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PlantOrDB: a genome-wide ortholog database for land plants and green algae.

Li L, Ji G, Ye C, Shu C, Zhang J, Liang C - BMC Plant Biol. (2015)

Bottom Line: It is widely accepted that orthologs are homologous genes evolved from speciation events while paralogs are homologous genes resulted from gene duplication events.With the rapid increase of genomic data, identifying and distinguishing these genes among different species is becoming an important part of functional genomics research.PlantOrDB not only allows users to identify orthologs or paralogs from phylogenetic trees, but also provides all orthologs that are built using Reciprocal Best Hit (RBH) pairwise alignment method.Users can upload their own sequences to find the best matched gene families, and visualize their query sequences within the relevant phylogenetic trees and sequence alignments.

View Article: PubMed Central - PubMed

Affiliation: Department of Automation, Xiamen University, Fujian, 361005, China. leilioxford@hotmail.com.

ABSTRACT

Background: Genes with different functions are originally generated from some ancestral genes by gene duplication, mutation and functional recombination. It is widely accepted that orthologs are homologous genes evolved from speciation events while paralogs are homologous genes resulted from gene duplication events.With the rapid increase of genomic data, identifying and distinguishing these genes among different species is becoming an important part of functional genomics research.

Description: Using 35 plant and 6 green algal genomes from Phytozome v9, we clustered 1,291,670 peptide sequences into 49,355 homologous gene families in terms of sequence similarity. For each gene family, we have generated a peptide sequence alignment and phylogenetic tree, and identified the speciation/duplication events for every node within the tree. For each node, we also identified and highlighted diagnostic characters that facilitate appropriate addition of a new query sequence into the existing phylogenetic tree and sequence alignment of its best matched gene family. Based on a desired species or subgroup of all species, users can view the phylogenetic tree, sequence alignment and diagnostic characters for a given gene family selectively. PlantOrDB not only allows users to identify orthologs or paralogs from phylogenetic trees, but also provides all orthologs that are built using Reciprocal Best Hit (RBH) pairwise alignment method. Users can upload their own sequences to find the best matched gene families, and visualize their query sequences within the relevant phylogenetic trees and sequence alignments.

Conclusion: PlantOrDB ( http://bioinfolab.miamioh.edu/plantordb ) is a genome-wide ortholog database for land plants and green algae. PlantOrDB offers highly interactive visualization, accurate query classification and powerful search functions useful for functional genomic research.

No MeSH data available.


The snapshots of the main web interface of PlantOrDB. Panel a: the navigation bar of PlantOrDB. Panel b: Summary Information. Panel c: Download. Panel d: Consensus Sequence Viewer. Panel e: Pie Viewer. Panel f: Datagrid Viewer. Panel g: Tree Viewer. Panel h: Tree-alignment Combined Viewer. Panel i: gene information panel. Panel j: navigation panel
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Fig1: The snapshots of the main web interface of PlantOrDB. Panel a: the navigation bar of PlantOrDB. Panel b: Summary Information. Panel c: Download. Panel d: Consensus Sequence Viewer. Panel e: Pie Viewer. Panel f: Datagrid Viewer. Panel g: Tree Viewer. Panel h: Tree-alignment Combined Viewer. Panel i: gene information panel. Panel j: navigation panel

Mentions: The major web portal of PlantOrDB is divided into six components: “USER GUIDE”, “SUMMARY”, “DATABASE BROWSER”, “GENE FAMILY SEARCH”, “PAIRWISE ORTHOLOG SEARCH” and “QUERY CLASSIFICATION”, shown as in the navigation bar in Fig. 1a. The “USER GUIDE” is a tutorial page that helps users utilize and be familiar with our web interfaces. The “SUMMARY” has two submenus items: “About PlantOrDB” and “Data Source”, which provide a database overview and some descriptions of our data source respectively. The “DATABASE BROWSER” contains four submenus items: “Gene Families”, “Protein Sequences”, “Gene Annotation” and “Individual Gene Sequence-Annotation Viewer”. Through these items, users can navigate, browse, view and search both the summary and detailed information of gene families, protein sequences and their functional annotations. The “GENE FAMILY SEARCH” allows users to search homolog gene families by a gene family ID, full gene name and gene sequence ID. The “PAIRWISE ORTHOLOG SEARCH” allows users to search all RBH-pairwise-alignment-based orthologs for a given gene. After a user specifies a gene sequence ID, the interface will show an ortholog tree that contains all orthologs for the selected gene and their relevant orthologs recursively. Furthermore, the interface also can show the ortholog path between any two genes in the ortholog tree, which can describe how these two genes are linked through their orthologs. The “QUERY CLASSIFICATION” tab allows users to submit a single query sequence and classify it into an existing, best matched homolog gene family. The query sequence will be inserted into appropriate positions within the phylogenetic tree and multiple sequence alignment of the best matched gene family for interactive visualization.Fig. 1


PlantOrDB: a genome-wide ortholog database for land plants and green algae.

