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Open Access Highly Accessed Research article

Genomic analysis of expressed sequence tags in American black bear Ursus americanus

Sen Zhao13, Chunxuan Shao1, Anna V Goropashnaya2, Nathan C Stewart2, Yichi Xu1, Øivind Tøien2, Brian M Barnes2, Vadim B Fedorov2 and Jun Yan1*

Author Affiliations

1 CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes of Biological Sciences, 320 Yue Yang Road, Shanghai, 200031, China

2 Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA

3 Current address: Microbial Evolution Research Group (MERG), Department of Biology, University of Oslo, N-0316 Oslo, Norway

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BMC Genomics 2010, 11:201  doi:10.1186/1471-2164-11-201

Published: 26 March 2010

Abstract

Background

Species of the bear family (Ursidae) are important organisms for research in molecular evolution, comparative physiology and conservation biology, but relatively little genetic sequence information is available for this group. Here we report the development and analyses of the first large scale Expressed Sequence Tag (EST) resource for the American black bear (Ursus americanus).

Results

Comprehensive analyses of molecular functions, alternative splicing, and tissue-specific expression of 38,757 black bear EST sequences were conducted using the dog genome as a reference. We identified 18 genes, involved in functions such as lipid catabolism, cell cycle, and vesicle-mediated transport, that are showing rapid evolution in the bear lineage Three genes, Phospholamban (PLN), cysteine glycine-rich protein 3 (CSRP3) and Troponin I type 3 (TNNI3), are related to heart contraction, and defects in these genes in humans lead to heart disease. Two genes, biphenyl hydrolase-like (BPHL) and CSRP3, contain positively selected sites in bear. Global analysis of evolution rates of hibernation-related genes in bear showed that they are largely conserved and slowly evolving genes, rather than novel and fast-evolving genes.

Conclusion

We provide a genomic resource for an important mammalian organism and our study sheds new light on the possible functions and evolution of bear genes.