The zebrafish (Danio rerio) is a tropical freshwater fish belonging to the minnow family

(Cyprinidae) of the order Cypriniformes.

[1]
Native to the Himalayan region, it is a popular
aquarium fish, frequently sold under the trade name zebra danio.
[2]
The zebrafish is also an
important vertebrate model organism in scientific research. It is particularly notable for its
regenerative abilities,
[3]
and has been modified by researchers to produce several transgenic
strains.
[4][5][6]

Contents
1 Taxonomy
2 Distribution
3 Description
4 Reproduction
5 Feeding
6 Aquarium care
7 Strains
o 7.1 Wild-type strains
o 7.2 Hybrids
8 In scientific research
o 8.1 Model characteristics
o 8.2 Regeneration
o 8.3 Genetics
9 In medical research
o 9.1 Cancer
o 9.2 Cardiovascular disease
o 9.3 Immune system
o 9.4 Infectious diseases
o 9.5 Repairing retinal damage
o 9.6 Drug discovery
10 See also
11 References
12 Further reading
13 External links
Taxonomy
The zebrafish is a derived member of the genus Danio, of the family Cyprinidae. It has a
sister-group relationship with Danio kyathit.
[7]
Zebrafish are also closely related to the genus
Devario, as demonstrated by a phylogenetic tree of close species.
[8]
The zebrafish was
referred to in scientific literature as Brachydanio rerio for many years until its reassignment
to the genus Danio.
[9]

Distribution
The zebrafish is native to the streams of the southeastern Himalayan region,
[7]
and is found in
parts of India, Pakistan, Bangladesh, Nepal, and Burma.
[10]
The species arose in the Ganges
region in eastern India, and commonly inhabits streams, canals, ditches, ponds, and slow-
moving or stagnant water bodies, including rice fields.
[11]
Zebrafish have been introduced to
parts of the United States, presumably by deliberate release or by escape from fish farms.
[10]

Description
The zebrafish is named for the five uniform, pigmented, horizontal, blue stripes on the side of
the body, which are reminiscent of a zebra's stripes, and which extend to the end of the caudal
fin. Its shape is fusiform and laterally compressed, with its mouth directed upwards. The male
is torpedo-shaped, with gold stripes between the blue stripes; the female has a larger, whitish
belly and silver stripes instead of gold. Adult females exhibit a small genital papilla in front
of the anal fin origin. The zebrafish can grow to 6.4 cm (2.5 in) in length, although it seldom
grows larger than 4 cm (1.6 in) in captivity. Its lifespan in captivity is around two to three
years, although in ideal conditions, this may be extended to five years.
[11]

Reproduction


A juvenile zebrafish.
The approximate generation time for Danio rerio is three to four months. A male must be
present for ovulation and spawning to occur. Females are able to spawn at intervals of two to
three days, laying hundreds of eggs in each clutch. Upon release, embryonic development
begins; absent sperm, growth stops after the first few cell divisions. Fertilized eggs almost
immediately become transparent, a characteristic that makes D. rerio a convenient research
model species.
[11]



Diagram showing the life cycle of a zebrafish from fertilization to adulthood.
The zebrafish embryo develops rapidly precursors to all major organs appear within 36
hours of fertilization, and hatching takes place 1236 hours later, depending on the embryo's
internal conditions and the external temperature, which is ideally 28.5 C (83.3 F).
Swimming and feeding behavior begin about 36 hours later. The sex of juveniles cannot be
distinguished except by dissection, and sex determinants are not clearly understood.
To encourage the fish to spawn, some researchers use a fish tank with a sliding bottom insert,
which reduces the depth of the pool. The technique is most effective in the early morning,
given that ovulation and spawning are enhanced by light. Researchers have been able to
collect 10,000 embryos in 10 minutes using this method.
[12]
Male zebrafish are furthermore
known to respond to more pronounced markings on females, i.e., "good stripes", but in a
group, males will mate with whichever females they can find. What attracts females is not
currently understood. The presence of plants, even plastic plants, also apparently encourages
spawning.
[12]

