title: BambooGDB: a bamboo genome database with functional annotation and an analysis platform.
abstract: Bamboo, as one of the most important non-timber forest products and fastest-growing plants in the world, represents the only major lineage of grasses that is native to forests. Recent success on the first high-quality draft genome sequence of moso bamboo (Phyllostachys edulis) provides new insights on bamboo genetics and evolution. To further extend our understanding on bamboo genome and facilitate future studies on the basis of previous achievements, here we have developed BambooGDB, a bamboo genome database with functional annotation and analysis platform. The de novo sequencing data, together with the full-length complementary DNA and RNA-seq data of moso bamboo composed the main contents of this database. Based on these sequence data, a comprehensively functional annotation for bamboo genome was made. Besides, an analytical platform composed of comparative genomic analysis, protein-protein interactions network, pathway analysis and visualization of genomic data was also constructed. As discovery tools to understand and identify biological mechanisms of bamboo, the platform can be used as a systematic framework for helping and designing experiments for further validation. Moreover, diverse and powerful search tools and a convenient browser were incorporated to facilitate the navigation of these data. As far as we know, this is the first genome database for bamboo. Through integrating high-throughput sequencing data, a full functional annotation and several analysis modules, BambooGDB aims to provide worldwide researchers with a central genomic resource and an extensible analysis platform for bamboo genome. BambooGDB is freely available at http://www.bamboogdb.org/. Database URL: http://www.bamboogdb.org.
authors.affiliation: State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, International Center for Bamboo and Rattan, Beijing 100102, China, State key laboratory of tree genetics and breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China and Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
authors.forename: Hansheng
authors.initials: H
authors.lastname: Zhao
authors.forename: Zhenhua
authors.initials: Z
authors.lastname: Peng
authors.forename: Benhua
authors.initials: B
authors.lastname: Fei
authors.forename: Lubin
authors.initials: L
authors.lastname: Li
authors.forename: Tao
authors.initials: T
authors.lastname: Hu
authors.forename: Zhimin
authors.initials: Z
authors.lastname: Gao
authors.forename: Zehui
authors.initials: Z
authors.lastname: Jiang
mesh_terms: D031723:Bambusa / Q000235:genetics*; D030541:Databases, Genetic; D018745:Genome, Plant / Q000235:genetics*; D058977:Molecular Sequence Annotation / Q000379:methods*; D057386:Search Engine; D012984:Software; D013223:Statistics as Topic