Coevolution of Metabolic Pathways in Blattodea and Their Blattabacterium Endosymbionts, and Comparisons with Other Insect-Bacteria Symbioses

Many insects harbor bacterial endosymbionts that supply essential nutrients and enable their hosts to thrive on a nutritionally unbalanced diet. Comparisons of the genomes of endosymbionts and their insect hosts have revealed multiple cases of mutually-dependent metabolic pathways that require enzymes encoded in 2 genomes. Complementation of metabolic reactions at the pathway level has been described for hosts feeding on unbalanced diets, such as plant sap. However, the level of collaboration between symbionts and hosts that feed on more variable diets is largely unknown. In this study, we investigated amino acid and vitamin/cofactor biosynthetic pathways in Blattodea, which comprises cockroaches and termites, and their obligate endosymbiont Blattabacterium cuenoti (hereafter Blattabacterium). In contrast to other obligate symbiotic systems, we found no clear evidence of “collaborative pathways” for amino acid biosynthesis in the genomes of these taxa, with the exception of collaborative arginine biosynthesis in 2 taxa, Cryptocercus punctulatus and Mastotermes darwiniensis. Nevertheless, we found that several gaps specific to Blattabacterium in the folate biosynthetic pathway are likely to be complemented by their host. Comparisons with other insects revealed that, with the exception of the arginine biosynthetic pathway, collaborative pathways for essential amino acids are only observed in phloem-sap feeders. These results suggest that the host diet is an important driving factor of metabolic pathway evolution in obligate symbiotic systems

Enhanced mutation rate, relaxed selection, and the ‘domino effect’ drive gene loss in Blattabacterium, a cockroach endosymbiont

Intracellular endosymbionts have reduced genomes that progressively lose genes at a timescale of tens of million years. We previously reported that gene loss rate is linked to mutation rate in Blattabacterium, however, the mechanisms causing gene loss are not yet fully understood. Here, we carried out comparative genomic analyses on the complete genome sequences of a representative set of 67 Blattabacterium strains, with sizes ranging between 511kbp and 645kbp. We found that 200 of the 566 analysed protein-coding genes were lost in at least one lineage of Blattabacterium, with the most extreme case being one gene that was lost independently in 24 lineages. We found evidence for three mechanisms influencing gene loss in Blattabacterium. First, gene loss rates were found to increase exponentially with the accumulation of substitutions. Second, genes involved in vitamin and amino acid metabolism experienced relaxed selection in Cryptocercus and Mastotermes, possibly triggered by their vertically-inherited gut symbionts. Third, we found evidences of epistatic interactions among genes leading to a \u27domino effect\u27 of gene loss within pathways. Our results highlight the complexity of the process of genome erosion in an endosymbiont

Vicariance and dispersal events inferred from mitochondrial genomes and nuclear genes (18S, 28S) shaped global Cryptocercus distributions

Cryptocercus Scudder, a genus of wingless, subsocial cockroaches, has low vagility but exhibits a disjunct distribution in eastern and western North America, and in China, South Korea and the Russian Far East. This distribution provides an ideal model for testing hypotheses of vicariance through plate tectonics or other natural barriers versus dispersal across oceans or other natural barriers. We sequenced 45 samples of Cryptocercus to resolve phylogenetic relationships among members of the genus worldwide. We identified four types of tRNA rearrangements among samples from the Qin-Daba Mountains. Our maximum-likelihood and Bayesian phylogenetic trees, based on mitochondrial genomes and nuclear genes (18S, 28S), strongly supported six major lineages of Cryptocercus, which displayed a clear geographical distribution pattern. We used Bayesian molecular dating to estimate the evolutionary timescale of the genus, and reconstructed Cryptocercus ancestral ranges using statistical dispersal-vicariance analysis (S-DIVA) in RASP. Two dispersal events and six vicariance events for Cryptocercus were inferred with high support. The initial vicariance event occurred between American and Asian lineages at 80.5 Ma (95% credibility interval: 60.0–104.7 Ma), followed by one vicariance event within the American lineage 43.8 Ma (95% CI: 32.0–57.5 Ma), and two dispersal 31.9 Ma (95% CI: 25.8–39.5 Ma), 21.7 Ma (95% CI: 17.3–27.1 Ma) plus four vicariance events c. 29.3 Ma, 27.2 Ma, 24.8 Ma and 16.7 Ma within the Asian lineage. Our analyses provide evidence that both vicariance and dispersal have played important roles in shaping the distribution and diversity of these woodroaches

