Zebra Fish- A Model Organism

-SUBHRADEEP SARKAR M.Sc. in APPLIED GENETICS

Zebra fish biology and genome study

Introduction

The zebrafish, Danio rerio, is a tropical freshwater fish belonging to the family cyprinidae.

It is a popular aquarium fish, frequently sold under the trade name zebra Danio.

It is an important vertebrate model organism in scientific research.

Distribution

The zebrafish is native to the streams of the southeastern Himalayan region.

It arose in the Ganges region in Eastern india and is also native to Pakistan, Bangladesh, Nepal, and Myanmar.

It commonly inhabits streams, canals, ditches, ponds, and slow

moving to stagnant water bodies, including rice fields Zebrafish have been introduced in aquariums in Japan,

Canada, the united States and Australia.

Morphology The fish is named for the five uniform, pigmented,

horizontal blue stripes on the side of the body, all of which extend to the end of the caudal fin .

Males are torpedo shaped and have gold stripes between the blue stripes;

Females have a larger, whitish belly and have silver stripes instead of gold.

The zebrafish grows to 6.4 centimetres (2.5 in). Most zebrafish in captivity

live for 2–3 years, although in ideal conditions, they may live up to 5 years.

Zebra fish as a model organism Some of its advantages for biologists: It is a vertebrate, like us, and thus can provide clues to human biology . Its embryos develop outside the body where they can be easily

observed Its embryos are transparent so defects in development can be seen

easily. Embryonic development is quick (only 3 days). They can be made transgenic. Easier to house and care . Genetic similarity to humans.  Lots of offspring

Embryonic development The zebrafish is easy to raise and breed in the

laboratory. Its embryonic development is spectacularly fast It generates a typical vertebrate body plan – with a

neural tube, muscles, a vascular system and a beating heart – within 24 hours of fertilization .

Adults breed year-round, and natural matings generate large and synchronous batches of embryos

The eggs are fertilized externally, and an average clutch size is about 200.

Embryonic development

Stages of embryonic development zygote Period (0-45 min)

Cleavage Period (0.7- 2.2 h) Blastula Period (2 1/4 - 5 1/4 h) Gastrula Period (5 1/4 - 10 h) Segmentation Period (10-24 h) Pharyngula Period (24-48 h)

Hatching Period (48-72 h)

Embryonic development

The zygote is 0.7mm at the time of fertilization.• The chorion swells and lifts away from the newly fertilized egg

• During early development, cytoplasmic streaming movements in the egg generate an area of yolk-free cytoplasm – the blastodisc – at the top (animal) pole of

the embryo

1 ce

ll

Embryonic development Early cleavages occur every fifteen minutes. They divide the blastodisc, but not the yolk, generating

a mound of cells on top of the embryo. The embryo is now termed a blastula

                                                     

4 cell 2cell

Embryonic development

In the late blastula, the blastodisc thins and forms a blastoderm that spreads over the yolk, eventually completely engulfing it.

mid-blastula late blastula

Embryonic development

                                           

50% epiboly (side view

View from animal pole showing embryonic shield at top of image

Embryonic development This spreading movement is termed as epiboly. At 50% epiboly, the leading edge of the blastoderm

margin thickens and migrating cells begin to converge there, generating the embryonic shield.

These thickenings are the first sign of the gastrulation.

Embryonic development

gastrula stage

Embryonic development During segmentation period a variety of morphogenetic

movements now occur, the somites develop, the rudiments of the primary organs become visible, the tail bud becomes more prominent and the embryo elongates

Shortly after each somite forms, its surface appears epithelial.

The endoderm becomes morphologically distinctive at about the onset of the segmentation period

The notochord differentiates

Embryonic development Pharyngula period is the time of development when one

can most readily compare the morphologies of embryos of diverse vertebrates

The period name implies the appearance of primordia of the pharyngeal arches

The circulatory system forms , the heart begins to beat just at the onset of the period and forms well delineated chambers.

Blood begins to circulate though a closed set of channels. The fins begin to form There is marked behavioral development. Tactile sensitivity

appears, and the flexions that occurred in myotomes during the late stage become orchestrated into rhythmic bouts of swimming

Embryonic development During the hatching period the embryo continues to

grow at about the same rate as earlier

Morphogenesis of many of the organ rudiments is now rather complete.

Much easier to see are the rapidly developing rudiments of the pectoral fins, the jaws, and the gills.

Zebra fish genome 1)The zebrafish genome comprises 1.7x109 bp is

about half the size of the human genome 2)The chromosome complement of D.rerio is 2n=50 3)The are two metacentric (6,11), eight

submetacentric chromosomes (3,7,9,12,15,20,21 &23) and remaining15 chromosomes are subtelocentric.

4) In February 2001 the Sanger Institute started sequencing the genome of the zebrafish (Danio rerio)

5)The genome contains about 22000 genes.

Zebra fish genome 6)Analysis of gene maps shows that zebrafish

chromosomes have conserved syntenies with large segments of human chromosomes.

7) Zebrafish genes demonstrate on average greater than 75% similarity to human genes.

8) Comparative genomics using zebrafish and human gene maps has shown the existence of several blocks of synteny that existed in the common ancestor of these two species, app.450 million years ago

Zebra fish genome

9) Genetic maps show that segments of human chromosomes are generally present in zebrafish as two orthologous copies.

10) These data suggest a genome duplication event in the zebrafish lineage.

11) If the multiple copies of zebrafish chromosome segments arose by whole genome duplication , zebrafish should have twice as many chromosomes as humans .

12)But zebrafish, with 25 chromosomes, has just two more chromosomes in the haploid set than humans.

Zebra fish genome

13) It is hypothesized that last common ancestor of zebrafish and humans had app.24 chromosomes, and an excess of chromosome fusions in the fish lineage before or after the genome duplication reestablished the original number.

14) Due to extensive similarity between the zebrafish and human genomes so many human developmental and disease genes have counterparts in the zebrafish.

15) Mutations in zebrafish orthologues of human disease genes produce phenotypes similar to human disease states.

Zebra fish genome 16). Large numbers of mutations that disrupt embryonic

development have now been isolated in the zebrafish, many of which may serve as models for human disease syndromes.

17)For example, screening zebrafish populations has identified mutations in a number of genes - including sonic hedgehog - that result in a phenotype reminiscent of the holoprosencephaly syndrome.

Zebra fish genome 18) The genome of the zebrafish, Danio rerio,

contains two major classes of tandem repetitive elements (AT-rich and GC-rich).

19)The AT-rich sequences were found at the centromeres of all chromosome pairs and the GC-rich sequences were found in paracentromeric location on over half of the chromosomal pairs.

20) By comparing ESTs to whole-genome shotgun data, it is predicted that 50,000 high-quality candidate SNPs covers the zebrafish genome