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

Cloning and functional characterization of PjPORB, a member of the POR gene family in Pseudosasa japonica cv. Akebonosuji

“…The PjPORB amino acid sequences were aligned with the amino acid sequences of other POR homologues with DNAMAN, which were downloaded from GenBank (http://www.ncbi.nlm.nih.gov/) and BambooGDB (http:// www.bamboogdb.org/) (Zhao et al 2014). Phylogenetic tree based on the POR amino acid sequences was constructed using the neighbor-joining method with MEGA5 (Tamura et al 2011).…”

“…The amino acid sequences of 15 POR homologues from other higher plants were downloaded from GenBank (for non-bamboo species) and BambooGDB (for bamboo species, http://www.bamboogdb.org/index.jsp) (Zhao et al 2014), respectively. Then, a multiple alignment was carried out based on the amino acid sequences of these 15 PORs and the putative PjPOR.…”

Molecular characterization and primary functional analysis of PeMPEC, a magnesium-protoporphyrin IX monomethyl ester cyclase gene of bamboo (Phyllostachys edulis)

“…A search for the MPEC homologue sequence in the BambooGDB database (http://www.bamboogdb.org) constructed by our laboratory (Zhao et al 2014) was undertaken using the OsZIP1 sequence (FJ940751) (http:// www.ncbi.nlm.nih.gov/nuccore) as a reference. Primers (PM-1: 5 0 -ATGGCCTCCGCCATGAAGCT-3 0 ; PM-2: 5 0 -TCAGTAAACAAGCCGGGGCT-3 0 ) were designed according to the open reading frame (ORF) of the MPEC sequence in P. edulis.…”

First proteome study of sporadic flowering in bamboo species (Bambusa vulgaris and Dendrocalamus manipureanus) reveal the boom is associated with stress and mobile genetic elements

“…ACCEPTED MANUSCRIPT 4 Recent advances in bamboo biology and bamboo flowering studies includes the identification of syntenic genes between bamboo and other Poaceae (Gui et al, 2010), identification of programmed cell death related genes in bamboo after gregarious flowering (Rai and Dey, 2012), analysis of pollen structures from sporadic flowering of Bambusa vulgaris and Dendrocalamus manipureanus (Waikhom et al, 2014), and transcriptome analysis of bamboo floral tissues (Zhang et al, 2012;Gao et al, 2014).…”

“…The most distinctive feature in bamboo flowering boom is the prolonged vegetative phase that can last for decades (Janzen, 1976;John and Nagauda, 2002;Sharma et al, 2014). The question why bamboo flowering takes longer periods and often infrequently has stimulated scientists into dissecting the genome (Zhao et al, 2014) and also influenced folkloristic knowledge on rat-mediated famine linked to the flowering boom (John and Nadgauda, 2002). Bamboo sporadic flowering is hallmarked by an uneven distribution of flowers on fertile branches and fertile clumps (Waikhom et al, 2014), and in some cases, flowering leads to death of the whole clumps (Janzen, 1976;John and Nagauda, 2002).…”