C23The Vigna Genome Server, ‘VigGS’: A Genomic Knowledge Base of the Genus Vigna
The Vigna Genome Server, ‘VigGS’: A Genomic Knowledge Base of the Genus Vigna
Date: Wednesday, January 13, 2016
Time: 11:10 AM
Time: 11:10 AM
The genus Vigna includes legume crops such as cowpea, mungbean, and azuki bean as well as over 100 wild species. A number of the wild species are highly tolerant to severe environmental conditions including high salinity, acid or alkaline soil; drought; flooding; and pests and diseases, making it a good target for investigation of genetic diversity in adaptation to stressful environments. However, a lack of genomic information has hindered such research in this genus. Here, we present a genome database of the genus Vigna, Vigna Genome Server ‘VigGS’, based on the recently sequenced azuki bean genome, which incorporates annotated exon-intron structures, along with evidence for transcripts and proteins, visualized in GBrowse. VigGS also facilitates user construction of multiple alignments between azuki bean genes and those of six related dicots. In addition, the database displays sequence polymorphisms between azuki bean and its wild relatives and enables users to design primer sequences targeting any variant site. To incorporate up-to-date genomic information, VigGS automatically receives newly deposited mRNA sequences of preset species from the public database once a week. Users can refer to not only gene structures mapped on the azuki bean genome on GBrowse but also relevant literature of the genes. Currently genome sequencing of 13 wild Vigna species is in process. Comparative protein mapping data based on each species genome and genome alignment for each pair of closely related species will be implemented in VigGS, which will shed light on the genetic consequences of the adaptive evolution of the Vigna species.