Why use zebrafish as a model organism for research
work?
zebrafish as a model organism for research work
Introduction:
· 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)
|
Kingdom |
Animalia |
|
Phylum |
Chordata |
|
Class |
Actinopterygii |
|
Order |
Cypriniformes |
|
Family |
Cyprinidae |
|
Sub-Family |
Danioninae |
|
Genus |
Danio |
|
Species |
Danio |
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
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.