Feeding
Zebrafish are omnivorous, primarily eating zooplankton, phytoplankton, insects and insect
larvae, although they can eat a variety of other foods, such as worms and small crustaceans, if
their preferred food sources are not readily available.
[11]
Most zebrafish accept common food
flakes and tubifex worms in the aquarium.
Aquarium care
Zebrafish are hardy fish and considered good for beginner aquarists. Their enduring
popularity can be attributed to their playful disposition,
[13]
as well as their rapid breeding,
aesthetics, cheap price and broad availability. They also do well in schools or shoals of six or
more, and interact well with other fish species in the aquarium. However, they are susceptible
to Oodinium or velvet disease, microsporidia (Pseudoloma neurophilia), and Mycobacterium
species. Given the opportunity, adults eat hatchlings, which may be protected by separating
the two groups with a net, breeding box or separate tank.
Strains
In late 2003, transgenic zebrafish that express green, red, and yellow fluorescent proteins
became commercially available in the United States. The fluorescent strains are tradenamed
GloFish; other cultivated varieties include "golden", "sandy", "longfin" and "leopard".
The leopard danio, previously known as Danio frankei, is a spotted colour morph of the
zebrafish which arose due to a pigment mutation.
[14]
Xanthistic forms of both the zebra and
leopard pattern, along with long-finned subspecies, have been obtained via selective breeding
programs for the aquarium trade.
[15]

Wild-type strains
The Zebra Fish Information Network (ZFIN) provides up-to-date information about current
known wild-type (WT) strains of D. rerio, some of which are listed below.
[16]

AB (AB)
AB/C32 (AB/C32)
AB/TL (AB/TL)
AB/Tuebingen (AB/TU)
C32 (C32)
Cologne (KOLN)
Darjeeling (DAR)
HK/AB (HK/AB)
HK/Sing (HK/SING)
Hong Kong (HK)
India (IND)
Indonesia (INDO)
Nadia (NA)
RIKEN WT (RW)
SJA (SJA)
SJD (SJD)
SJD/C32 (SJD/C32)
Tuebingen (TU)
Tupfel long fin (TL)
Tupfel long fin nacre
(TLN)
WIK (WIK)
Ekkwill (EKW) Singapore (SING) WIK/AB (WIK/AB)
Hybrids
Hybrids between different Danio species may be fertile: for example, between D. rerio and
D. nigrofasciatus.
[8]

In scientific research


Zebrafish chromatophores, shown here mediating background adaptation, are widely studied
by scientists.


A zebrafish pigment mutant (bottom) produced by insertional mutagenesis.
[8]
A wild-type
embryo (top) is shown for comparison. The mutant lacks black pigment in its melanocytes
because it is unable to synthesize melanin properly.
D. rerio is a common and useful model organism for studies of vertebrate development and
gene function. Its use as a laboratory animal was pioneered by George Streisinger and
colleagues at the University of Oregon. Its importance has been consolidated by successful
large-scale forward genetic screens (commonly referred to as the Tbingen/Boston screens).
The fish has a dedicated online database of genetic, genomic, and developmental information,
the Zebrafish Information Network (ZFIN). D. rerio is also one of the few fish species to
have been sent into space.
Research with D. rerio has yielded advances in the fields of developmental biology,
oncology,
[17]
toxicology,
[18]
reproductive studies, teratology, genetics, neurobiology,
environmental sciences, stem cell research and regenerative medicine,
[19][20]
and evolutionary
theory.
[8]

Model characteristics
As a model biological system, the zebrafish possesses numerous advantages for scientists. Its
genome has been fully sequenced, and it has well-understood, easily observable and testable
developmental behaviors. Its embryonic development is very rapid, and its embryos are
relatively large, robust, and transparent, and able to develop outside their mother.
[21]

Furthermore, well-characterized mutant strains are readily available.
Other advantages include the species' nearly constant size during early development, which
enables simple staining techniques to be used, and the fact that its two-celled embryo can be
fused into a single cell to create a homozygous embryo. The zebrafish is also demonstrably
similar to mammalian models and humans in toxicity testing, and exhibits a diurnal sleep
cycle with similarities to mammalian sleep behavior.
[22]

Regeneration
Zebrafish have the ability to regenerate their fins, skin, heart and, in larval stages, brain.
[23]

Zebrafish heart muscle regeneration does not make use of stem cells; instead, mature heart
muscle cells regress to a stem cell-like state and redifferentiate.
[23]
In 2011, the British Heart
Foundation ran an advertising campaign publicising their intention to study the applicability
of this ability to humans, by raising 50 million in research funding.
[24][25]

Zebrafish have also been found to regenerate photoreceptor cells and retinal neurons
following injury, which has been shown to be mediated by the dedifferentiation and
proliferation of Mller glia.
[26]
Researchers frequently amputate the dorsal and ventral tail
fins and analyze their regrowth to test for mutations. It has been found that histone
demethylation occurs at the site of the amputation, switching the zebrafish's cells to an
"active", regenerative, stem cell-like state.
[27]
In 2012, Australian scientists published a study
revealing that zebrafish use a specialised protein, known as fibroblast growth factor, to ensure
their spinal cords heal without glial scarring after injury.
[3]

