Research On The Evolution Of Plant Pathogens And Disease Resistance Genes

Phytopathogen is the general term of the biological factors causing plant diseases,including bacteria,viruses,fungi,nematodes,and oomycetes.The phytopathogens evolve different strategies to infect plants.Plants,in turn,evolve different defense mechanisms to fight against pathogens.The conflict between plants and pathogens results in a recurring evolutionary arms race,which is also known as the "Red Queen" evolutinary dynamics.With the recent development of next-generation sequencing,the genomes of a variety of plants and phytopathogens have been sequenced,which provide important resources for studying the evolution of phytopathogens and plant resistance(R)genes.In this study,based on genome-scale data of plants and phytopathogens,we use comparative genomics and phylogenetic methods to systemically explore the effect of gene duplication on the evolution of DNA viruses and the origin and evolution of plant R genes.Gene duplication is one of machanisms that generate new genes,which plays an important role in shaping the complexity of genome.Previous studies suggest that gene duplication is rare within RNA viruses.However,it remains unclear about the extent and evolution of gene duplication within DNA viruses.Many phytopathogens are DNA viruses,such as Cauliflower mosaic virus,Cassava vein mosaic virus,and Emiliania huxleyi virus 86.We assemble a dataset of 250 viruses that represent all knowed DNA virus genera.We use a homology search and phylogenetic analysis combined method to systemically identify gene duplication events within 250 DNA viruses.We identify a total of 612 gene duplication events in 85 double-stranded DNA(dsDNA)viruses,but find no gene duplication event in 40 sing-stranded DNA(ssDNA)viruses or 9 reverse-transcribing dsDNA(dsDNA-RT)viruses.Our results suggest that the frequency of gene duplication is different among different DNA viruses,and gene duplication occurs frequently in dsDNA viruses.Moreover,the number of gene duplication events in dsDNA viruses exhibits a strong positive correlation with the complexity(measured by genome size and the number of genes)of dsDNA viruses,suggesting that gene duplication is an importatn mechanism shaping the complexity of dsDNA virus genomes.We find?27.4%of duplicates in dsDNA viruses are tandemly arranged,suggesting tandenm gene duplication is one of the main mechanisms of gene duplication in dsDNA viruses.Selection pressure analysis of all duplicate genes suggests that most of duplicate genes evolve under purifying selection.Most of plant R genes encode proteins with nucleotide binding site and leucine-rich repeat(NBS-LRR)domains.Plant NBS-LRR proteins can be divided into two classes,NBS-LRR proteins with Toll/interleukin-1 receptor(TIR)domain(TIR-NBS-LRRs,TNLs)and NBS-LRR proteins without TIR domain(non-TIR-NBS-LRRs,nTNLs).Previous studies suggest that R genes are widely distributed in land plants.However,much remains unknown about the origin and evolution of R genes.In this study,we perform comparative genomic and phylogenetic analyses to mine R genes within 24 representative plant genomes and 8 charophyte transcriptomes,which cover a broad diversity of plants.We identify a total of 3,712 R proteins and find R proteins in charophyte for the first time.Phylogenetic analyses suggest that R genes originated in charophytes.Both TNLs and nTNLs are present in the charophyte genomes,and TNL might originate from nTNLs by gain of TIR domain.Selection pressure analysis of 34 R gene groups of charophytes and bryophytes show that positive selection occur in the majority of these R gene groups,suggesting R genes in these plants may involve in the interaction between plants and microorganisms.TIR domain is a kind of intracellular signal transduction domain,and plays an important role in the innate immune system.TIR domain-containing proteins are widely distributed in cellular organisms.Our study shows that TNLs may originate by inserting TIR domain into nTNL.However,the source and evolution of TIR domain remian unclear.We perform phylogenetic analyses of TIR domain in plants,animals,bacteria,and archaea,and find TIR domain in TNL of plants cluste together,suggesting TIR domain of plant TNLs have a common origin.Resistance to powdery mildew 8(RPW8)is a kind of broad-spectrum resistance domain that was first found in Arabidopsis thaliana.RPW8 domain-containing proteins appear to be widely distributed in the land plants except monocots and lycophytes.We perform comparative genomic and phylogenetic analyses of RPW8 domain-containing proteins in the genomes of 24 representative plant species.We identify a total of 148 RPW8 domain-containing proteins within 11 land plants,127 of which are R proteins.We find frequent domain gains and losses shape the diversity of RPW8 domain-containing proteins.In conclusion,this study systemically analyzes gene duplication events in DNA viruses and the origin and evolution of plant R genes.We find that the frequency of gene duplication is different among different DNA viruses and gene duplication plays an important role in shaping the genome complexity of dsDNA viruses.We find R genes in charophytes and propose that the origin of R genes may have a great effect on the colonization of terrestrial environments by plants.Our study might have important implications in understanding the evolution of plants-pathogen interactions.