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gb4gv: a genome browser for geminivirus

View Article: PubMed Central - HTML - PubMed

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus

Web interface of gb4gv.(A) The home page of gb4gv. The evolutionary tree under represented species shows the available viruses including the three genera of Geminiviruses and two satellites. Users can view a particular genus or satellite by clicking on the virus or satellite name in the evolutionary tree. Users can also make use of the “Species Search” box to look up for a particular virus by keywords. Additionally, users can enter keywords in the “Position/Search Term” box search for a particular virus and/or gene. Click the blue GO button to navigate into the genomic information of a particular viral species. (B) This page provides various annotation information about the selected genome in which they are organized in tracks. (C) Information of a protein-coding gene. It tells the genomic location of the gene, size, and strand that codes for the protein. In addition, there is a short description about the current gene including the name of the protein, whether the virus is a New World or an Old World virus, the full name of the virus and its acronym, the RefSeq and GenBank accession numbers with hyperlink linked to the corresponding GenBank entry in the NCBI website.
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fig-3: Web interface of gb4gv.(A) The home page of gb4gv. The evolutionary tree under represented species shows the available viruses including the three genera of Geminiviruses and two satellites. Users can view a particular genus or satellite by clicking on the virus or satellite name in the evolutionary tree. Users can also make use of the “Species Search” box to look up for a particular virus by keywords. Additionally, users can enter keywords in the “Position/Search Term” box search for a particular virus and/or gene. Click the blue GO button to navigate into the genomic information of a particular viral species. (B) This page provides various annotation information about the selected genome in which they are organized in tracks. (C) Information of a protein-coding gene. It tells the genomic location of the gene, size, and strand that codes for the protein. In addition, there is a short description about the current gene including the name of the protein, whether the virus is a New World or an Old World virus, the full name of the virus and its acronym, the RefSeq and GenBank accession numbers with hyperlink linked to the corresponding GenBank entry in the NCBI website.

Mentions: The web interface of gb4gv is organized in a hierarchy consisting of three levels. The highest level presents all the genera of Geminiviridae maintained in gb4gv including two satellites despite they are considered as genera (Fig. 3A). Figure 3B displays information about the genome of an individual virus and corresponding annotation tracks. Detailed information about a particular annotation e.g., a gene, a protein or a specific genomic sequence, is presented at the lowest level (Fig. 3C)


gb4gv: a genome browser for geminivirus
Web interface of gb4gv.(A) The home page of gb4gv. The evolutionary tree under represented species shows the available viruses including the three genera of Geminiviruses and two satellites. Users can view a particular genus or satellite by clicking on the virus or satellite name in the evolutionary tree. Users can also make use of the “Species Search” box to look up for a particular virus by keywords. Additionally, users can enter keywords in the “Position/Search Term” box search for a particular virus and/or gene. Click the blue GO button to navigate into the genomic information of a particular viral species. (B) This page provides various annotation information about the selected genome in which they are organized in tracks. (C) Information of a protein-coding gene. It tells the genomic location of the gene, size, and strand that codes for the protein. In addition, there is a short description about the current gene including the name of the protein, whether the virus is a New World or an Old World virus, the full name of the virus and its acronym, the RefSeq and GenBank accession numbers with hyperlink linked to the corresponding GenBank entry in the NCBI website.
© Copyright Policy
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC5391787&req=5

fig-3: Web interface of gb4gv.(A) The home page of gb4gv. The evolutionary tree under represented species shows the available viruses including the three genera of Geminiviruses and two satellites. Users can view a particular genus or satellite by clicking on the virus or satellite name in the evolutionary tree. Users can also make use of the “Species Search” box to look up for a particular virus by keywords. Additionally, users can enter keywords in the “Position/Search Term” box search for a particular virus and/or gene. Click the blue GO button to navigate into the genomic information of a particular viral species. (B) This page provides various annotation information about the selected genome in which they are organized in tracks. (C) Information of a protein-coding gene. It tells the genomic location of the gene, size, and strand that codes for the protein. In addition, there is a short description about the current gene including the name of the protein, whether the virus is a New World or an Old World virus, the full name of the virus and its acronym, the RefSeq and GenBank accession numbers with hyperlink linked to the corresponding GenBank entry in the NCBI website.
Mentions: The web interface of gb4gv is organized in a hierarchy consisting of three levels. The highest level presents all the genera of Geminiviridae maintained in gb4gv including two satellites despite they are considered as genera (Fig. 3A). Figure 3B displays information about the genome of an individual virus and corresponding annotation tracks. Detailed information about a particular annotation e.g., a gene, a protein or a specific genomic sequence, is presented at the lowest level (Fig. 3C)

View Article: PubMed Central - HTML - PubMed

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus