GB4GV: A GENOME BROWSER FOR GEMINIVIRUS

Catherine M. Newsom-Stewart*, Eric S. Ho Department of Biology, Lafayette College, Easton, Pennsylvania, 18042, United States. *Presenter

Geminivirus is a prevalent plant virus that imperils farming globally, causing serious economic loss to agriculture, particularly in developing countries. The virus has a quickly evolving genome attributed to its single-stranded structure. Studies have shown that substitution rate in single-stranded DNA viruses is comparable to the rate in RNA viruses, resulting in widespread and diverse, viable Geminivirus genomes. Therefore it is important to study, and eventually eradicate, this devastating virus. Genomics is a major approach taken by researchers in elucidating viral infection. 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, viral genomes often pertain peculiar characteristics that do not fit into the genome architecture of living organisms. The unified annotation scheme imposed by NCBI on viral genomes may therefore downplay the signature features of different viruses. For example, Begomovirus is the most pervasive genus in Geminiviridae. It encapsulates two similar-sized circular genomes in one virion, constituting a bipartite genome. Intriguingly, the bipartite genomes share a pair of nearly identical non-coding regions with a distinctive hairpin secondary structure, which plays a crucial role in DNA replication. Unfortunately, this association between the bipartite genomes is missing from NCBI Viral Genome. Our goal is to integrate biologically relevant annotations into a new open access Geminivirus genomics database e.g. the association between the main genome and its helper satellite, targeted host, location, etc. We have manually curated 508 Geminiviruses from four major genera, and 161 satellites obtained from NCBI RefSeq and PubMed databases. These data are hosted in the website (http://gb4gv.lafayette.edu/cgi-bin/hgGateway) that we built with a user-friendly browser interface adopted from the UCSC Genome Browser. The readily accessible genomic information provided by gb4gv will facilitate researchers to formulate insights in conquering the devastation caused by Geminivirus.


Additional Abstract Information

Presenter: Catherine Newsom-Stewart

Institution: Lafayette College

Type: Poster

Subject: Biology

Status: Approved


Time and Location

Session: Poster 7
Date/Time: Fri 1:20pm-2:20pm
Location: University Center Ballroom - Tripod 10 Side C