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Friday, 7 August 2020

Why use zebrafish as a model organism for research work?

        Why use zebrafish as a model organism for research work?

                 zebrafish as a model organism for research work


·        Danio rerio (Zebrafish) are small tropical freshwater fish in the minnow family (Cyprinidae), native to Northeast India and Pakistan.
·       They are well-known as a common aquarium fish, retailed under the name Zebra danio.
·        It is a vertebrate modal organism used in the laboratory to help the scientists in the biological process.

Taxonomy of Danio rerio (F. Hamilton, 1822) 
















Danio rerio

Biology features :

·         This fish has unchanging five pigmented horizontal blue bands on the side of the body, all stripes spread up to the end of the caudal fin.

·         Growth of the zebrafish is up to 6.4 cm (2.5 in)

·          Mouth directed upwards and body laterally compressed.

·          It is Omnivorous in feeding  i.e both plant and animal

·         Zebrafish have a life span of 1-2 years.

Sexual Dimorphism:

·         Males are slender, the body shape is torpedo mostly with a pink or yellow tinge, gold stripes are present in between the blue stripes.

·          Females tend to be less pink than males.

·         Females are fatter as they carry eggs in their belly.

·         Females fish have whitish belly and silver stripes are present in amid the blue stripes instead of gold.

Why use zebrafish as a model organism for research work?

Scientists and researchers across the globe acclaimed zebrafish as a model organism due to its diverse features that make its use as a model organism. Some of them are given below.

1.      External Fertilization: Zebrafish eggs are fertilized outside the fish body. It can be used for studying early embryonic development and Organogenesis.

2.      More progeny: Zebrafish lays hundreds of eggs, average clutch size is about 200 which ultimately leads more offspring available for research work as compared to other model organisms like Mouse or Caenorhabditis elegans

3.      Small generation interval: As compared to other model organisms, Zebrafish matures 3-4 months only

4.      Transparent eggs or Embryos: Zebrafish eggs are nearly crystal clear or transparent which allows scientists and researchers to easily examine the development of internal structures. It takes only 3 days for embryonic development. Transparent eggs or embryos: can be used easily gene manipulation study.  

5.      Genomic Information: Whole-genome of   Zebrafish is available at different public databases ( like NCBI or Ensembl) and it has a alike genomics structure to humans. More than 70 % of genes are the same as human and 84% of the genes known to be associated with human diseases have a zebrafish equivalent. The genome of this fish has been fully sequenced to a very high quality and accuracy. This has permitted scientists and researchers across the globe to create mutations easily in any genes to study their function or impact.

6.      Vertebrate animal: Zebrafish has the same main organs and tissues as other vertebrate animals.

7.       As compared to other model organism zebrafish is cheaper to maintain

8.      Zebrafish grow at a tremendously fast rate as compared to other model organisms.

9.      It is small-sized fish needs less space for residence

10.  Zebrafish have the exceptional ability to repair and regeneration power of  muscle

        Figure 1:  Characteristics of  zebrafish as a model organism

Applications of Zebrafish As a Model Organism:
Human diseases successfully modeled in zebrafish are
·         Duchenne muscle dystrophy.
·         Cancers: leukemia, pancreatic cancer, hepatocellular carcinoma, melanoma.
·         Metabolic disorders (atherosclerosis, Nonalcoholic fatty liver disease, and diabetes)
·         Cardiovascular diseases ( blood clotting, blood vessel development, heart failure, congenital heart)
·         Infectious diseases ( mycobacterial  infections like tuberculosis)
·         Neurological diseases (Alzheimer’ s diseases, anxiety,  depression)

Zebrafish Genome information

1.      The haploid zebrafish genome has 25 chromosomes (Daga et al., 1996; Gornung et al., 1997). The chromosome contains about 1.7×109 base pairs of  DNA (Hinegardner and Rosen, 1972). Zebrafish genome has been fully sequenced and over 26,000 protein coding genes are present

2.      The chromosome complement of is 2n= 50.

3.      There are two metacentrics (6, 11), eight sub-metacentric chromosomes (3, 7, 9, 12, 21 &23) and the remaining 15 chromosomes are sub-telocentric.

4.      There are about 26,206 protein-encoding genes encoding around 50,000 proteins.

5.      There are about 293 pseudogenes (loss of function) and non-coding RNA genes (ncRNA) genes.

6.      The mitochondrial genome is 16,596bp and encodes 13 proteins, 22 transfer RNA, and 2 ribosomal RNAs.

7.      First genetic map of zebrafish included about 400 genetic markers mostly random amplified polymorphic DNAs (RAPDs) along with few genes and mutations (Postlethwait et al., 1994; Johnson et al., 1996).

8.      The genetic map comprises of 25 linkage groups (LG), each of which corresponds to a single chromosome. On nearly every chromosome the apparent orthologues of genes that are syntenic in mammals are also syntenic in zebrafish.11orthologues or highly homologous genes are syntenic on LG9 and the long arm of human chromosome 2 (Hsa2q).

