Background: The evolutionary history of species is frequently derived from molecular sequences, and the resulting phylogenetic trees do not include explicit functional information. Here, the biological processes of 42,489 proteins of the reference proteomes of 34 species of Spirochaetes were used to test the functional relation among bacteria in this phylum. We tested the hypothesis of whether the species of the genus Borreliaare as different as to be splitted in two different genera.
Results: Detrended Canonical Analysis demonstrated that the presence/absence of BPs among selected bacteria contains a strong phylogenetic signal and did not separate species of Borrelia. Examining the ten biological processes in which more proteins are involved consistently demonstrated that species in Borreliaare more similar among them than free-life species ( Sediminispirochaeta, Spirochaeta, Sphaerochaeta) or pathogenic without vectors ( Leptospira, Treponema, Brachyspira), which are highly divergent. A dendrogram based on presence/absence of proteins in the reference proteomes demonstrated that the distance between species of the same genus in free-life or pathogenic non-vector species are higher than among the 19 species (27 strains) of Borrelia. A phyloproteomic network supported the close functional association between species of Borreliaand their peculiarities about the extreme reduction of its proteome.
Conclusions: The proteome of 27 strains of Borreliademonstrated that only a few proteins have separately evolved in the relapsing fever and Lyme borreliosis groups, while most prominent proteins and processes of Borreliaare a subset of those found in free life and non-vectored pathogenic species. In addition, the functional innovation (i.e. unique biological processes or proteins) of Borreliais very low compared with other genera of Spirochaetes. Functional differences among Borreliaspecies were found to be marginal. Phyloproteomic networks including all pairwise combinations between species, proteins and processes contribute better than other methods to evaluate the evolutionary relationships among the taxa. With the limitations of data availability, results do not support the split of the arthropod-transmitted spirochaetes into the proposed genera Borreliaand Borreliella.