Genomic characteristics of the Neisseria-related symbionts suggest an intermediate stage of the evolution
We propose that the Neisseria -related symbionts are in an early or intermediate state of symbiosis evolution. We base this view on comparisons with other known symbionts. Full genomes are currently available for four lineages of lice-associated symbionts. Three are highly reduced and display strong compositional shift towards AT, typical for many P-symbionts (Table 1). The fourth possesses a large genome and is supposedly a recent acquisition (Boyd et al., 2016). The genomes of the two Neisseria -related symbionts can thus be compared to various lice P-symbionts and to “free living” members of Neisseriales. Both “Neisseria ”-H and “Neisseria ”-P display significantly weaker genome degeneration than the highly reducedRiesia , Puchtella, and Legionella (Boyd et al., 2017; Rihova et al., 2017). They have higher GC content, considerably larger genomes (approximately three times higher number of genes), and consequently more complete metabolic pathways (SupplementaryData1). On the other hand, their genomes are recognizably reduced and the GC content decreased when compared to their relatives (e.g. the genusNeisseria , but also the bee symbiont Snodgrassella ) or to the presumably young Sodalis -like symbiont from the louseProechinophthirus fluctus (Boyd et al., 2016). The comparison of selected metabolic pathways shows that the Neisseria -related symbionts retain considerably greater numbers of genes in various categories than the reduced genomes of L. polyplacis and R. pediculicola (SupplementaryData1). This difference is particularly strong in the Recombination and repair category (as one example) but also in several amino acid biosynthesis pathways. An interesting example of differences between the two Neisseria -related symbionts is the complete histidine pathway in the “Neisseria- P” symbiont, entirely lost in the more reduced “Neisseria- H” (as well as in L. polyplacis and R. pediculicola ). Another conspicuous difference between theNeisseria -related symbionts and the other two louse symbionts regards their capacity to build the cell walls. Similar to the L. polyplacis and R. pediculicola , the Neisseria -related symbionts retain the path for peptidoglycan synthesis, but unlike them, they also possess the genes for penicillin binding protein class A and a complete pathway for lipid A, required for synthesis of lipopolysaccharide. In contrast, both Neisseria -related symbionts seem to lack the rod-shape coding genes. Finally, the genomes of bothNeisseria -related symbionts retain various genes connected to DNA exchange and/or transport, such as mobile elements, type IV pili, and secretion systems (SupplementaryData1). If, as suggested by many of the described genomic features, “Neisseria” -H is a young symbiont in an early state of evolution, we could assume that it only recently replaced a more ancient P-symbiont, which was fulfilling the nutritional role prior to the acquisition of the Neisseria -related symbiont. As discussed below, such a putative P-symbiont was indeed detected in the majority of the H. acanthopus microbiomes. Also, the FISH survey indicated that the bacteriocytes might be inhabited by two different bacteria. However, this interpretation should be taken with caution since the non-overlapping signal may reflect different properties of the used chromophores (Figure 4).