DNA Polymorphism Annotation Database (DNApod): Toward an Integration of SRA-Driven Genotypic Data and Public Phenotypic Data

With advances in next-generation sequencing (NGS), datasets for DNA polymorphism among various species and strains have been produced, stored and distributed. However, reliability among datasets varies because the experimental and analytical conditions are different among assays. Furthermore, such datasets have often been distributed from the websites of individual sequencing projects. It is desirable to integrate DNA polymorphism data into a database with uniform quality control distributed from a single platform in a single place. The DNA polymorphism annotation database (DNApod) (http://tga.nig.ac.jp/dnapod/) is an integrated database that stores genome-wide DNA polymorphism datasets acquired under uniform analytical conditions, including the quality of raw data, reference genome version and evaluation algorithms. DNApod genotypic data is re-analysed whole-genome shotgun (WGS) datasets extracted from the Sequence Read Archive (SRA) and distributes genome-wide DNA polymorphism datasets and known-gene annotations for each DNA polymorphism. The purpose of the database is to store genome-wide DNA polymorphism datasets of plants, with crops as a first priority. The DNApod genotypic database currently contains 679 rice lines, 404 maize lines, and 66 sorghum lines. The analytical methods are available as a DNApod workflow in the DNA Data Bank of Japan (DDBJ) Read Annotation Pipeline (DDBJ pipeline) that allows users to perform NGS analyses with their own data. To advance the sharing of organism knowledge, DNApod offers basic and ubiquitous functions towards multiple alignment and phylogenetic tree construction using orthologous gene information. Then, DNApod provides the tables of id links between DNApod and public phenotypic data.