To facilitate the query for germplasms, QTLs and RNA-seq data stored in VitisGDB, we have built the search index for different types of information, including search germplasm, search QTLs and search transcriptome. For germplasm, there are two basic ways for users to access data stored in VitisGDB: search and browse. On the ‘Search germplasm’ page, a basic search form is provided, it allows users to input a specific name for retrieving the corresponding germplasm, or to select one category in species, berry color, utilization and flower sex for retrieving a list of germplasms whose information fit such criteria. Similarly, ‘Search QTLs’ and ‘Search Transcriptome’ page allows uses to narrow down the list by trait type, species, chromosome or species, cultivar, tissue type and treatment type, respectively. Additionally, one useful aspects of query in VitisGDB is the “wildcard” character “%”. By default, every search has a wildcard at the end. For instance, when entering “Cabernet” will show both Cabernet Franc and Cabernet Suavigon (and other two variations). User can also insert a wildcard elsewhere in the string. When inputting “%Sauvignon”, it will get back five germplasms which have Suavignon somewhere in the name.
To perform sequence similarity searches on genome assemblies and annotations, we have implemented NCBI’s BLAST tools in VitisGDB. All of 12 genome assembly, and their corresponding CDS and protein sequences are provided for comparison in this BLAST interface. To prevent uses from selecting incompatible BLAST programs and dataset, the list of dataset is automatically fixed based on the selected BLAST programs. The final BLAST result can be downloaded in HTML formats.
Sets of genomic and genetic features on assembled genomes can be explored at VitisGDB through genome browser implemented in JBrowse (11). As a combination of database and interactive web pages, JBrowse is an efficient visualization module which facilitates viewing various types of data, such as gene models, CDS, heterozygous SNPs and RNA-seq, in different colors in the context of genomic region. Currently, all collected Vitis genomes and gene models are imported into JBrowse. In addition, by clicking one specific data entry, the detailed feature page of data entries can be reached. In the future updates, other interesting data, such as expression abundances derived from the RNA-seq, messenger RNA will be added to the genome browser.
In the ‘Download’ page, VitisGDB provides download of all datasets, which contains genome assembly sequence, annotation result and genomic variations in fasta format, gff format and vcf format, respectively. Considering the large data size of raw sequence for de novo assembly, re-sequencing and RNA-seq, the NCBI BioProject and BioSample ID as well as the corresponding links are provided on the download page. In addition, by searching for keywords, such as species, trait or treatment which is followed by clicking ‘Download’, the export of data is supported for search results of interest to the users.