Plant Genome Database Japan (PGDBj) in 2017: A Research Infrastructure for Genomics and Genetics of Plants

The Plant Genome DataBase Japan (PGDBj, http://pgdbj.jp/en) provides an aggregate of the genomic and genetic databases that were automatically generated or manually curated from the various information sources in relation to plant biology and plant breeding. As the component databases, PGDBj currently consists of the Ortholog DB, the Plant Resource DB, and the DNA Marker DB, respectively having database entries related to clusters of similar amino acid sequences, ESTs and full-length cDNA clones, and DNA markers and QTLs, for example. The Ortholog DB (http://pgdbj.jp/od3), which is a fundamental layer of PGDBj, stores the relationships among the entries across the organisms based on sequence similarity, and thereby provides hub structures that can connect the relevant entries distributed in the component databases. To generate the orthologous information in the Ortholog DB, we obtained the amino acid sequences of green plants and cyanobacteria from the NCBI RefSeq Database and carried out all-against-all BLAST search among them. By categorizing the similar sequences, we generated their clusters, each of which is referred to as an “ortholog” in this database. Besides integrated search functionality for the database entries, the orthologous information in the Ortholog DB can provide prediction mechanisms by transferring and comparing the data among the organisms and taxonomic clades. We are developing client application software utilizing the phylogenetic and syntenic profiles generated from the Ortholog DB.