Comparative Genomics And Phylogeny Of Paraburkholderia Rhizobia

The Burkholderia genus comprises widely distributed gram-negative bacteria with varying functional and morphological characteristics.Despite this,its taxonomy status remains unresolved.Burkholderia rhizobia(later mainly transferred to the Paraburkholderia genus),as the major nodulating group within the beta-proteobacteria,have significant implications for the evolutionary study of rhizobia.These rhizobia can form symbiotic nodules with legumes from the subfamily Papilionoideae and the genus Mimosa,which have two centers of geographic distribution.However,it is still unclear how Paraburkholderia rhizobia was recruited as two distinct rhizobia and why symbiotic genes can be integrated into their genomes,even if their genomic background is highly divergent from other rhizobia in the alpha-proteobacteria.Therefore,this study primarily utilizes comparative genomics methods to conduct a large-scale genomic analysis of all Paraburkholderia rhizobia and determine their phylogenetic positions,infer the origin,transfer,and possible acquisition modes of symbiotic-related genes.The following results will be investigated:This dissertation utilized average nucleotide identity(ANI)analysis to evaluate and revise the taxonomic status of 71 Burkholderia rhizobia strains.We identified 32 distinct nodulating groups and observed no divergent host symbiotic variants within populations,as supported by the core gene tree.Our examination of pan-genomes showed substantial genetic diversity in Burkholderia rhizobia,with frequent genetic exchanges taking place with other groups,indicating the lateral transfer of symbiotic genes among strains.Through analysis of symbiotic and homologous genes in Paraburkholderia rhizobia,this study investigated horizontal transfer events in rhizobia.4 strains of rhizobia that nodulating Papilionoideae plants were isolated from the nodulation center of Mimosa in South America.Large-scale recent horizontal transfer events were detected between these strains and non-nodulating Mimosa rhizobia that are closely related but different from the nodulating host.The transferred genes were primarily located on plasmids.Reconstruction of symbiotic gene cluster structures revealed that the symbiotic gene clusters of these Papilionoideae-nodulating strains that originated from the nodulation center of Mimosa in South America were highly similar to those of Mimosa rhizobia,but different from those of other Papilionoideae rhizobia.These findings indicate that these four root-nodulating bacteria on Papilionoideae plants have the same origin as Mimosa rhizobia.Their symbiotic ability may have been acquired through horizontal transfer between rhizobia with similar ecological niches.In this study,we aimed to investigate the classification status of Paraburkholderia rhizobia.Similar to the phylogenetic position of rhizobia in alpha-proteobacteria,Paraburkholderia rhizobia exhibit scattered phylogenetic relationships,indicating that the acquisition of symbiotic ability in Paraburkholderia rhizobia involves horizontal gene transfer.In contrast to most alpha-proteobacterial rhizobia,the nitrogenase of Paraburkholderia rhizobia predominantly acts through the synthesis of high citrate synthase by the nif V gene.Therefore,to investigate the origin of symbiotic ability in Paraburkholderia rhizobia,molecular evolutionary analysis was conducted on the nif V gene in Paraburkholderia rhizobia and nitrogen-fixing bacteria.The results indicated that no significant positive selection site was found,suggesting that the nitrogen fixation ability in the symbiotic gene cluster of Paraburkholderia rhizobia may not come from rhizobial species within the Paraburkholderia genus but may have been transferred along with symbiosis-related genes.Unlike the clear monophyletic origin information of Mimosa rhizobia,the apparent bifurcation of nif V in Papilionoideae rhizobia may support that their nitrogen fixation ability has multiple origins.In this paper,we determined the phylogenetic position of Paraburkholderia rhizobia at genomic level.We compared the differentiation levels of symbiotic genes and core genes in Paraburkholderia rhizobia and utilized symbiotic gene trees and gene clusters to identify two distinct symbiotic genotypes.Detecting horizontal transfer events helped to explain inconsistencies between some rhizobial genotypes and phenotypes.Additionally,we found the Papilionoideae plant family to exhibit strong compatibility with Mimosa rhizobia.We also analyzed the possible origins of nitrogen fixation genes in Paraburkholderia rhizobia and speculated on the reasons that led to the development of distinctly different symbiotic genotypes from a specific perspective.These findings are significant for exploring the evolution and nitrogen fixation mechanism of Paraburkholderia rhizobia.