Plant Genome DataBase Japan (PGDBj): A Portal Website for the Integration of Plant Genome-Related Databases

Abstract

The Plant Genome DataBase Japan (PGDBj, http://pgdbj.jp/?ln=en) is a portal website that aims to integrate plant genome-related information from databases (DBs) and the literature. The PGDBj is comprised of three component DBs and a cross-search engine, which provides a seamless search over the contents of the DBs. The three DBs are as follows. (i) The Ortholog DB, providing gene cluster information based on the amino acid sequence similarity. Over 500,000 amino acid sequences of 20 Viridiplantae species were subjected to reciprocal BLAST searches and clustered. Sequences from plant genome DBs (e.g. TAIR10 and RAP-DB) were also included in the cluster with a direct link to the original DB. (ii) The Plant Resource DB, integrating the SABRE DB, which provides cDNA and genome sequence resources accumulated and maintained in the RIKEN BioResource Center and National BioResource Projects. (iii) The DNA Marker DB, providing manually or automatically curated information of DNA markers, quantitative trait loci and related linkage maps, from the literature and external DBs. As the PGDBj targets various plant species, including model plants, algae, and crops important as food, fodder and biofuel, researchers in the field of basic biology as well as a wide range of agronomic fields are encouraged to perform searches using DNA sequences, gene names, traits and phenotypes of interest. The PGDBj will return the search results from the component DBs and various types of linked external DBs.

Plant-PrAS: A Database of Physicochemical and Structural Properties and Novel Functional Regions in Plant Proteomes

“…In order to improve functional annotation of genes in plants, various initiatives have been undertaken, such as inclusion of an experimental method that uses cross-species expressed sequence tag (EST) information ( Chen et al 2007 ), integration of plant genomic information ( Asamizu et al 2014 ), integration of Arabidopsis transcriptomic information ( Obayashi et al 2014 ), utilization of transcriptomic and metabolic profiles among plant tissues ( Sakurai et al 2013 ), integrative analysis of plant hormone accumulation and gene expression among rice tissues ( Kudo et al 2013 ), inclusion of the phenotypic information on mutant Arabidopsis lines ( Sakurai et al 2011 , Myouga et al 2013 , Akiyama et al 2014 ), inclusion of experimental and computational methods using gene expression data and experimentally derived (or predicted) protein–protein interactions ( Kourmpetis et al 2011 ), and inclusion of similarity clustering among protein sequences in the SALAD database ( http://salad.dna.affrc.go.jp/salad/ ) ( Mihara et al 2010 ).…”

Metabolonote: A Wiki-Based Database for Managing Hierarchical Metadata of Metabolome Analyses

“…In Metabolonote, all of the metadata at the upper levels of the hierarchy are displayed as a single webpage. A link to PGDBj (Asamizu et al, 2014 ), which provides integrated information around plant genome data, is attached to the metadata of the sample set (SE). At the metadata of the samples, a link to the record of KomicMarket (Sakurai et al, 2014 ), the peak annotation database is present.…”

Translational genomics for plant breeding with the genome sequence explosion

“…For the comparative analysis of QTL among different crop species, it is necessary to integrate published QTLs of the crop species into a single database. For this purpose, a Japanese research group published the database, PGDBj (Asamizu et al ., ) (http://pgdbj.jp/), which combines the genetic markers and QTL data from various plant species. The primer sequences are available for 98 333 genetic markers of 40 plant species, and 3144 QTLs of 27 plant species are listed (Figure c).…”