Li L, Ji G, Ye C, Shu C, Zhang J, Liang C - BMC Plant Biol. (2015)

The snapshots of the main web interface of PlantOrDB. Panel a: the navigation bar of PlantOrDB. Panel b: Summary Information. Panel c: Download. Panel d: Consensus Sequence Viewer. Panel e: Pie Viewer. Panel f: Datagrid Viewer. Panel g: Tree Viewer. Panel h: Tree-alignment Combined Viewer. Panel i: gene information panel. Panel j: navigation panel
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4481079&req=5

Fig1: The snapshots of the main web interface of PlantOrDB. Panel a: the navigation bar of PlantOrDB. Panel b: Summary Information. Panel c: Download. Panel d: Consensus Sequence Viewer. Panel e: Pie Viewer. Panel f: Datagrid Viewer. Panel g: Tree Viewer. Panel h: Tree-alignment Combined Viewer. Panel i: gene information panel. Panel j: navigation panel
Mentions: The major web portal of PlantOrDB is divided into six components: “USER GUIDE”, “SUMMARY”, “DATABASE BROWSER”, “GENE FAMILY SEARCH”, “PAIRWISE ORTHOLOG SEARCH” and “QUERY CLASSIFICATION”, shown as in the navigation bar in Fig. 1a. The “USER GUIDE” is a tutorial page that helps users utilize and be familiar with our web interfaces. The “SUMMARY” has two submenus items: “About PlantOrDB” and “Data Source”, which provide a database overview and some descriptions of our data source respectively. The “DATABASE BROWSER” contains four submenus items: “Gene Families”, “Protein Sequences”, “Gene Annotation” and “Individual Gene Sequence-Annotation Viewer”. Through these items, users can navigate, browse, view and search both the summary and detailed information of gene families, protein sequences and their functional annotations. The “GENE FAMILY SEARCH” allows users to search homolog gene families by a gene family ID, full gene name and gene sequence ID. The “PAIRWISE ORTHOLOG SEARCH” allows users to search all RBH-pairwise-alignment-based orthologs for a given gene. After a user specifies a gene sequence ID, the interface will show an ortholog tree that contains all orthologs for the selected gene and their relevant orthologs recursively. Furthermore, the interface also can show the ortholog path between any two genes in the ortholog tree, which can describe how these two genes are linked through their orthologs. The “QUERY CLASSIFICATION” tab allows users to submit a single query sequence and classify it into an existing, best matched homolog gene family. The query sequence will be inserted into appropriate positions within the phylogenetic tree and multiple sequence alignment of the best matched gene family for interactive visualization.Fig. 1

Bottom Line: It is widely accepted that orthologs are homologous genes evolved from speciation events while paralogs are homologous genes resulted from gene duplication events.With the rapid increase of genomic data, identifying and distinguishing these genes among different species is becoming an important part of functional genomics research.PlantOrDB not only allows users to identify orthologs or paralogs from phylogenetic trees, but also provides all orthologs that are built using Reciprocal Best Hit (RBH) pairwise alignment method.Users can upload their own sequences to find the best matched gene families, and visualize their query sequences within the relevant phylogenetic trees and sequence alignments.

View Article: PubMed Central - PubMed

Affiliation: Department of Automation, Xiamen University, Fujian, 361005, China. leilioxford@hotmail.com.

ABSTRACT

Background: Genes with different functions are originally generated from some ancestral genes by gene duplication, mutation and functional recombination. It is widely accepted that orthologs are homologous genes evolved from speciation events while paralogs are homologous genes resulted from gene duplication events.With the rapid increase of genomic data, identifying and distinguishing these genes among different species is becoming an important part of functional genomics research.

Description: Using 35 plant and 6 green algal genomes from Phytozome v9, we clustered 1,291,670 peptide sequences into 49,355 homologous gene families in terms of sequence similarity. For each gene family, we have generated a peptide sequence alignment and phylogenetic tree, and identified the speciation/duplication events for every node within the tree. For each node, we also identified and highlighted diagnostic characters that facilitate appropriate addition of a new query sequence into the existing phylogenetic tree and sequence alignment of its best matched gene family. Based on a desired species or subgroup of all species, users can view the phylogenetic tree, sequence alignment and diagnostic characters for a given gene family selectively. PlantOrDB not only allows users to identify orthologs or paralogs from phylogenetic trees, but also provides all orthologs that are built using Reciprocal Best Hit (RBH) pairwise alignment method. Users can upload their own sequences to find the best matched gene families, and visualize their query sequences within the relevant phylogenetic trees and sequence alignments.

Conclusion: PlantOrDB ( http://bioinfolab.miamioh.edu/plantordb ) is a genome-wide ortholog database for land plants and green algae. PlantOrDB offers highly interactive visualization, accurate query classification and powerful search functions useful for functional genomic research.

No MeSH data available.