9.      Zebrafish genome appears to have two copies of many chromosome segments that exist as single copies in mammalian genomes. Zebrafish have two copies of each of the HOX-bearing chromosomes of mammals.

10.  Zebra fish gene demonstrates on average greater than 75% similarity to human genes.

11.  Using zebrafish and human gene maps, comparative genomics has shown the existence of several blocks of synteny existed in the common ancestor of these two species, app.450 million years ago. The Zebrafish genome has orthologues of paralogous chromosome segments in mammals. The mammalian genome has up to four copies of the chromosome segment present in the vertebrate ancestor. For example, much of Hsa4 and 5, segments of Hsa1, 6, 9 and 19 contain four mammalian Notch alleles ( Katsanis et al., 1996, Kasahara et al., 1996), parts of Hsa11, 15, and 19, and portions of Hsa2, 7, 12, and 17 which contain the four mammalian HOX clusters and associated genes.

12.  Comparative molecular embryology suggests that zebrafish may have two copies of many unique genes in mammals. Examples include ssh and twhh, which are both equally related to mammalian SHH  ( Ekker S et al., 1995; Zardoya et al., 1996) , and snap25a and snap25b, which are both similar to human SNAP gene.

13.  By whole genome duplication if multiple copies of zebrafish chromosomes arose, Danio rerio should have twice as many chromosomes as humans.

14.  Zebrafish has just two more chromosomes in the haploid set than human chromosomes.

15.  Human developmental and diseases genes have counterparts in zebrafish due to extensive similarity between genomes.

16.  Mutations in zebrafish orthologues of human diseases, genes produce phenotypes similar to human disease states.

17.  AT rich and GC rich sequence is present as major class of tandem repeats in the genome of zebrafish.

18.  At the centromeres of all chromosomes pairs AT-rich sequences were found.

19.  Over half of the chromosome pairs GC- rich sequences are found at the pericentromeric locations.

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

Zebrafish Genome Project:   

Zebrafish genome sequencing project was initiated at the Wellcome Trust Sanger Institute in Cambridge, UK, in,  Feburary2001. They choose the Tubingen as the zebrafish reference strain,  as it has been used extensively to identify mutations affecting embryogenesis. Two strategies were chosen to obtain genome sequence:

1.      Whole Genome Shotgun (WGS) sequencing assemblies.

2.      Clone mapping and sequencing from BAC and PAC libraries.

        Sanger Institute also committed to identifying all zebrafish genes.Zv9 assembly is the recently integrated assembly of the zebrafish genome. It is based on a 90% clone sequence and remaining gaps are filled using a sequence from novel Whole Genome Sequence assembly, WGS31, with a total size of 1.412 gigabases (Gb). 

            The zebrafish genome sequence reveals the interesting factors about the comparison of zebrafish and human protein-coding genes. First, 71.4% of human genes have at least one zebrafish orthologue, as defined by Ensembl. Reciprocally 69% of zebrafish genes have at least one human orthologue. A few human genes have not clearly identifiable zebrafish orthologue; For example., Leukemia inhibitory factor (LIF), oncostatin M (OSM),or interleukin -6 (IL6)genes, even though the receptors lifra, osmr, il6r are clearly present in zebrafish. The zebrafish contain proteins with the same functionality as LIF, OSM, IL-6 but there is a large divergence in a sequence that they can’t be recognized as orthologue.

               Zv9 shows overall repeat content of 52.2% which is the highest reported repeat sequence so far in vertebrates as all other teleosts sequenced exhibit much lower content, with an average of less than 30%.

11% of the zebrafish genome is covered by type I transposable element (retro transposable), whereas, the human genome contains 44% of type I transposable element. Zebrafish genome contains an excess of type II DNA transposable elements covering 39% of the genome.

The long arm of chromosome 4 is unique among zebrafish genome, lack of protein-coding genes with its extensive heterochromatin. Chromosome 4 is late replicating and contains genomic copies of 5S ribosomal DNA (rDNA) which are not present in any other chromosomes and about 80% of the genes present on chromosome 4 have no identifiable orthologues in humans. Among zebrafish chromosomes, chromosome 16 and chromosome 19 is unique in their one-to-one conservation of synteny. Although the zebrafish reference genome sequencing is complete, a few poorly assembled regions remain which are being resolved by Genome Reference Consortium.

Conclusion: Zebrafish is a positive and versatile model the vertebrate organism, bestowing a means to model a gene function, drug discovery, toxicology, cancer studies, development of various organ system, human diseases and disorders, etc. because of easy manipulation, high fecundity, quick embryonic development and high fecundity favor the Danio rerio an attractive model for in vivo and in vitro assays with simplicity.

                 zebrafish as a model organism for research work

Note: Credit for writing the above article goes to Azra Nabi, Masters Student Division of Fish Genetics and Biotechnology, Faculty of Fisheries Ganderbal, Sher-e- Kashmir University of Agricultural Science and Technology- Kashmir. 

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