A sequence-based variation map of zebrafish

Ashok Patowary, Ramya Purkanti, Meghna Singh, Rajendra Chauhan, Angom Ramcharan Singh, Mohit Swarnkar, Naresh Singh, Vikas Pandey, Carlos Torroja, Matthew D. Clark, Jean-Pierre Kocher, Karl J Clark, Derek L. Stemple, Eric W Klee, Stephen C Ekker, Vinod Scaria, Sridhar Sivasubbu

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

Zebrafish (Danio rerio) is a popular vertebrate model organism largely deployed using outbred laboratory animals. The nonisogenic nature of the zebrafish as a model system offers the opportunity to understand natural variations and their effect in modulating phenotype. In an effort to better characterize the range of natural variation in this model system and to complement the zebrafish reference genome project, the whole genome sequence of a wild zebrafish at 39-fold genome coverage was determined. Comparative analysis with the zebrafish reference genome revealed approximately 5.2 million single nucleotide variations and over 1.6 million insertion-deletion variations. This dataset thus represents a new catalog of genetic variations in the zebrafish genome. Further analysis revealed selective enrichment for variations in genes involved in immune function and response to the environment, suggesting genome-level adaptations to environmental niches. We also show that human disease gene orthologs in the sequenced wild zebrafish genome show a lower ratio of nonsynonymous to synonymous single nucleotide variations.

Original languageEnglish (US)
Pages (from-to)15-20
Number of pages6
JournalZebrafish
Volume10
Issue number1
DOIs
StatePublished - Mar 1 2013

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Zebrafish
Danio rerio
Genome
genome
Nucleotides
nucleotides
Laboratory Animals
human diseases
Genes
laboratory animals
Vertebrates
complement
niches
genes
vertebrates
Phenotype
phenotype
genetic variation
organisms

ASJC Scopus subject areas

  • Animal Science and Zoology
  • Developmental Biology

Cite this

Patowary, A., Purkanti, R., Singh, M., Chauhan, R., Singh, A. R., Swarnkar, M., ... Sivasubbu, S. (2013). A sequence-based variation map of zebrafish. Zebrafish, 10(1), 15-20. https://doi.org/10.1089/zeb.2012.0848

A sequence-based variation map of zebrafish. / Patowary, Ashok; Purkanti, Ramya; Singh, Meghna; Chauhan, Rajendra; Singh, Angom Ramcharan; Swarnkar, Mohit; Singh, Naresh; Pandey, Vikas; Torroja, Carlos; Clark, Matthew D.; Kocher, Jean-Pierre; Clark, Karl J; Stemple, Derek L.; Klee, Eric W; Ekker, Stephen C; Scaria, Vinod; Sivasubbu, Sridhar.

In: Zebrafish, Vol. 10, No. 1, 01.03.2013, p. 15-20.

Research output: Contribution to journalArticle

Patowary, A, Purkanti, R, Singh, M, Chauhan, R, Singh, AR, Swarnkar, M, Singh, N, Pandey, V, Torroja, C, Clark, MD, Kocher, J-P, Clark, KJ, Stemple, DL, Klee, EW, Ekker, SC, Scaria, V & Sivasubbu, S 2013, 'A sequence-based variation map of zebrafish', Zebrafish, vol. 10, no. 1, pp. 15-20. https://doi.org/10.1089/zeb.2012.0848
Patowary A, Purkanti R, Singh M, Chauhan R, Singh AR, Swarnkar M et al. A sequence-based variation map of zebrafish. Zebrafish. 2013 Mar 1;10(1):15-20. https://doi.org/10.1089/zeb.2012.0848
Patowary, Ashok ; Purkanti, Ramya ; Singh, Meghna ; Chauhan, Rajendra ; Singh, Angom Ramcharan ; Swarnkar, Mohit ; Singh, Naresh ; Pandey, Vikas ; Torroja, Carlos ; Clark, Matthew D. ; Kocher, Jean-Pierre ; Clark, Karl J ; Stemple, Derek L. ; Klee, Eric W ; Ekker, Stephen C ; Scaria, Vinod ; Sivasubbu, Sridhar. / A sequence-based variation map of zebrafish. In: Zebrafish. 2013 ; Vol. 10, No. 1. pp. 15-20.
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