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Background  The  Bacillus subtilis -group and the  Bacillus cereus -group are two well-studied groups of species in the genus  Bacillus . Bacteria in this genus can produce a highly resistant cell type, the spore, which is encased in a complex protective protein shell called the coat. Spores in the  B. cereus -group contain an additional outer layer, the exosporium, which encircles the coat. The coat in  B. subtilis  spores possesses inner and outer layers. The aim of this study is to investigate whether differences in the spore structures influenced the divergence of the coat protein genes during the evolution of these two  Bacillus  species groups.    Results  We designed and implemented a computational framework to compare the evolutionary histories of coat proteins. We curated a list of  B. subtilis  coat proteins and identified their orthologs in 11  Bacillus  species based on phylogenetic congruence. Phylogenetic profiles of these coat proteins show that they can be divided into conserved and labile ones. Coat proteins comprising the  B. subtilis  inner coat are significantly more conserved than those comprising the outer coat. We then performed genome-wide comparisons of the nonsynonymous/synonymous substitution rate ratio, dN/dS, and found contrasting patterns: Coat proteins have significantly higher dN/dS in the  B. subtilis -group genomes, but not in the  B. cereus -group genomes. We further corroborated this contrast by examining changes of dN/dS within gene trees, and found that some coat protein gene trees have significantly different dN/dS between the  B subtilis -clade and the  B. cereus -clade.    Conclusions  Coat proteins in the  B. subtilis - and  B. cereus -group species are under contrasting selective pressures. We speculate that the absence of the exosporium in the  B. subtilis  spore coat effectively lifted a structural constraint that has led to relaxed negative selection pressure on the outer coat.

Contrasting evolutionary patterns of spore coat proteins in two Bacillus species groups are linked to a difference in cellular structure