Abstract
BackgroundGenes 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.DescriptionUsing 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.ConclusionPlantOrDB (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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0531-4) contains supplementary material, which is available to authorized users.
Highlights
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 [1,2,3]
For any two gene sequences, either from the same species or different species, if their BLAST e-value is within the 1e-10 cutoff (e-value threshold) and the overlapped region is more than 80 % of the longer sequence, they will be treated as homologous genes
Summary
Built on 35 plant and 6 green algal genomes released from Phytozome v9, PlantOrDB is a genome-wide ortholog database for land plants and green algae. The highly interactive web interfaces provided by PlantOrDB can display useful information on individual gene, and its homolog gene families and ortholog genes interactively and dynamically. PlantOrDB provides accurate query classification and useful data visualization of query sequences within phylogenetic tree and multiple sequence alignment, with powerful search functions useful for functional genomics research. Some other databases such as PLAZA 3.0 and EnsemblPlants are able to provide many comparative genomics tools (e.g., collinear region plot and localization plot) that PlantOrDB currently does not offer. We will incorporate these tools into our database and make PlantOrDB more useful to the research community. We have tested our web interfaces using Google Chrome, Mozilla Firefox (8.0 or above) and Microsoft Internet Explorer (9.0 or above) under different Operation Systems including Macintosh, Linux and Windows. For the best visualization effect and performance, we recommend Mozilla FireFox and Google Chrome
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