An automated system for evaluation of the potential functionome: MAPLE version 2.1.0

Abstract

Metabolic and physiological potential evaluator (MAPLE) is an automatic system that can perform a series of steps used in the evaluation of potential comprehensive functions (functionome) harboured in the genome and metagenome. MAPLE first assigns KEGG Orthology (KO) to the query gene, maps the KO-assigned genes to the Kyoto Encyclopedia of Genes and Genomes (KEGG) functional modules, and then calculates the module completion ratio (MCR) of each functional module to characterize the potential functionome in the user's own genomic and metagenomic data. In this study, we added two more useful functions to calculate module abundance and Q-value, which indicate the functional abundance and statistical significance of the MCR results, respectively, to the new version of MAPLE for more detailed comparative genomic and metagenomic analyses. Consequently, MAPLE version 2.1.0 reported significant differences in the potential functionome, functional abundance, and diversity of contributors to each function among four metagenomic datasets generated by the global ocean sampling expedition, one of the most popular environmental samples to use with this system. MAPLE version 2.1.0 is now available through the web interface (http://www.genome.jp/tools/maple/) 17 June 2016, date last accessed.

Keywords: MAPLE; global ocean sampling (GOS); metabolic pathway; metagenome.

Figure 1

Comparison of the complete module patterns among the four GOS sites. A: Classification of complete modules based on the module type defined by the KEGG database. 1: Ratio of each module type in the KEGG module. 2: Comparison of the ratio of complete modules in each type of KEGG module among the four GOS sites. B: Classification of complete modules by module class based on the MCR patterns of 1,488 prokaryotes. 1: Ratio of each module class in the KEGG module. 2: Comparison of ratios of complete modules in each module class among the four GOS sites. ITR: individual taxonomic rank. WC: whole community, OWC: only whole community.

Figure 2

Comparison of biodiversity contributing to the complete module and relative module abundance in the pathway and structural complex modules among the four GOS sites. The upper histogram shows MCR patterns of the KEGG module. The bars outlined by dashed lines indicate the MCRs of the WC. Uppercase characters A to D under the upper histogram show the module class used in Fig. 1, and ‘R’ indicates rare modules. The middle histogram shows the number of ITRs that completed the functional module. The lower histogram shows the relative module abundance ratio (MAR). The MAR was calculated by dividing abundance of each module by the minimum abundance among the four GOS sites. The modules showing 2-fold greater differences in the MAR among the four GOS sites are represented.

Figure 3

Comparison of abundance ratios of the modules completed by ITRs. Three typical pathway modules categorized into classes A (universal), B (restricted), and C (diversified). There were no substantial differences in relative module abundances among the four GOS sites selected for comparison of the contributions of ITR patterns to the module abundance.

Figure 4

Comparison of MCR and Q-value patterns of pathway modules by ITRs and WCs among the four GOS sites. (A) GS000c, (B) GS000d, (C) GS030, and (D) GS031. 1: ITR, 2: WC. Triangle: photorespiration (M00532), diamond: ethylmalonyl pathway (M00373), square: C₅-isoprenoid biosynthesis (M00095). Number of modules with the Q-value <0.5 in ITR and WC is shown in each sample. Among those with the Q-value <0.5, the number of modules with that of nearly zero is shown in the parentheses. The number of modules with the Q-value <0.5 in WC is somewhat larger than that in ITR in all GOS sites.

Figure 5

Microbial community structure for the four GOS sites based on ribosomal proteins. (A) GS000c, (B) GS000d, (C) GS030, and (D) GS031.