Literature DB >> 26110276

BGD: a database of bat genomes.

Jianfei Fang1, Xuan Wang1, Shuo Mu1, Shuyi Zhang1, Dong Dong1.   

Abstract

Bats account for ~20% of mammalian species, and are the only mammals with true powered flight. For the sake of their specialized phenotypic traits, many researches have been devoted to examine the evolution of bats. Until now, some whole genome sequences of bats have been assembled and annotated, however, a uniform resource for the annotated bat genomes is still unavailable. To make the extensive data associated with the bat genomes accessible to the general biological communities, we established a Bat Genome Database (BGD). BGD is an open-access, web-available portal that integrates available data of bat genomes and genes. It hosts data from six bat species, including two megabats and four microbats. Users can query the gene annotations using efficient searching engine, and it offers browsable tracks of bat genomes. Furthermore, an easy-to-use phylogenetic analysis tool was also provided to facilitate online phylogeny study of genes. To the best of our knowledge, BGD is the first database of bat genomes. It will extend our understanding of the bat evolution and be advantageous to the bat sequences analysis. BGD is freely available at: http://donglab.ecnu.edu.cn/databases/BatGenome/.

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Year:  2015        PMID: 26110276      PMCID: PMC4482021          DOI: 10.1371/journal.pone.0131296

Source DB:  PubMed          Journal:  PLoS One        ISSN: 1932-6203            Impact factor:   3.240


  17 in total

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Authors:  Jillian D L Smith; T Ryan Gregory
Journal:  Biol Lett       Date:  2009-03-04       Impact factor: 3.703

2.  Using OrthoCluster for the detection of synteny blocks among multiple genomes.

Authors:  Ismael A Vergara; Nansheng Chen
Journal:  Curr Protoc Bioinformatics       Date:  2009-09

3.  Convergent sequence evolution between echolocating bats and dolphins.

Authors:  Yang Liu; James A Cotton; Bin Shen; Xiuqun Han; Stephen J Rossiter; Shuyi Zhang
Journal:  Curr Biol       Date:  2010-01-26       Impact factor: 10.834

4.  Adaptive evolution of energy metabolism genes and the origin of flight in bats.

Authors:  Yong-Yi Shen; Lu Liang; Zhou-Hai Zhu; Wei-Ping Zhou; David M Irwin; Ya-Ping Zhang
Journal:  Proc Natl Acad Sci U S A       Date:  2010-04-26       Impact factor: 11.205

5.  The hearing gene Prestin reunites echolocating bats.

Authors:  Gang Li; Jinhong Wang; Stephen J Rossiter; Gareth Jones; James A Cotton; Shuyi Zhang
Journal:  Proc Natl Acad Sci U S A       Date:  2008-09-05       Impact factor: 11.205

6.  A high-resolution map of human evolutionary constraint using 29 mammals.

Authors:  Kerstin Lindblad-Toh; Manuel Garber; Or Zuk; Michael F Lin; Brian J Parker; Stefan Washietl; Pouya Kheradpour; Jason Ernst; Gregory Jordan; Evan Mauceli; Lucas D Ward; Craig B Lowe; Alisha K Holloway; Michele Clamp; Sante Gnerre; Jessica Alföldi; Kathryn Beal; Jean Chang; Hiram Clawson; James Cuff; Federica Di Palma; Stephen Fitzgerald; Paul Flicek; Mitchell Guttman; Melissa J Hubisz; David B Jaffe; Irwin Jungreis; W James Kent; Dennis Kostka; Marcia Lara; Andre L Martins; Tim Massingham; Ida Moltke; Brian J Raney; Matthew D Rasmussen; Jim Robinson; Alexander Stark; Albert J Vilella; Jiayu Wen; Xiaohui Xie; Michael C Zody; Jen Baldwin; Toby Bloom; Chee Whye Chin; Dave Heiman; Robert Nicol; Chad Nusbaum; Sarah Young; Jane Wilkinson; Kim C Worley; Christie L Kovar; Donna M Muzny; Richard A Gibbs; Andrew Cree; Huyen H Dihn; Gerald Fowler; Shalili Jhangiani; Vandita Joshi; Sandra Lee; Lora R Lewis; Lynne V Nazareth; Geoffrey Okwuonu; Jireh Santibanez; Wesley C Warren; Elaine R Mardis; George M Weinstock; Richard K Wilson; Kim Delehaunty; David Dooling; Catrina Fronik; Lucinda Fulton; Bob Fulton; Tina Graves; Patrick Minx; Erica Sodergren; Ewan Birney; Elliott H Margulies; Javier Herrero; Eric D Green; David Haussler; Adam Siepel; Nick Goldman; Katherine S Pollard; Jakob S Pedersen; Eric S Lander; Manolis Kellis
Journal:  Nature       Date:  2011-10-12       Impact factor: 49.962

