BacNeMu: neutral mutation spectra reconstruction pipeline for bacteria

Abstract

The mutational spectrum is an increasingly important molecular phenotype that quantitatively describes mutagenesis in a given gene and species, enabling future comparative analyses to reveal differences in underlying mutagenic processes, whether internal, such as DNA repair processes, or external, such as ecological niches and conditions. Mutation accumulation experiments, although time-consuming and costly, remain the standard approach for reconstructing bacterial neutral mutation spectra. Here, we present BacNeMu, a phylogenetically informed pipeline that reconstructs neutral mutational spectra of bacterial genomes using open databases GTDB1, AnnoTree2 and KEGG Orthology3, building on previously developed NeMu pipeline4. BacNeMu reconstructs mutation spectra that closely match mutation accumulation experiments results while requiring substantially less time, enabling comparative analyses across diverse bacterial taxa. Applied to obligate aerobes and anaerobes, BacNeMu recovered the expected excess of T:A>C:G transitions, consistent with oxidative-damage-associated mutational patterns previously described in mitochondrial genomes and yeast single-strand5,6. We further asked if any other ecologic factors influence a mutational spectrum. As a pilot we compared three species living under different temperatures: one strong thermophile - Thermotoga maritima7, one psychrophile - Clostridium algidicarnis8, and one with intermediate temperature tolerance - Psychrobacter sanguinis9. In the thermophile, the relative frequency of T:A>C:G substitutions was higher than in the psychrophile, although C:G>T:A transitions predominate across all three species. BacNeMu provides a rapid, phylogenetically informed framework for generating biologically meaningful mutation spectra from open databases. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/735404v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@bfe7adorg.highwire.dtl.DTLVardef@1033010org.highwire.dtl.DTLVardef@48a77aorg.highwire.dtl.DTLVardef@1eb7533_HPS_FORMAT_FIGEXP M_FIG C_FIG