Construction Of Transcription Factor,SSR Databases And Computational Identification Of MiRNAs In Vitis Vinifera L.

Vitis vinifera L. is one of the most important horticultural crops in the world, being used for the production of wine and juice, and as fresh and dried fruit。The completion of the Vitis vinifera L. genome sequence provides an opportunity for people to learn about grape in new review. Here we used bioinformatics approach to search transcription factors (TFs), SSRs, and miRNAs at grape genome levels, and constructed grape transcription factors and SSR database by compute and web technology.We collected HMMs of domains that occur in TFs. Then these HMMs were used to search against the whole genome of Vitis vinifera L.. All significant hits were kept. Then, the rule was implemented in a Perl script-Class.pl to classify proteins into different families. Annotations of grape putative TFs are obtained by bioinformaics tools and public databases. Data for all TFs are stored in several tables of a MySQL relational database on a server. The web interface is based on PHP and Perl scripts. Using the pipeline we developed,1625putative TFs in grape were identified and classified into67families. The database of grape transcription factors (DGTF) comprehensively collected and annotated grape TFs. The DGTF contains1625putative grape TFs in67families. The DGTF provides detailed annotations for individual members of each TF family, including sequence feature, domain architecture, expression information, and orthologs in other plants. Cross-links to other public databases make its annotations more extensive. The web site of DGTF is http://www.yaolab.sh.cn/dgtf/.We developed a Perl script-SSRFinder to detect SSRs in grape genome sequence. A total of114,520SSRs were isolated from342.63Mb of publicly available Vitis vinifera L. genome DNA sequence. Among them, SSRs with poly(AT)n repeats represented the most abundant type, whereas (G+C)-rich motifs were the rarest type. We also assessed the distribution of SSRs on genome fragment. The results showed that the SSRs distributed mainly in intergenic region and were moderately abundant in UTRs. In coding region, the distribution of all repeat types was less frequent except tri-and hexa-nucleotide repeats. To make use of these SSRs, we developed a database on internet web. The database of grape SSRs (DGSSR) is a database comprehensively collecting and annotating grape SSRs. The DGSSR contains all the SSRs with their related information detected in the study. It provides flexible query interface and detailed annotations for individual SSR. It also contains SSRs detected from Vitis vinifera L. ESTs dataset. The DGSSR is available at http://www.yaolab.sh.cn/ssr/.Here we developed a program-MirFinder for prediction of grape miRNAs. The characteristic features of known plant miRNAs were used as criteria to search for new miRNAs. After searching the Vitis vinifera L. genome by MirFinder, we identified146miRNAs, of which98miRNAs were the same as known miRNAs and48are new identified miRNAs. The48miRNAs were classified into21families, of which8families are newly identified in grape. A total of15potential targets were identified for6of the8new miRNA families based on the fact that miRNAs exhibit perfect or nearly perfect complementarity with their target sequences.