Increased Mutation Rate Is Linked to Genome Reduction in Prokaryotes

The evolutionary processes that drive variation in genome size across the tree of life remain unresolved. Effective population size (Ne) is thought to play an important role in shaping genome size [1, 2, 3]—a key example being the reduced genomes of insect endosymbionts, which undergo population bottlenecks during transmission [4]. However, the existence of reduced genomes in marine and terrestrial prokaryote species with large Ne indicate that genome reduction is influenced by multiple processes [3]. One candidate process is enhanced mutation rate, which can increase adaptive capacity but can also promote gene loss. To investigate evolutionary forces associated with prokaryotic genome reduction, we performed molecular evolutionary and phylogenomic analyses of nine lineages from five bacterial and archaeal phyla. We found that gene-loss rate strongly correlated with synonymous substitution rate (a proxy for mutation rate) in seven of the nine lineages. However, gene-loss rate showed weak or no correlation with the ratio of nonsynonymous/synonymous substitution rate (dN/dS). These results indicate that genome reduction is largely associated with increased mutation rate, while the association between gene loss and changes in Ne is less well defined. Lineages with relatively high dS and dN, as well as smaller genomes, lacked multiple DNA repair genes, providing a proximate cause for increased mutation rates. Our findings suggest that similar mechanisms drive genome reduction in both intracellular and free-living prokaryotes, with implications for developing a comprehensive theory of prokaryote genome size evolution

Parallel and Gradual Genome Erosion in the Blattabacterium Endosymbionts of Mastotermes darwiniensis and Cryptocercus Wood Roaches

Almost all examined cockroaches harbor an obligate intracellular endosymbiont, Blattabacterium cuenoti. On the basis of genome content, Blattabacterium has been inferred to recycle nitrogen wastes and provide amino acids and cofactors for its hosts. Most Blattabacterium strains sequenced to date harbor a genome of approximately 630 kbp, with the exception of the termite Mastotermes darwiniensis ( approximately 590 kbp) and Cryptocercus punctulatus ( approximately 614 kbp), a representative of the sister group of termites. Such genome reduction may have led to the ultimate loss of Blattabacterium in all termites other than Mastotermes. In this study, we sequenced 11 new Blattabacterium genomes from three species of Cryptocercus in order to shed light on the genomic evolution of Blattabacterium in termites and Cryptocercus. All genomes of Cryptocercus-derived Blattabacterium genomes were reduced ( approximately 614 kbp), except for that associated with Cryptocercus kyebangensis, which comprised 637 kbp. Phylogenetic analysis of these genomes and their content indicates that Blattabacterium experienced parallel genome reduction in Mastotermes and Cryptocercus, possibly due to similar selective forces. We found evidence of ongoing genome reduction in Blattabacterium from three lineages of the C. punctulatus species complex, which independently lost one cysteine biosynthetic gene. We also sequenced the genome of the Blattabacterium associated with Salganea taiwanensis, a subsocial xylophagous cockroach that does not vertically transmit gut symbionts via proctodeal trophallaxis. This genome was 632 kbp, typical of that of nonsubsocial cockroaches. Overall, our results show that genome reduction occurred on multiple occasions in Blattabacterium, and is still ongoing, possibly because of new associations with gut symbionts in some lineages