osmunda cinna
momea: Physical organization, gene
localization and comparison to an

giosperm chloroplast DNA. Curro Genet.
5 : 1 65-70
82. Palmer, J. D . , Thompson ,
Rearrangements
in
the
W . F.
1 98 1 .
chloroplast
genomes of mung bean and pea. Pmc.
Natl. Acad. Sci. USA 78:5533-37
83. Palmer, J. D . , Thompson , W. F. 1 982.

Chloroplast DNA rearrangements are
more frequent when a large inverted re
peat is lost. Cell 29:537-50
84. Palmer, J. D . , Zamir, D. 1 982. Chloro
plast DNA evolution and phylogenetic
relationships in Lycopersicon. Proc.
Natl. Acad. Sci. USA 79:5006- 1 0

8 5 . Phillips, A . L. , Gray, J . C. 1 984. Loca
tion and nucleotide sequence of the gene

for the 1 5 . 2 kDa polypeptide of the
cytochrome b-f complex from pea chlo-
352
86.

87.
88.
89.
PALMER
roplasts. Mol. Gen. Genet. 1 94:47784

Pilot, T. J . , Fox, J. L. 1 984. Cloning and
sequencing of the genes encoding the
alpha and beta subunits of C-phyco
cyanin
from
the
cyanobacterium
Agmenellum
quadruplicatum.
Proc.
Natl. Acad. Sci. USA 8 1 :6983-87
Posno, M . , Torenvliet, D. J . , Lustig, H . ,
van Noort, M . , Groot, G . S . P . 1985.
Localization of three chloroplast ribo
somal protein genes at the left junction of
the large single copy region and the in
verted repeat of Spirodela oligorhiza
chloroplast DNA. Curro Genet. 9:2 1 119
Poulsen, C. R. 1983. The barley chloro
plast genome: physical structure and
transcriptional activity in vivo. Carlsberg
Res. Commun. 48:57-80
Rasmussen, O. F . , Bookjans, G . , Stum
mann, B. M. , Henningsen, K. W. 1984.
Localization and nucleotide sequence of
the gene for the membrane polypeptide
02 from pea chloroplast DNA. Plant
Mol. Bioi. 3 : 1 9 1-99
90. Ravel-Chapuis, P . , Heizmann, P . ,

Nigon, V . 1982. Electron microscopic
localization of the replication origin of
Euglena gracilis chloroplast DNA. Na
ture 300:78-8 1
9 1 . Ravel-Chapuis" P . , Flamant, F. , Nico
las, P . , Heizmann, P . , Nigon, V. 1 984.
Diversity of the ribosomal structures in
the Euglena gracilis chloroplast genome:
description of a mutant with two ribo
somal operons and possible mechanism
for its production. Nucleic Acids Res.
1 2 : 1 039-48
92. Rochaix, J. D. 1 97 8 . Restriction en
donuclease map of the chloroplast DNA
of Chlamydomonas reinhardii. J. Mol.
BioI. 1 26:597-6 1 7
9 3 . Rochaix, J . D . , Darlix, J . L. 1 982. Com
posite structure of the chloroplast 23S
ribosomal RNA genes i n Chlamydomo
nas reinhardii: evolutionary and func
tional implications. J. Mol. BioI. 1 59:
383-95
94. Rochaix, J. D . , Dron, M . , Rahire, M . ,
Malnoe, P . 1 984. Sequence homology
between the 32K dalton and the D2 chlo
roplast membrane polypeptides
of
Chlamydomonas reinhardii. Plam Mol.
Bioi. 3:363-70
95 . Rochaix, J. D . , Malnoe, P. 1 97 8 . Anat
omy ofthe chloroplast ribosomal DNA of
Chlamydomonas reinhardii. Cell 1 5 :
661-70
96. Roux, E. , Graf, L . , Stutz, E. 1 98 3 . Nu
cleotide sequence of a ' truncated rRNA
operon' of the Euglena gracilis chloro-
97.
98.
99.
100.
101.
plast genome. Nucleic Acids Res. 1 1 :

1 957-68
Roux, E. , Stutz, E. 1985. The chloro
plast genome of Euglena gracilis: the
mosaic structure of a DNA segment link
ing the extra 16S rRNA gene with the rrn
operon A . Curro Genet. 9:22 1-27
Saits, Y . , Herrmann, R. G . , Peleg, N . ,
Lavi, U . , Izhar, S . , Frankel, R . , Beck
mann, J. S . 1984. Physical mapping of
plastid DNA variation among eleven
Nicotiana species. Theor. Appl. Genet.
69: 1- 1 4
Schlunegger, B . , Stutz, E . 1984. The
Euglena gracilis chloroplast genome:
structural features of a DNA region possi
bly carrying the single origin of DNA
replication. Curro Genet. 8:629-34
Schmidt, R. J . , Hosler, J. P . , Gillham,
N . W . , Boynton, J. B. 1985. Biogenesis
and evolution of chloroplast ribosomes:
cooperation of nuclear and chloroplast
genomes. See Ref. 74. In press
Scott, N. S . , Timmis, J. N. 1 984.
Homologies between nuclear and plastid
DNA in spinach . Theor. Appl. Genet.
67:279-88
102. Scott, N. S . , Tymms, M. J . , Possing