In probing disorders of the nervous system, including neurodegenerative diseases, movement
disorders, psychiatric disorders and deafness, researchers are using the zebrafish to
understand how the genetic defects underlying these conditions cause functional
abnormalities in the human brain, spinal cord and sensory organs. Researchers have also
studied the zebrafish to gain new insights into the complexities of human musculoskeletal
diseases, such as muscular dystrophy.
[28]
Another focus of zebrafish research is to understand
how a gene called Hedgehog, a biological signal that underlies a number of human cancers,
controls cell growth.
Genetics
Gene expression
Due to their short lifecycles and relatively large clutch sizes, zebrafish are a useful model for
genetic studies. A common reverse genetics technique is to reduce gene expression or modify
splicing using Morpholino antisense technology. Morpholino oligonucleotides (MO) are
stable, synthetic macromolecules that contain the same bases as DNA or RNA; by binding to
complementary RNA sequences, they reduce the expression of specific genes. MO can be
injected into one cell of an embryo after the 32-cell stage, reducing gene expression in only
cells descended from that cell. However, cells in the early embryo (less than 32 cells) are
interpermeable to large molecules,
[29][30]
allowing diffusion between cells.
A known problem with gene knockdowns is that, because the genome underwent a
duplication after the divergence of ray-finned fishes and lobe-finned fishes, it is not always
easy to silence the activity one of the two gene paralogs reliably due to complementation by
the other paralog.
[31]
Despite the complications of the zebrafish genome, a number of
commercially available global platforms exist for analysis of both gene expression by
microarrays and promoter regulation using ChIP-on-chip.
[32]

Genome sequencing
The Wellcome Trust Sanger Institute started the zebrafish genome sequencing project in
2001, and the full genome sequence of the Tuebingen reference strain is publicly available at
the National Center for Biotechnology Information (NCBI)'s Zebrafish Genome Page. The
zebrafish reference genome sequence is annotated as part of the Ensembl project, and is
maintained by the Genome Reference Consortium.
[33]

In 2009, researchers at the Institute of Genomics and Integrative Biology in Delhi, India,
announced the sequencing of the genome of a wild zebrafish strain, containing 1.7 billion
genetic letters.
[34][35]
The genome of the wild zebrafish was sequenced at 39-fold coverage.
Comparative analysis with the zebrafish reference genome revealed over 5 million single
nucleotide variations and over 1.6 million insertion deletion variations. The zebrafish
reference genome sequence was published by Kerstin Howe et al. in 2013.
[36]

Mitochondrial DNA
In October 2001, researchers from the University of Oklahoma published D. rerio's complete
mitochondrial DNA sequence.
[37]
Its length is 16,596 base pairs. This is within 100 base pairs
of other related species of fish, and it is notably only 18 pairs longer than the goldfish
(Carassius auratus) and 21 longer than the carp (Cyprinus carpio). Its gene order and content
are identical to the common vertebrate form of mitochondrial DNA. It contains 13 protein-
coding genes and a noncoding control region containing the origin of replication for the
heavy strand. In between a grouping of five tRNA genes, a sequence resembling vertebrate
origin of light strand replication is found. It is difficult to draw evolutionary conclusions
because it is difficult to determine whether base pair changes have adaptive significance via
comparisons with other vertebrates' nucleotide sequences.
[37]

Pigmentation genes
In December 2005, a study of the golden strain identified the gene responsible for its unusual
pigmentation as SLC24A5, a solute carrier that appeared to be required for melanin
production, and confirmed its function with a Morpholino knockdown. The orthologous gene
was then characterized in humans and a one base pair difference was found to strongly
segregate fair-skinned Europeans and dark-skinned Africans.
[38]

Transgenesis
Transgenesis is a popular approach to study the function of genes in zebrafish. Construction
of transgenic zebrafish is rather easy by a method using the Tol2 transposon system.
[39]

Transparent adult bodies
In 2008, researchers at Boston Children's Hospital developed a new strain of zebrafish,
named Casper, whose adult bodies had transparent skin.
[5]
This allows for detailed
visualization of cellular activity, circulation, metastasis and many other phenomena. Because
many gene functions are shared between fish and humans, the Casper strain is expected to
yield insights into human diseases such as leukemia and other cancers.
[5]
In January 2013,
Japanese scientists genetically modified a transparent zebrafish specimen to produce a visible
glow during periods of intense brain activity, allowing the fish's "thoughts" to be recorded as
specific regions of its brain lit up in response to external stimuli.
[6]

Use in environmental monitoring
In January 2007, Chinese researchers at Fudan University genetically modified zebrafish to
detect oestrogen pollution in lakes and rivers, which is linked to male infertility. The
researchers cloned oestrogen-sensitive genes and injected them into the fertile eggs of
zebrafish. The modified fish turned green if placed into water that was polluted by
oestrogen.
[4]