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
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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 |
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Subject |
CH1 Chemical Biology
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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.
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Date |
2013
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Type |
Article
NonPeerReviewed |
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Format |
application/pdf
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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. |
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Relation |
http://openaccess.igib.res.in/153/
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