Oomycete Gene Table: an online database for comparative genomic analyses of the oomycete microorganisms

Abstract

Oomycetes form a unique group of the fungal-like, aquatic, eukaryotic microorganisms. Lifestyle and pathogenicity of the oomycetes are diverse. Many pathogenic oomycetes affect a broad range of plants and cause enormous economic loss annually. Some pathogenic oomycetes cause destructive and deadly diseases in a variety of animals, including humans. No effective antimicrobial agent against the oomycetes is available. Genomic data of many oomycetes are currently available. Comparative analyses of the oomycete genomes must be performed to better understand the oomycete biology and virulence, as well as to identify conserved and biologically important proteins that are potential diagnostic and therapeutic targets of these organisms. However, a tool that facilitates comparative genomic studies of the oomycetes is lacking. Here, we described in detail the Oomycete Gene Table, which is an online user-friendly bioinformatic tool, designed to search, analyze, compare and visualize gene contents of 20 oomycetes in a customizable table. Genomic contents of other oomycete species, when available, can be added to the existing database. Some of the applications of the Oomycete Gene Table include investigations of phylogenomic relationships, as well as identifications of biologically important and pathogenesis-related genes of oomycetes. In summary, the Oomycete Gene Table is a simple and useful tool for comparative genomic analyses of oomycetes.

Figure 1

Components of the Oomycete Gene Table. Each row represents a gene cluster. Several columns are arranged to present (i) Row numbers, (ii) Cluster identification numbers, (iii) COG, (iv) Functional descriptions, (v) Expected gene lengths and (vi) organism names (e.g. 20 oomycetes and 2 diatoms). Percent completeness of a gene in each cell is indicated by color shading. A light-gray cell shows that a sequence with significant similarity (but without a complete open reading frame) is identified in a particular organism. A black cell indicates that no gene is identified in the corresponding genome.

Figure 2

User interface of the Oomycete Gene Table comprises of six drop-down windows: (a) Keyword search, (b) BLAST search, (c) Row sorting and cell coloring options, (d) Row filtering options, (e) Column (s) to display and (f) Show genes only present in.

Figure 3

The ‘Keyword search’ window of the Oomycete Gene Table: (a) a single or combined keyword(s) (e.g. cluster ID, COG number and protein/gene name) can be entered in the ‘input’ box for searching the genomic data of all 22 organisms and (b) the Oomycete Gene Table shows a search result of the matched gene contents of all or selected genomes.

Figure 4

The ‘Row sorting and cell coloring’ options of the Oomycete Gene Table. Display of the gene clusters and their associated data can be customized, arranged and sorted based on: (a) cluster IDs, functional annotations, expected gene lengths and COG categories; (b) position or copy number of gene(s) in the genome; and (c) a selected property, such as gene completeness, gene order in a genome, gene copy number or CG content.

Figure 5

The ‘Row filtering’ options of the Oomycete Gene Table. The drop-down window is used to customize and display only gene clusters with a desired COG category. The COG codes (e.g. [D], [M] and [N]), together with the number and percentage of each gene cluster identified in the organism(s) are listed.

Figure 6

Genomic data retrieval features of the Oomycete Gene Table: (a) when a gene cluster ID is selected, several links are shown as gateways to access the genomic data of all organisms contained in that gene cluster; (b) overview genomic data includes genome IDs, contig/gene IDs, genomic location and length of the genes, functional annotations, links to gene/protein sequences, links to source databases and links to NCBI Protein-BLAST tool; and (c) when an individual cell is selected, the genomic data of an individual organism can be obtained.