7.  phyloXML: XML for evolutionary biology and comparative genomics.

Authors:  Mira V Han; Christian M Zmasek
Journal:  BMC Bioinformatics       Date:  2009-10-27       Impact factor: 3.169

8.  Using GBrowse 2.0 to visualize and share next-generation sequence data.

Authors:  Lincoln D Stein
Journal:  Brief Bioinform       Date:  2013-02-01       Impact factor: 11.622

9.  Genome analysis reveals insights into physiology and longevity of the Brandt's bat Myotis brandtii.

Authors:  Inge Seim; Xiaodong Fang; Zhiqiang Xiong; Alexey V Lobanov; Zhiyong Huang; Siming Ma; Yue Feng; Anton A Turanov; Yabing Zhu; Tobias L Lenz; Maxim V Gerashchenko; Dingding Fan; Sun Hee Yim; Xiaoming Yao; Daniel Jordan; Yingqi Xiong; Yong Ma; Andrey N Lyapunov; Guanxing Chen; Oksana I Kulakova; Yudong Sun; Sang-Goo Lee; Roderick T Bronson; Alexey A Moskalev; Shamil R Sunyaev; Guojie Zhang; Anders Krogh; Jun Wang; Vadim N Gladyshev
Journal:  Nat Commun       Date:  2013       Impact factor: 14.919

10.  InterPro: the integrative protein signature database.

Authors:  Sarah Hunter; Rolf Apweiler; Teresa K Attwood; Amos Bairoch; Alex Bateman; David Binns; Peer Bork; Ujjwal Das; Louise Daugherty; Lauranne Duquenne; Robert D Finn; Julian Gough; Daniel Haft; Nicolas Hulo; Daniel Kahn; Elizabeth Kelly; Aurélie Laugraud; Ivica Letunic; David Lonsdale; Rodrigo Lopez; Martin Madera; John Maslen; Craig McAnulla; Jennifer McDowall; Jaina Mistry; Alex Mitchell; Nicola Mulder; Darren Natale; Christine Orengo; Antony F Quinn; Jeremy D Selengut; Christian J A Sigrist; Manjula Thimma; Paul D Thomas; Franck Valentin; Derek Wilson; Cathy H Wu; Corin Yeats
Journal:  Nucleic Acids Res       Date:  2008-10-21       Impact factor: 16.971

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  2 in total

1.  Discovery of an endogenous Deltaretrovirus in the genome of long-fingered bats (Chiroptera: Miniopteridae).

Authors:  Helena Farkašová; Tomáš Hron; Jan Pačes; Pavel Hulva; Petr Benda; Robert James Gifford; Daniel Elleder
Journal:  Proc Natl Acad Sci U S A       Date:  2017-03-09       Impact factor: 11.205

2.  Differential Evolution of Antiretroviral Restriction Factors in Pteropid Bats as Revealed by APOBEC3 Gene Complexity.

Authors:  Joshua A Hayward; Mary Tachedjian; Jie Cui; Adam Z Cheng; Adam Johnson; Michelle L Baker; Reuben S Harris; Lin-Fa Wang; Gilda Tachedjian
Journal:  Mol Biol Evol       Date:  2018-07-01       Impact factor: 16.240

  2 in total

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