gb4gv: A genome browser for geminivirus

Background: Geminivirus (family Geminiviridae) is a prevalent plant virus that imperils agriculture globally, causing serious damage to the livelihood of farmers, particularly in developing countries. The virus evolves rapidly, attributing to its single-stranded genome propensity, resulting in worldwide circulation of diverse and viable genomes. Genomics is a prominent approach taken by researchers in elucidating the infectious mechanism of the virus. Currently, NCBI Viral Genome website is a popular repository of viral genomes that conveniently provides researchers a centralized data source of genomic information. However, unlike the genome of living organisms, viral genomes most often maintain peculiar characteristics that fit into no single genome architecture. By imposing a unified annotation scheme on the myriad of viral genomes may downplay their hallmark features. For example, virion of Begomovirus prevailing in America encapsulates two similar-sized circular genomes and both are required to maintain virulence. But, the two bipartite genomes are kept separately in NCBI with no explicit association in linking them. Thus, our goal is to build a comprehensive Geminivirus genomics database, namely gb4gv, that not only preserves genomic characteristics of the virus, but also supplements biologically relevant annotations that help to interrogate this virus e.g. the targeted host, putative iterons, siRNA targets etc. Methods: We have employed manual and automatic methods to curate 508 genomes from four major genera of Geminiviruses, and 161 associated satellites obtained from NCBI RefSeq and PubMed databases. Results: These data are available for free access without registration from our website. Besides genomic content, our website provides visualization capability inherited from UCSC Genome Browser. Discussion: With the genomic information readily accessible, we hope that our database will inspire researchers in gaining better understanding about this virus, resulting in insightful strategies to conquer the devastation inflicted agriculture. Availability and Implementation: Database URL: http://gb4gv.lafayette.edu .