MBGD update 2013: the microbial genome database for exploring the diversity of microbial world

Abstract

The microbial genome database for comparative analysis (MBGD, available at http://mbgd.genome.ad.jp/) is a platform for microbial genome comparison based on orthology analysis. As its unique feature, MBGD allows users to conduct orthology analysis among any specified set of organisms; this flexibility allows MBGD to adapt to a variety of microbial genomic study. Reflecting the huge diversity of microbial world, the number of microbial genome projects now becomes several thousands. To efficiently explore the diversity of the entire microbial genomic data, MBGD now provides summary pages for pre-calculated ortholog tables among various taxonomic groups. For some closely related taxa, MBGD also provides the conserved synteny information (core genome alignment) pre-calculated using the CoreAligner program. In addition, efficient incremental updating procedure can create extended ortholog table by adding additional genomes to the default ortholog table generated from the representative set of genomes. Combining with the functionalities of the dynamic orthology calculation of any specified set of organisms, MBGD is an efficient and flexible tool for exploring the microbial genome diversity.

Figure 1.

Occurrence pattern display with the reduced pattern representation. Displayed is a histogram of occurrence patterns (with color in histogram bar representing functional category) in the entire orthologous cluster table of the superkingdom Bacteria (highlighted in the left-hand taxonomy tree). Here, occurrence patterns are compressed in the phylum level (as selected in ‘Group by’ menu), meaning that each element in an occurrence pattern corresponds to a phylum; the corresponding phylum name in each element is shown in the table below the histogram, where users can specify a condition of presence or absence of each taxon to filter the pattern. The colors in the occurrence patterns represents: dark green, r = 1 (1); green, 0.5 ≤ r < 1 (+); light green, 0 < r < 0.5 (-); none, r = 0 (0); where r is the ratio of the genomes that have the orthologs in that taxon and the characters in parentheses (1,+,-,0) are the quantized characters for reduced pattern.

Figure 2.

Core genome alignment display showing the core structure of the family Bacillaceae. In this diagram, each column corresponds to an extracted ‘core’ orthologous group and each row corresponds to genome. A dot represents an orthologous gene and a line represents a neighborhood relation between genes in each genome. Red line indicates that there is an inversion and green line indicates that there are some inserted genes between them. Note that core alignments are available only for taxonomic groups whose ranks are family or below that contain sufficiently diverse genomes, which are highlighted yellow in the taxonomy tree viewer in the left-hand panel.