ham, J. V. 1984. Plastid-DNA levels in
the different tissues of potato. Planta
1 6 1 : 1 2- 1 9
103. Sears, B . B . 1 983. Genetics and evolu
tion of the chloroplast. Stadler Symp.
1 5 : 1 1 9-39
1 04 . Sederoff, R . R . 1984. Structural varia
tion in mitochondrial DNA. Adv. Genet.
22: 1 - 1 08
1 0 5 . Seyer, P . , Herrmann , R. G . , Lescure, A.
M . 1 982. Purification of plastid DNA
from tobacco cell suspensions. Plam Sci.
Lett. 25:342-52
106. Shen, G. F. , Chen, K . , Wu, M . , Kung,
S. D.
1982. Nicotiana chloroplast
genome. IV. N. accuminata has larger
inverted repeats and genome size. Mol.
Gen. Genet. 1 87 : 1 2- 1 8
1 0 7 . Shinozaki, K . , Sugiura, M . 1983. The
gene for the small subunit of ribulose
I ,5-bisphosphate carboxylase/oxygenase
is located close to the gene for the large
subunit in the cyanobacterium Anacystis
nidulans 630 1 . Nucleic Acids Res. 1 1 :
6957-64
1 08 . Siu, C. H . , Chiang, K. S . , Swift, H .
1975 . Characterization of cytoplasmic
and nuclear genomes in the colorless alga
Polytoma. V . Molecular structure and
heterogeneity of leucoplast DNA. J.
Mol. BioI. 98:369-9 1
109. Spielmann, A . , Stutz, E. 1983. Nucle
otide sequence of soybean chloroplast
DNA regions which contain the psbA and

trnH genes and cover the ends of the large
single copy region and one end of the
inverted repeats. Nucleic Acids Res.
1 1 : 7 1 57-67
1 1 0. Starnes, S. M . , Lambert, D . H . , Max
well, E. S . , Stevens, S . E . Jr. , Porter, R.
D . , Shively, J . M. 1985. Cotranscription
of the large and small subunit genes of

ribulose-I ,5-bisphosphate carboxylase!

oxygenase in Cyanophora paradoxa .
FEMS Micro. Lett. 28 : 1 65-69
I I I . Steinmuller, K. , Kaling, M . , Zetsche, K .
1 983. In vitro synthesis o f phycob ilipro
teins and ribulose- I ,5-bisphosphate car

box ylase by non-polyadenylated-RNA of
Cyanidium caldarium and Porphyridium
aerugineum. Planta 1 59:308- 1 3
1 12. Stem , D . B . , Lonsdale, D . M . 1982 .
Mitochondrial and chloroplast genomes
of maize have a 1 2-kilobase DNA se
quence in common. Nature 299:698702
1 1 3 . Stem, D. B . , Palmer, J. D. 1984. Exten
sive and widespread homologies between
mitochondrial and chloroplast DNA in
plants. Proc. Natl. Acad. Sci. USA
8 1 : 1 9450
1 1 4 . Strittmayer, G . , Kossel, H. 1 984. Co
transcription and processing of 23S , 4. 5S
and 5S rRNA in chloroplasts from Zea
mays . Nucleic Acids Res. 1 2:7633-47
1 1 5 . Sugita, M . , Kato, A . , Shimada, H . ,
Sugiura, M. 1 984. Sequence analysis of
the junctions between a large inverted
repeat and single -copy regions in tobacco
chloroplast DNA. Mol.
Gen.
Genet.
1 94:200--5
1 1 6 . Takaiwa, F. , Sugiura, M. 1 982. Nucle
otide sequence of the 1 6S-23S spacer re
gion in an rRNA gene cluster from tobac
co chloroplast DNA. Nucleic Acids Res.
10:2665-76
1 1 7 . Thompson, J. A. 1 980. Apparent identity
of chromoplast and chloroplast DNA in
the daffodil, Narcissus pseudonarcissus.
Z. Naturforsch. 35c: I 1 0 1-3
1 1 8 . Thompson, J . A . 1 980. Isolation and
characterization of DNA from different
plastid types of Tropaeolum majus. Eur.
J. Cell Bioi. 2 1 :37-42
1 1 9. Timmis, J. N . , Scott, N. S. 1983. Se
quence homology between spinach nu
clear and chloroplast genomes. Nature
305 :65-67
1 20. Tomioka, N . , Sugiura, M. 1984. Nucle
otide sequence of the 16S-23S spacer re
gion in the rrnA operon from a blue
green alga, Anacystis nidulans. Mol.
Gen. Genet. 1 93 :427-30
1 2 1 . Tymms, M. J . , Schweiger, H . -G . 1 985 .
Tandemly repeated nonribosomal DNA
sequences in the chloroplast genome of
353
an Acetabularia mediterranea strain.

