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Background Long-term persistent symbiotic associations may result in co-speciation and can be inferred if species trees of hosts and symbionts are congruent in topology and divergence times. Co-speciation has been seen to occur relatively frequently in obligate associations, but is less common in parasitic or facultative ones, mainly due to the difference in horizontal transmission rates. The long-term vertical inheritance and close host association of obligate endosymbionts also generally result in smaller genomes than in facultative endosymbionts. Here, we investigate co-speciation and genome reduction using highly similar strains of the endosymbiont Wolbachia infecting Drosophila species from the willistoni and saltans groups, where only one strain, w Pau, infecting D. paulistorum , is obligate. Results We sequenced the Wolbachia genomes from five species of the willistoni and saltans groups and constructed phylogenies. Topological congruence was found between these Wolbachia strains and the nuclear DNA of their hosts, except for w Pau and D. paulistorum , but full topological congruence was observed between Wolbachia and the host mitochondrial DNA. However, assuming temporal congruence, we estimated extremely low evolutionary rates in Wolbachia of 10 − 10 -10 − 11 changes/site/year. Additionally, the obligate w Pau strain was found to have a larger genome than closely related facultative strains, mainly due to an ongoing expansion of an IS4 element. Furthermore, w Pau has lost a large proportion of its prophage WO genes, but the cif genes, known to be involved in the CI phenotype, are intact. Finally, nine of the eleven genes from the prophage WO-associated Undecim cluster are uniquely duplicated. Conclusions The congruent topologies between Wolbachia and their willistoni and saltans group hosts indicate co-speciation. However, the high similarity between Wolbachia strains, which results in low mutation rate estimates, challenges this interpretation. Contrary to the expectations of the genome reduction theory, we observed an increase in genome size in the obligate w Pau strain, potentially driven by a decreased population size. Finally, the duplication of the Undecim cluster, despite a major loss of other prophage-associated genes, suggests that the genes in the Undecim cluster are under strong selection and potentially play a role in the obligate association between w Pau and their D. paulistorum hosts.

Background Retama dasycarpa , a drought-resistant legume endemic to Morocco’s High Atlas Mountains, thrives in harsh conditions due to its association with nitrogen-fixing Bradyrhizobium strains. Despite the ecological significance of this symbiosis, the genetic diversity, symbiotic mechanisms, and stress adaptation strategies of these microsymbionts remain poorly understood. In this study we employed a comparative genomic approach to elucidate the genomic and functional traits of five strains isolated from R. dasycarpa nodules, with a focus on their symbiotic and stress-responsive gene repertoires. Results Phylogenomic analysis revealed that four of the five strains likely represent novel Bradyrhizobium species, as indicated by average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values below species delineation thresholds. Genomic comparisons identified core symbiotic genes, including nod , nif , and fix genes, essential for nodulation and nitrogen fixation. Interestingly, strain RDT46 lacked canonical nod genes but retained a minimal Type III Secretion System (T3SS), suggesting alternative symbiotic pathways. Pangenome analysis of 56 Bradyrhizobium genomes highlighted an open pangenome with extensive accessory gene content, reflecting adaptive versatility. Stress adaptation genes, such as those involved in osmoprotectant synthesis, oxidative stress response, and heat shock, were conserved across the five strains, underscoring their resilience to semi-arid conditions. Conclusions This study uncovers previously unknown genomic diversity in R. dasycarpa -associated Bradyrhizobim spp., including evidence for non-canonical symbiosis mechanisms. The strains’ genetic toolkit for stress tolerance highlights their potential as inoculants for revegetation of degraded semi-arid lands.

Background Recent evidence shows that arbuscular mycorrhizal (AM) symbiosis, as defined by the presence of arbuscules, is established by two distinct fungal groups, with the distinctive ‘fine root endophyte’ morphotype formed by fungi from the subphylum Mucoromycotina rather than the sub-phylum Glomeromycotina. While FRE forming fungi are globally distributed, there is currently no understanding of the genomic basis for their symbiosis or how this symbiosis compares to that of other mycorrhizal symbionts. Results We used culture-independent metagenome sequencing to assemble and characterise the metagenome-assembled genome (MAG) of a putative arbuscule forming fine root endophyte, which we show belonged to the family Planticonsortiaceae within the order Densosporales. The MAG shares key traits with Glomeromycotina fungi, which indicate obligate biotrophy, including the absence of fatty acid and thiamine biosynthesis pathways, limited enzymatic abilities to degrade plant cell walls, and a high abundance of calcium transporters. In contrast to Glomeromycotina fungi, it exhibits a higher capacity for degradation of microbial cell walls, a complete cellulose degradation pathway, low abundances of copper, nitrate and ammonium transporters, and a complete pathway for vitamin B6 biosynthesis. Conclusion These differences, particularly those typically associated with saprotrophic functions, highlight the potential for contrasting interactions between Mucoromycotina and Glomeromycotina fungi with their host plant and the environment. In turn, this could support niche differentiation in resource acquisition and complementary ecological functions.

