Gb4gv: a genome browser for geminivirus.

Eric S Ho,Caroline S Mccauley,Catherine M Newsom-Stewart,Lysa Diarra

doi:10.7717/peerj.3165

Abstract

BackgroundGeminiviruses (family Geminiviridae) are prevalent plant viruses that imperil 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, the 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, the viron of begomoviruses prevailing in America encapsulates two similar-sized circular DNA components and both are required for systemic infection of plants. However, the bipartite components are kept separately in NCBI as individual genomes 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, for example, the targeted host, putative iterons, siRNA targets, etc.MethodsWe have employed manual and automatic methods to curate 508 genomes from four major genera of Geminiviridae, and 161 associated satellites obtained from NCBI RefSeq and PubMed databases.ResultsThese data are available for free access without registration from our website. Besides genomic content, our website provides visualization capability inherited from UCSC Genome Browser.DiscussionWith the genomic information readily accessible, we hope that our database will inspire researchers in gaining a better understanding of the incredible degree of diversity of these viruses, and of the complex relationships within and between the different genera in the Geminiviridae.Availability and ImplementationThe database can be found at: http://gb4gv.lafayette.edu.

Highlights

Geminiviruses have emerged as one of the most prevalent and problematic plant pathogens especially in developing countries (Sattar et al, 2013; Scholthof et al, 2011; Shepherd et al, 2010)
We will highlight the unique features offered by gb4gv that are helpful in studying the genomics of geminiviruses
While the software architecture of gb4gv is based on Genome Browser, the operations of our website is highly similar to UCSC Genome Browser

Summary

Introduction

Geminiviruses (family Geminiviridae) have emerged as one of the most prevalent and problematic plant pathogens especially in developing countries (Sattar et al, 2013; Scholthof et al, 2011; Shepherd et al, 2010). They have become the largest group of plant viruses to exist today It posts significant threat both socially and economically as geminiviruses are the most destructive pathogens in subsistence agriculture like beans, cotton, maize, sweet potato, and tomato (Jeske, 2009; Sattar et al, 2013; Scholthof et al, 2011; Shepherd et al, 2010). With the genomic information readily accessible, we hope that our database will inspire researchers in gaining a better understanding of the incredible degree of diversity of these viruses, and of the complex relationships within and between the different genera in the Geminiviridae. The database can be found at: http://gb4gv.lafayette. edu

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