Proc. Natl. Acad. Sci. USA 82: 1 70 1 O
1 2 2 . Van Ee, J . H . , Vos, Y . J . , Bohnert, H .
J . , Planta, R . J . 1 982. Mapping o f genes
on the chloroplast DNA of Spirodela oli

gorhiza . Plant Mol. Bioi. 1 : 1 1 7-3 1
1 23 . Vaughn, K. c . , DeBonte, L. R . , Wilson,
K. G . , Schaeffer, G. W. 1980. Organelle
alteration as a mechanism for maternal
inheritance. Science 208: 1998
1 24 . Waddell, J . , Wang, X . M . , Wu, M .

1 984. Electron microscopic localization
of the chloroplast DNA repl icative ori
gins in Chlamydomonas reinhardii.
Nucleic Acids Res. 1 2: 3843-56
1 25 . Walbot, V. 1 977 . The dimorphic chloro

plasts of the C4 plant Panicum maximum
contain identical genomes . Cell 1 1 :72937
1 26 . Ward , B . L . , Anderson, R. S . , Bendich,
A. J. 1 98 1 . The mitochondrial genome is
large and variable i n a family of plants
(Cucurbitaceae). Cell 25:793-803
1 27 . Watson , J . C . , Palmer, J. D . , Thompson,
W. F. 1983. Chloroplast genes for com
ponents of the translational apparatus.
Carnegie Inst. Yearb . 82:24-26
1 :48. Westhoff, P . , Alt, J . , Nelson, N . , Herr
mann, R. G . 1 985. Genes and transcripts
for the ATP synthase CFo subunits I and
II from spinach thylakoid membranes.
Mol. Gen. Genet. 1 99:290--99
1 29 . Whatley, J. M. 1 983. Plastids-past,
present, and future. Int. Rev. Cytol.
Suppl. 14:329-74
1 30. Whitfeld, P. R . , Bottomley, W. 1 983.
Organization and structure of chloroplast
genes. Ann. Rev. Plant Physiol. 34:279310
I 3 1 . Willey, D . L . , Howe, C . J . , Auffret, A .
D . , Bowman, C . M . , Dyer, T. A . , Gray,
J. C. 1 984. Location and nucleotide se
quence of the gene for cytochrome f in
wheat chloroplast DNA. Mol. Gen.
Genet. 194:41 22
1 32. Woessner, J. P. , Masson, A. , Harris, E.
H . , Bennoun, P . , Gillham, N. W . , Boyn
ton, J. E. 1 984. Molecular and genetic
analysis of the chloroplast ATPase of
Chlamydomonas. Plant Mol. Bioi. 3 :
1 77-90
1 33 . Wurtz, E. A . , Buetow, D. E. 1 98 1 . In
traspecific variation in structural organi
zation and redundancy of chloroplast
ribosomal DNA cistrons in Euglena gra
cilis. Curro Genet. 3: 1 8 1-87
1 34. Wurtz, E. A . , Boynton, J. E . , Gillham,
N . W. 1977 . Perturbation of chloroplast
gene transmission in Chlamydomonas
reinhardtii by 5-fluorodeoxyuridine.
Proc. Natl. Acad. Sci. USA 74:4552-56
1 3 5 . Wunz, E. A . , Sears, B. B . , Raber!, D .
354
PALMER
K . , Shepherd , H. S . , Gillham, N. W . ,
Boynton, J . E. 1979. A specific increase
in chloroplast gene mutations following

growth of Chlamydomonas in 5fluorodeoxyuridine. Mol. Gen. Genet.
1 70:235-42
1 36 . Yamada, T. 1 983. Characterization of
inverted repeat sequences and ribosomal
RNA genes of chloroplast DNA from

Chiarella ellipsoidea. Curro Genet. 7 :

48 1-87
1 37 . Zurawski, G . , Bottomley, W . , Whitfeld,
P. R. 1984. Junctions of the large single
copy region and the inverted repeats in

Spinacia oleracea and Nicotiana debneyi
chloroplast DNA: sequence of the genes
for tRNAH" and the ribosomal proteins
S 1 9 and L2 . Nucleic Acids Res. 1 2:6547-
58
1 38 . Zurawski, G . , Clegg, M . T . , Brown, A .
H . D . 1984. The nature o f nucleotide
sequence divergence between barley and

maize chloroplast DNA. Genetics 1 06:
735-49

Palmer 1985

Transféré par

Informations du document

Copyright

Formats disponibles

Partager ce document

Partager ou intégrer le document

Options de partage

Avez-vous trouvé ce document utile ?

