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10/306997/PMU/6710 11/322094/PMU/6977

 Introduction of plant gene and genome

Differences of Nuclear and Organelle


Mechanism involved in dna quantitiy



What is GENE?

Region of DNA or RNA that encode for a polypeptide or for an RNA chain that has a function in the organism A modern definition : "a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions, and or other functional sequence regions“

What is GENOME?
• GENOME is all of a living thing's genetic material, includes both the genes and the non-coding sequences encoded either in DNA or RNA

Tree of plant genomes • Nuclear genome • Mitochondrial Genomes • Chloroplast Genomes

Endosymbiotic evolution

Mitochondria arose from α-proteobacteria and chloroplasts arose from cyanobacteria

Nuclear vs Organelle genomes


Nuclear genome structure
A chromosome is the visible state of genetic material during a phase of the division of the cell (prometafase/metaphase) DNA in metaphase chromosomes must be shortened 10,000-fold by very efficient packing. The DNA molecule is twisted onto itself, and the supercoiled molecule is wrapped around proteins which maintain its shape.

These proteins are histone proteins. The complex DNA protein is called chromatin, while the structure formed by two turns of DNA around one histone is called a nucleosome.

Chromosome nuclear structure

Overview of the many orders of DNA condensation into chromatin

Euchromatine & Heterochromatin

DNA containing genes is called euchromatin Non-genic DNA is called heterochromatin. Heterochromatin and euchromatin stain differently. This difference causes the bands we see in a karyotype.

Genome composition

Euchromatin (genes) usually contains a higher proportion of GC. Euchromatin has more unique DNA sequences. Heterochromatin (non-coding) usually contains a higher proportion of AT. Heterochromatin contains more repetitive sequence.s

Differences of organelle and nuclear genomes
No. 1 2 3 4 5 DNA Structure Circular DNA Differences Organelle genomes Packing with No histone proteine Intron in DNA No sequence Inheritance Maternal Yes Yes Nuclear genomes Linear DNA

Result of recombination from male and female DNA polymerase DNA polymerase I, low DNA polymerase 1, 2, 3 and proofreading activity ε with intrinsic proofreading activity

Nuclear genome size in different species

Sizes and coding content of some organelle and prokaryote genomes


Sizes and coding content of some organelle and prokaryote genomes

• •

Polyploidization Revetitive sequence - rRNA gene - centromers - telomeres - transposons

Ribosomal RNA genes



• •

The telomeres of most organisms' chromosomes consist of short sequence-asymmetric repeated sequences. Lengths are typically greater than 50 repeats in holotrichous ciliates, less than 350 repeats in Arabidopsis and 300 to 500 bp in Saccharomyces. A Drosophila chromosome, an exception, has a transposable element at the end of one of its chromosomes. Examples:

telomere Sentromere


T Transposable Elements (TEs)
50-80% of plant genomes are TEs Discovered by Barbara McClintock by studying unstable corn kernel phenotypes Fragments of DNA that can insert into new chromosomal locations Often duplicate themselves during the process of moving around

Class 1 TEs use RNA intermediates to move around and undergo duplicative transposition Class 2 TEs are excised during transposition and may undergo “cut and paste” transposition with no duplication or “gap repair” where the gap is filled with a copy of the transposon Autonomous elements contain necessary genes for transposition Non-autonomous elements rely on products of other elements for transposition

Class II Transposons
• Move by a "cut and paste" process: the transposon is cut out of its location and inserted into a new location • Requires a transposase to cut and insert DNA fragment. • Transposon has terminal inverted repeats • Excision generates direct repeats (~ target insertion sites)



The genomes are very dynamic Genome of plant is located in nuclues, mitochondria and chloroplast Genetic element is changed at different scales: • Gene • Chromosome segments • Genome

1. Jenik, P.D. Jurkuta, R.E. and Barton, M.K. 2005.

Interactions between the cell cycle and embryonic patterning in Arabidopsis uncovered by a mutation in DNA polymerase epsilon. Plant Cell 17: 3362–3377

2. Parent, J. Lepage, E. and Brisson, N. 2011.

Divergent Roles for the Two PolI-Like Organelle DNA Polymerases of Arabidopsis. Plant Physiology 156 (1): 254-262 Nature 441: 398-401

3. Pearson, H. 2006. Genetics: what is a gene?. 4. Quiroz, H.C.2002. Plant genomics: an

5/15/12 overview. Biological Research 35: 3-4 

7. Casacuberta and Santiago, 2003, Plant LTRretransposons and MITEs: control of transcription and impact on the evolution of plants genes and genomes. Elsevier Gene 311 (2003) 1-11.


Terima kasih…..

Coordination between the nucleus and organelle genomes

Anterogade signaling

Anterogade signaling

Retrogade signaling

Retrogade signaling

Polyploidy (here, autopolyploidy)

Structure of the different types of plant transposable elements