title: The Vigna Genome Server, 'VigGS': A Genomic Knowledge Base of the Genus Vigna Based on High-Quality, Annotated Genome Sequence of the Azuki Bean, Vigna angularis (Willd.) Ohwi & Ohashi.
abstract: The genus Vigna includes legume crops such as cowpea, mungbean and azuki bean, as well as >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. These features of the genus Vigna make 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', http://viggs.dna.affrc.go.jp), 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 dicot species. 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. VigGS offers a simple keyword search in addition to sequence similarity searches using BLAST and BLAT. To incorporate up to date genomic information, VigGS automatically receives newly deposited mRNA sequences of pre-set 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. VigGS will contribute to genomic research into plant biotic and abiotic stresses and to the future development of new stress-tolerant crops.
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan hirsakai@affrc.go.jp.
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Sakai
authors.affiliation: Genetic Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan.
authors.forename: Ken
authors.initials: K
authors.lastname: Naito
authors.affiliation: Genetic Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan.
authors.forename: Yu
authors.initials: Y
authors.lastname: Takahashi
authors.affiliation: Mizuho Information & Research Institute, Inc., 2-3 Kanda-Nishikicho, Chiyoda-ku, Tokyo, 101-8443 Japan.
authors.forename: Toshiyuki
authors.initials: T
authors.lastname: Sato
authors.affiliation: BITS Co., Ltd., 5-201 Kandamatsunaga-cho, Chiyoda-ku, Tokyo, 101-0023 Japan.
authors.forename: Toshiya
authors.initials: T
authors.lastname: Yamamoto
authors.affiliation: BITS Co., Ltd., 5-201 Kandamatsunaga-cho, Chiyoda-ku, Tokyo, 101-0023 Japan.
authors.forename: Isamu
authors.initials: I
authors.lastname: Muto
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Itoh
authors.affiliation: Genetic Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan.
authors.forename: Norihiko
authors.initials: N
authors.lastname: Tomooka
mesh_terms: D018556:Crops, Agricultural; D030541:Databases, Genetic; D056426:Genetic Loci / Q000235:genetics; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D051188:Knowledge Bases; D058977:Molecular Sequence Annotation; D014584:User-Computer Interface; D000070658:Vigna / Q000235:genetics*
keywords: Genome database; Legume; Vigna