Construction Study Of A Database For Rice Comparative Genomics And Evolutionary Biology

Rice is one of the important economical crops in the world. With the development of sequencing technologies and the implementation of the International Rice Genome Sequencing Project, the genome sequences of cultivated rice subspecies japonica Nipponbare and indica93-11, along with other cultivated and wild rice species, were released successively. Accompanying with the study for rice functional genome and the rice agronomic traits, the annotation data is accumulating rapidly. Though several databases and platforms were constructed to organize these data, most databases comprised only one kind of data and the data for all aspects still scatter dispersedly. Comparative genomics is an effective strategy for functional genomics. It is necessary to analyze and integrate these distributed annotation data from comparative genomics sight, so that these rice data could be well utilized.Based on the LAMP(Linux-Apache-MySQL-PHP) web service platform, we have integrated all the latest annotation data for rice into the Rice Genome Knowledgebase (RGKbase), and visualization for different kinds of data and a variety of bioinformatic analysis modules were also supported. Currently, RGKbase has included data from five rice cultivars and species: Nipponbare(japonica),93-11(indica), PA64s{indica), the African rice(Oryza glaberrima) and a wild rice species (Oryza brachyantha). According to those public annotation data, new annotation for rice was performed with a series of bioinformatics softwares. The intraspecific and interspecific syntenic analysis for these rice genomes were also carried out and the results were also included in RGKbase. In the study for RGKbase, the main three sections were list as follows:i) Integrate all latest annotation data and experiment data for rice, which includes:genome sequence, transcriptomic and epigenomic data, genetic variations, quantitative trait loci (QTLs) and single-nucleotide polymorphisms (SNP) information.ii) Develop online bioinformatics analysis modules with known programs, including data searching, identification of gene function, analysis of gene expression regulation and study of genetics structure and evolution.iii) Develop online visualization modules for the data and results from genome annotation, and evolutionary analysis and collinearity features with Gbrowse, GeneBrowse and Circos. The RGKbase could provide the molecular biologists and agriculturists with the well-organized annotation data and the comparative results, which would be helpful to study the discriminative patterns among various rice subspecies, hybrid vigour, gene related to important agronomic traits, rice breeding and the domestication processes. Moreover, it would also be valuable for the sustainable development of agriculture.