title: A sequence-based variation map of zebrafish.
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.
authors.affiliation: CSIR- Institute of Genomics and Integrative Biology, Delhi, India.
authors.forename: Ashok
authors.initials: A
authors.lastname: Patowary
authors.forename: Ramya
authors.initials: R
authors.lastname: Purkanti
authors.forename: Meghna
authors.initials: M
authors.lastname: Singh
authors.forename: Rajendra
authors.initials: R
authors.lastname: Chauhan
authors.forename: Angom Ramcharan
authors.initials: AR
authors.lastname: Singh
authors.forename: Mohit
authors.initials: M
authors.lastname: Swarnkar
authors.forename: Naresh
authors.initials: N
authors.lastname: Singh
authors.forename: Vikas
authors.initials: V
authors.lastname: Pandey
authors.forename: Carlos
authors.initials: C
authors.lastname: Torroja
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Clark
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Kocher
authors.forename: Karl J
authors.initials: KJ
authors.lastname: Clark
authors.forename: Derek L
authors.initials: DL
authors.lastname: Stemple
authors.forename: Eric W
authors.initials: EW
authors.lastname: Klee
authors.forename: Stephen C
authors.initials: SC
authors.lastname: Ekker
authors.forename: Vinod
authors.initials: V
authors.lastname: Scaria
authors.forename: Sridhar
authors.initials: S
authors.lastname: Sivasubbu
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D014644:Genetic Variation; D016678:Genome; D054643:INDEL Mutation; D008297:Male; D013058:Mass Spectrometry; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D015027:Zebrafish / Q000235:genetics*