Horizontal Gene Transfer Of Rhizobial Symbiosis-related Genes And Fungal Secondary Metabolic Gene Clusters

Horizontal gene transfer?HGT?is the sharing of genetic material between organisms which are not in a parent-offspring relationship.Genes can be transferred to another organism through various mechanisms of HGT such as transformation,transduction and plasmid conjugation.HGT allows gain of novel molecular functions and can provide selective evolutionary advantages to species.Large-scale genome analysis will significantly advance the systematical understanding of HGT in the context of microbial genome evolution.Accordingly,we first developed a new strategy for detecting recent HGT events at a whole-genome scale.Next,we analysed the HGT events of symbiosis modules among rhizobia,and secondary metabolic biosynthetic gene clusters among fungi,respectively.Additionally,we implemented a large-scale analysis of Rhizobium plasmids.A new computational strategy for detecting recent HGT Here,we developed a novel strategy,named RecentHGT.The number of genes undergoing recent HGT between two bacterial genomes was estimated by a novel algorithm derived from the expectation-maximization?EM?algorithm and is based on the theoretical Weibull distribution fitting of the sequence-similarity values of all orthologous genes.Then we tested the proposed strategy by applying it to a simulated HGT dataset and two cheese-associated bacteria with confirmed HGT events.We also found that our strategy was more sensitive and efficient than other state-of-art HGT detection methods.Detecting HGT events among Phaseolus vulgaris rhizobia Here,the RecentHGT strategy was adopted to detect HGT events among 29 representative Phaseolus vulgaris microsymbionts?21 Rhizobium strains,four Sinorhizobium strains,and four Bradyrhizobium strains?with their 48 closely related reference strains.The results confirmed that large-scale HGT events exclusively mediated by the symbiotic plasmids leading to expanded diversity of bean-nodulating rhizobial species.For Rhizobium,HGT only occurred among the strains nodulating P.vulgaris,which shows strong host-specificity.However,for Sinorhizobium and Bradyrhizobium,the P.vulgaris microsymbionts only shared symbiotic modules with Glycine max microsymbionts instead of themselves reflecting symbiotic compatibility between microsymbionts of common bean and other hosts such as soybean.In addition,there are two independent HGT groups among Rhizobium strains.This phenomenon indicate that the HGT could contribute the recipients to adapt particular soil environment such as acid soils.Comparative genomics analysis of Rhizobium plasmids Here,we present a large-scale analysis of 216 plasmids from 49 complete genomes of Rhizobium by constructing a bipartite network that consists of two classes of nodes,the plasmids and homologous protein families that connect them.Dissection of the network using a hierarchical clustering strategy reveals extensive variety,with 34 homologous plasmid clusters.Four large and common clusters?one symbiotic cluster and three accessory clusters?reflect a fundamental composition of the Rhizobium plasmids,whereas the other clusters are quite small and rare.Symbiotic clusters and rare accessory clusters are exogenetic and do not appear to have co-evolved with the common accessory clusters;the latter ones have a large coding potential and functional complementarity for different lifestyles in Rhizobium.The bipartite network also provides preliminary evidence of Rhizobium plasmid variation and formation including genetic exchange,plasmid fusion and fission,exogenetic plasmid transfer,host plant selection,and environmental adaptation.Deciphering origination,differentiation and HGT of fusidane biosynthetic gene clusters?BGCs?This research analyzed compositions and evolution histories of three typical fusidane BGCs.Based on the fungal genome and transcriptome,we predicted the BGCs of fusidic acid and cephalosporin P₁,and observed six core genes among all three fusidane BGCs.Accordingly,we hypothesized that the six-gene-mediated reaction is likely to be a common pathway in the early-stage biosynthesis of all fusidane-type antibiotics and different fusidane-type antibiotics are subsequently generated under the action of different post-modification enzymes.The fusidane BGCs in fungi have complex evolutionary histories:1)The clusters evolved by gene duplication and differentiation from an ancestry cyclase,a P450 monooxygenase and an acyltransferase genes,and three dehydrogenases;2)fusidic acid and cephalosporin P₁ catalytic gene clusters possibly derived from ancient helvolic acid BGCs;3)The occasionally horizontal transfers of whole biosynthetic gene clusters contributed to the spreading of fusidane BGCs among distantly-related fungi.In summary,this research systematically analyzed HGT events in some important microorganisms.Importantly,we put forward a novel strategy for detecting recent HGT and reveal the influences of the plasmids and the HGT genes on the rhizobia-legume symbiosis.Additionally,we provide evidences of the horizontal transfer of secondary metabolite gene clusters between fungi.The results could bring us closer to the goal of understanding HGT‘s contribution to adaptive evolution in microorganisms.