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

29 Scopus citations

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

ASJC Scopus subject areas

  • Animal Science and Zoology
  • Developmental Biology

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    Patowary, A., Purkanti, R., Singh, M., Chauhan, R., Singh, A. R., Swarnkar, M., Singh, N., Pandey, V., Torroja, C., Clark, M. D., Kocher, J. P., Clark, K. J., Stemple, D. L., Klee, E. W., Ekker, S. C., Scaria, V., & Sivasubbu, S. (2013). A sequence-based variation map of zebrafish. Zebrafish, 10(1), 15-20. https://doi.org/10.1089/zeb.2012.0848