SeSaMe:Metagenome Sequence Classification of Arbuscular Mycorrhizal Fungi-associated Microorganisms

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 of 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 study,we introduce a novel bioinformatics program,Spore-associated Symbiotic Microbes(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 a three consecutive codon DNA 9-mer encoding 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 mean percentages of correct predictions of the CDS and the non-CDS test sets at the genus level were 71% and 50% for bacteria,68% and 73% for fungi(excluding AMF),and 49% and 72% for AMF(Rhizophagus irregularis),respectively.SeSaMe provides not only a means for estimating taxonomic diversity and abundance but also the gene reservoir of the reference taxonomic groups associated with AMF.Therefore,it enables users to study the symbiotic roles of associated microorganisms.It can also be applicable to other microorganisms as well as soil metagenomes.SeSaMe is freely available at www.fungalsesame.org.

SeSaMe PS Function:Functional Analysis of the Whole Metagenome Sequencing Data of the Arbuscular Mycorrhizal Fungi

In this study,we introduce a novel bioinformatics program,Spore-associated Symbiotic Microbes Position-specific Function(SeSaMe PS Function),for position-specific functional analysis of short sequences derived from metagenome sequencing data of the arbuscular mycorrhizal fungi.The unique advantage of the program lies in databases created based on genus-specific sequence properties derived from protein secondary structure,namely amino acid usages,codon usages,and codon contexts of 3-codon DNA 9-mers.SeSaMe PS Function searches a query sequence against reference sequence database,identifies 3-codon DNA 9-mers with structural roles,and creates a comparative dataset containing the codon usage biases of the 3-codon DNA 9-mers from 54 bacterial and fungal genera.The program applies correlation principal component analysis in conjunction with K-means clustering method to the comparative dataset.3-codon DNA 9-mers clustered as a sole member or with only a few members are often structurally and functionally distinctive sites that provide useful insights into important molecular interactions.The program provides a versatile means for studying functions of short sequences from metagenome sequencing and has a wide spectrum of applications.SeSaMe PS Function is freely accessible at www.fungalsesame.org.