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A Sequence-Based Variation Map of Zebrafish

IR@IGIB: CSIR-Institute of Genomics & Integrative Biology, New Delhi

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Title A Sequence-Based Variation Map of Zebrafish
 
Creator 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
 
Subject CH1 Chemical Biology
 
Description 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.
 
Date 2013
 
Type Article
NonPeerReviewed
 
Format application/pdf
 
Identifier http://openaccess.igib.res.in/153/1/Patowary%20et%20al%202013_ASWT_Genome.pdf
Patowary, Ashok and Purkanti, Ramya and Singh, Meghna and Chauhan, Rajendra and Singh, Angom Ramcharan and Swarnkar, Mohit and Singh, Naresh and Pandey, Vikas and Torroja, Carlos and Clark, Matthew D and Kocher, Jean-Pierre and Clark, Karl J and Stemple, Derek L and Klee, Eric W and Ekker, Stephen C and Scaria, Vinod and Sivasubbu, Sridhar (2013) A Sequence-Based Variation Map of Zebrafish. A Sequence-Based Variation Map of Zebrafish, 10 (1). pp. 10-1089.
 
Relation http://openaccess.igib.res.in/153/