Genome assembly and functional annotation of Mycoplasma pneumoniae M129 strain

Mycoplasma pneumoniae, a genome-reduced bacterium that causes community‐acquired pneumonia, is a model organism extensively used in systems biology studies, and is considered to be one of the smallest known self-replicating organisms. The Mycoplasma pneumoniae M129 strain cultured in the laboratory presents many unknown genetic variants when compared to the reference genome NC_000912.1. In order to fully characterize the laboratory strain, whole-genome sequencing and genome assembly were performed. Cells were cultured for several passages (0, 6, 10, 14 and 18), and genomic DNA samples were sequenced on Illumina MiSeq platform at 1000x coverage, 2x300 bp (paired-end). Genome assembly was performed using SPAdes genome assembler. Misassemblies were resolved using the NC_000912.1 genome as a reference. Annotations were extensively updated and curated based on genome sequence and recent experimental data.