SeSaMe: Metagenome Sequence Classification of Arbuscular Mycorrhizal Fungi Associated Microorganisms

Abstract

Arbuscular mycorrhizal fungi (AMF) are plant root symbionts that play key roles in plant growth and soil fertility. They are obligate biotrophic fungi that form coenocytic multinucleated hyphae and spores. Numerous studies have shown that diverse microorganisms live on the surface and inside their mycelia, resulting in a metagenome when whole genome sequencing (WGS) data are obtained from sequencing AMF cultivated in vivo. The metagenome contains not only the AMF sequences, but also those from associated microorganisms. In this article, we introduce a novel bioinformatics program, SeSaMe, designed for taxonomic classification of short sequences obtained by next-generation DNA sequencing. A genus-specific usage bias database was created based on amino acid usage and codon usage of three consecutive codon DNA 9-mers encoding for an amino acid trimer in a protein secondary structure. The program distinguishes between coding sequence (CDS) and non-CDS, and classifies a query sequence into a genus group out of 54 genera used as reference. The average correct prediction percentages of the CDS and the non-CDS test sets at the genus level were 71% and 50% for bacteria, 65% and 73% for fungi (excluding AMF), and 49% and 72% for AMF (Rhizophagus irregularis), respectively. The program provides a means for estimating not only taxonomic diversity and abundance but also the gene reservoir of the reference taxonomic groups associated with AMF. Therefore, the program enables users to study the symbiotic roles of associated microorganisms. SeSaMe can be applicable to other microorganisms as well as soil metagenomes. It is freely available at www.journal.com and www.fungalsesame.org.