Ce contenu est-il inapproprié ?

Droits d'auteur :

Formats disponibles

Palmer 1985

Transféré par

Droits d'auteur :

Formats disponibles

ANNUAL

Quick links to online content

Ann. Rev. Genet.

All rights reserved

DIVERSITY OF CHLOROPLAST DNA ARRANGEMENTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Genome Size and Conformation . . . . . . . . . . . . . .. . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

EVOLUTIONARY TRENDS IN CHLOROPLAST GENOME ORGANIZATION . . . . . . .

INDUCED ALTERATIONS IN CHLOROPLAST GENOME STRUCTURE . . . . . . . . . . . . .

0066-4197/85 /1215 -0325 $02. 00

Annu. Rev. Genet. 1985.19:325-354. Downloaded from www.annualreviews.org

interested in the sequence and expression of chloroplast genes are referred to

DIVERSITY OF CHLOROPLAST DNA ARRANGEMENTS

Genome Size and Conformation

CHLOROPLAST DNA ORGANIZATION

Size and structure of chloroplast DNAs

Annu. Rev. Genet. 1985.19:325-354. Downloaded from www.annualreviews.org

bData summarized from tables in

13(1) and from J. Palmer and

'J. Palmer, D. Stein (unpublished data).

dM. Reith, R. Cattolico (unpublished data).

34,35 , 73). If this inference is true, then the

endosymbiotic origin (reviewed in

larger genome size in Acetabularia is likely the result of secondary increases

Annu. Rev. Genet. 1985.19:325-354. Downloaded from www.annualreviews.org

from Acetabularia and angiosperms synthesize much the same pattern of

Annu. Rev. Genet. 1985.19:325-354. Downloaded from www.annualreviews.org

CHLOROPLAST DNA ORGANIZATION

sativum) data are from (85,89,127; J. Gray,T. A. Dyer,D. L. Willey,G. R. M. Courtice,T. M .

luteus data are from (M. Reith, R. Cattolico, unpublished data).

Annu. Rev. Genet. 1985.19:325-354. Downloaded from www.annualreviews.org

235 165 ...Q-""

Annu. Rev. Genet. 1985.19:325-354. Downloaded from www.annualreviews.org

CHLOROPLAST DNA ORGANIZATION

Annu. Rev. Genet. 1985.19:325-354. Downloaded from www.annualreviews.org

Gene Content, Order, and Structure

Annu. Rev. Genet. 1985.19:325-354. Downloaded from www.annualreviews.org

CHLOROPLAST DNA ORGANIZATION

Ribosomal RNA transcription units of chloroplasts and cyanobacteria. Filled boxes

Annu. Rev. Genet. 1985.19:325-354. Downloaded from www.annualreviews.org

CHLOROPLAST DNA ORGANIZAnON

The most prominent structural differences found among individual chloro

EVOLUTIONARY TRENDS IN CHLOROPLAST GENOME

SIZE VARIATION AND REPEAT CONTENT

Annu. Rev. Genet. 1985.19:325-354. Downloaded from www.annualreviews.org

unpuhlished data) are shown with their inverted repeats paired .

complexity . At one extreme , the 2 17-kb geranium cpDNA chromosome

Annu. Rev. Genet. 1985.19:325-354. Downloaded from www.annualreviews.org

CHLOROPLAST DNA ORGANIZAnON

Annu. Rev. Genet. 1985.19:325-354. Downloaded from www.annualreviews.org

Much of the variation in sequence complexity of angiosperm cpDNA appears

Annu. Rev. Genet. 1985.19:325-354. Downloaded from www.annualreviews.org

CHLOROPLAST DNA ORGANIZATION

Annu. Rev. Genet. 1985.19:325-354. Downloaded from www.annualreviews.org

events; however, modeling efforts suggest that a minimum of about 12 in

Annu. Rev. Genet. 1985.19:325-354. Downloaded from www.annualreviews.org

CHLOROPLAST DNA ORGANIZATION

Annu. Rev. Genet. 1985.19:325-354. Downloaded from www.annualreviews.org

example, although their 22-23-kb rRNA-encoding inverted repeats differ by

CHLOROPLAST DNA ORGANIZATION

Annu. Rev. Genet. 1985.19:325-354. Downloaded from www.annualreviews.org

INDUCED ALTERATIONS IN CHLOROPLAST GENOME

Annu. Rev. Genet. 1985.19:325-354. Downloaded from www.annualreviews.org

CHLOROPLAST DNA ORGANIZATION

double-stranded ends close together, facilitating their joining and repair. Un