Plant Genome Database Japan (PGDBj) in 2015: A Comprehensive Database Covering Information of Plant Genome-Related Databases in Japan

Plant genetic and genomic research in Japan has made significant contribution to high-resolution analyses of genome structures and functions. The outcomes have been provided in independent databases (DBs). Various types of information, such as DNA sequences, transcript, protein and phenotypic data derived from numerous DBs are described by original format for each DB. Moreover, these data contain the results from studies of various plant species. This situation makes it difficult for researchers to retrieve the sufficient information.

We aim to solve this problem by promoting integration of these DBs in Japan from three standpoints. First is integration of plant genome DBs by using an ortholog DB as a HUB for connecting sequences by similarity. 22 external plant genome-related DBs such as ‘RAP-DB’ and ‘KEGG’ have been linked. Next is integration of plant resource DBs. The resources of EST and cDNA clones in RIKEN BioResource Center (RIKEN BRC), National BioResource Projects (NBRP), Kinki University, and National Institute of Fruit Tree Science (NIFTS) from 15 species have become searchable. Final is integration of plant genome DBs with DNA marker and linkage map information. The information for more than 30 species has been provided. We have also developed a portal website named PGDBj (Plant Genome DataBase Japan; http://pgdbj.jp) providing an interface to access information in integrated-DBs. Currently, we pursue the integration by using semantic web technology.

The goal of PGDBj is to provide integrated information like data of genes relevant to beneficial plant traits, which accelerate the crop improvement and development.