MarkerMAG: linking metagenome-assembled genomes (MAGs) with 16S rRNA marker genes using paired-end short reads.

Abstract

Metagenome-assembled genomes (MAGs) have substantially extended our understanding of microbial functionality. However, 16S rRNA genes, which are commonly used in phylogenetic analysis and environmental surveys, are often missing from MAGs. Here, we developed MarkerMAG, a pipeline that links 16S rRNA genes to MAGs using paired-end sequencing reads. Assessment of MarkerMAG on three benchmarking metagenomic datasets with various degrees of complexity shows substantial increases in the number of MAGs with 16S rRNA genes and a 100% assignment accuracy. MarkerMAG also estimates the copy number of 16S rRNA genes in MAGs with high accuracy. Assessments on three real metagenomic datasets demonstrate 1.1- to 14.2-fold increases in the number of MAGs with 16S rRNA genes. We also show that MarkerMAG-improved MAGs increase the accuracy of functional prediction from 16S rRNA gene amplicon data. MarkerMAG is helpful in connecting information in MAG databases with those in 16S rRNA databases and surveys and hence contributes to our increasing understanding of microbial diversity, function and phylogeny. MarkerMAG is implemented in Python3 and freely available at https://github.com/songweizhi/MarkerMAG. Supplementary data are available at Bioinformatics online.