Background The Hawaiian Pariaconus psyllid radiation represents a unique system to study the co-evolution of nuclear, mitochondrial, and endosymbiont genomes. These psyllids, which diversified across the Hawaiian Islands during the last 3–3.5 million years vary with their ecological niches on their plant host ‘Ōhi’a lehua ( Metrosideros polymorpha ) (free-living, open-gall, and closed-gall lifestyles) and harbor one to three beneficial bacterial endosymbionts. Co-evolutionary studies of other multi-endosymbiont insect systems have shown decoupled rates of sequence evolution between mitochondria and endosymbionts. Here we examine the evolutionary trends in Pariaconus psyllids, their mitochondria and their endosymbionts to determine if they fit this paradigm. Results We sequenced a new Carsonella genome from the ohialoha species group (closed-gall, one symbiont), revealing a remarkable degree of gene conservation between two of the most divergent species from this diverse species group that has dispersed across multiple islands. Further, despite the rapid radiation of psyllid species, we observed complete synteny among mitochondrial genomes from all six Pariaconus species in this study, suggesting the preservation of genome structure due to strong purifying selection. Phylogenetic analyses of the nuclear, mitochondrial, and endosymbiont genomes across these six Pariaconus species revealed correlated rates of substitutions, contrary to prior reports of decoupling between mitochondrial and endosymbiont genomes in other insect systems with multiple symbiont partners. Finally, we found that free-living psyllids with three symbionts exhibited elevated mutation rates (~ 1.2–1.6x) across all genomes and elevated rates of fixation of nonsynonymous substitutions in the insect nuclear genome and one of the endosymbionts. Conclusions This study highlights the interplay between ecological diversification and genomic evolution in Pariaconus . Further, these data indicate that multiple endosymbiont partners alone are not sufficient to result in decoupling rates of sequence evolution. Future work on basal members of this species radiation will refine our understanding of the mechanisms shaping this dynamic insect-symbiont system and its implications for genome evolution.

Tsetse ( Glossina spp.) are vectors of African trypanosomes, the causative agents of Human and African Animal trypanosomiases, diseases that remain significant medical and socioeconomic challenges in sub-Saharan Africa. In addition to trypanosomes, tsetse harbor both obligate and facultative symbiotic bacteria that can influence vector competence and reproductive biology. One such facultative symbiont, Spiroplasma glossinidia , infects several tsetse species within the Palpalis subgroup. In Glossina fuscipes fuscipes ( Gff ), the Spiroplasma glossinidia strain s Gff induces a trypanosome-refractory phenotype and negatively impacts reproductive fitness by reducing female fecundity. However, the mechanisms behind these Spiroplasma -derived phenotypes remain poorly understood. Here, we report successful in vitro cultivation of s Gff and present complete genomes from three sources: in vitro cultured s Gff and s Gff isolated from both laboratory-maintained and wild-caught (Uganda) Gff flies. Comparative genomic analyses revealed a high degree of similarity in gene content and synteny among these s Gff samples, confirming that they represent isolates of the same strain. Phylogenomic analyses placed s Gff within the Spiroplasma poulsonii clade. We found the s Gff genome to be highly dynamic, containing numerous mobile genetic elements. Additionally, in silico annotations indicated that s Gff relies on its host for both lipids and carbohydrates and can produce several toxins, all of which could be implicated in the observed trypanosome refractory phenotype. Finally, comparative transcriptomic analysis of s Gff from host hemolymph versus in vitro culture provided insights into potential factors relevant to host-symbiont interactions. Our findings provide a foundation for understanding the nutritional dialogue between s Gff and its host and identify symbiotic products that may contribute to trypanosome resistance. Furthermore, the establishment of an in vitro culture system for s Gff represents a significant resource for future functional studies with potential implications for vector control.

Background Dendroctonus rhizophagus is a bark beetle of great forest importance, due to its aggressive root colonization of seedlings and young pine trees. To successfully complete their life cycle, these insects and associated microorganisms must overcome the trees’ complex defense system. However, little is known about the enzymes and metabolic pathways involved in xenobiotic detoxification by microbial symbionts of bark beetles. We investigated the genomic potential for detoxification in bacteria Acinetobacter , Pseudomonas , Rahnella and Serratia , as well as the yeasts Candida [ Ogataea clade], Danielia , Cyberlindnera and Zygoascus , dominant members of the gut core microbiome of D . rhizophagus , through assembly, annotation, and comparison of their genomes. Results Genome analysis identified 1,293 genes in bacteria and yeasts related to 22 KO xenobiotic-degradation pathways. These pathways include those for aromatic compounds (benzoate, ferulate, vanillin), monoterpenes (pinene, camphor, geraniol, limonene) and diterpenes ( dit genes). Additionally, the genomes contained genes encoding members of the following enzymatic families: cytochrome P450, carboxylesterases, laccases, aldehyde and alcohol dehydrogenases, flavin binding-monooxygenases, intradiol and extradiol dioxygenases, glutathione S-transferases, and multidrug resistance transporters (ABC, MFS, MATE, and RND) implicated in the detoxification process. Conclusions Integration of these genes across the phases of xenobiotic detoxification reveals potential functional complementarity between bacteria and yeasts, suggesting that members of the gut microbiota of D. rhizophagus may enhance the beetle’s fitness by facilitating the metabolism and tolerance to the tree´s toxic compounds.

The complete nucleotide sequence of the genome of the soybean symbiont Bradyrhizobium japonicum strain USDA6T was determined. The genome of USDA6T is a single circular chromosome of 9,207,384 bp. The genome size is similar to that of the genome of another soybean symbiont, B. japonicum USDA110 (9,105,828 bp). Comparison of the whole-genome sequences of USDA6T and USDA110 showed colinearity of major regions in the two genomes, although a large inversion exists between them. A significantly high level of sequence conservation was detected in three regions on each genome. The gene constitution and nucleotide sequence features in these three regions indicate that they may have been derived from a symbiosis island. An ancestral, large symbiosis island, approximately 860 kb in total size, appears to have been split into these three regions by unknown large-scale genome rearrangements. The two integration events responsible for this appear to have taken place independently, but through comparable mechanisms, in both genomes.