Comparative Genomics of Microorganism Traits

We retrieved 214 genome sequences, 1 per species, from GenBank Genomes (ftp://ftp.ncbi.nih.gov/genomes/Bacteria/). Genes were extracted from annotation data and pseudo-genes were ignored. Genes of the transcription/translation machinery (RNA polymerase, rRNAs, ribosomal proteins) were identified by the annotation fields, or, when not possible, by homology from the genomes of closely related species. A pair of genes were regarded as orthologous if they were reciprocal best hits with more than 40% sequence similarity and less than 20% difference in protein length, as measured by a end-gaps free sequence alignment. tRNAs were searched with tRNAscanSE [88] (link) using the default parameters for bacteria or archaea. When the tRNA anticodon matched a previously published list of nearly ubiquitous tRNAs [35] (link) it was included in the list of ubi-tRNAs. Optimal growth temperatures (OGT) were retrieved for 204 of the 214 organisms from the DSMZ database (http://www.dsmz.de/microorganisms/). Psychrophiles and thermophiles were defined as organisms whose OGT is under 15°C and over 60°C, respectively. We extracted from primary literature the minimal generation times (d) for the 214 species of bacteria and archaea (Table S1).