gb4gv: a genome browser for geminivirus
Background Geminiviruses (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 worl...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2017-04-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/3165.pdf |
| _version_ | 1827606465722974208 |
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| author | Eric S. Ho Catherine M. Newsom-Stewart Lysa Diarra Caroline S. McCauley |
| author_facet | Eric S. Ho Catherine M. Newsom-Stewart Lysa Diarra Caroline S. McCauley |
| author_sort | Eric S. Ho |
| collection | DOAJ |
| description | Background Geminiviruses (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. Methods We 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. 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 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 Implementation The database can be found at: http://gb4gv.lafayette.edu. |
| first_indexed | 2024-03-09T06:38:40Z |
| format | Article |
| id | doaj.art-d91e46db61a54272aaaf626d778ccefb |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:38:40Z |
| publishDate | 2017-04-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-d91e46db61a54272aaaf626d778ccefb2023-12-03T10:55:22ZengPeerJ Inc.PeerJ2167-83592017-04-015e316510.7717/peerj.3165gb4gv: a genome browser for geminivirusEric S. Ho0Catherine M. Newsom-Stewart1Lysa Diarra2Caroline S. McCauley3Department of Biology, Lafayette College, Easton, PA, United StatesDepartment of Biology, Lafayette College, Easton, PA, United StatesDepartment of Biology, Lafayette College, Easton, PA, United StatesDepartment of Biology, Lafayette College, Easton, PA, United StatesBackground Geminiviruses (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. Methods We 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. 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 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 Implementation The database can be found at: http://gb4gv.lafayette.edu.https://peerj.com/articles/3165.pdfAlphasatelliteBetasatelliteBegomovirusCurtovirusGeminiviridaeGeminivirus |
| spellingShingle | Eric S. Ho Catherine M. Newsom-Stewart Lysa Diarra Caroline S. McCauley gb4gv: a genome browser for geminivirus PeerJ Alphasatellite Betasatellite Begomovirus Curtovirus Geminiviridae Geminivirus |
| title | gb4gv: a genome browser for geminivirus |
| title_full | gb4gv: a genome browser for geminivirus |
| title_fullStr | gb4gv: a genome browser for geminivirus |
| title_full_unstemmed | gb4gv: a genome browser for geminivirus |
| title_short | gb4gv: a genome browser for geminivirus |
| title_sort | gb4gv a genome browser for geminivirus |
| topic | Alphasatellite Betasatellite Begomovirus Curtovirus Geminiviridae Geminivirus |
| url | https://peerj.com/articles/3165.pdf |
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