Phylogenetic Relationships Construction And NLR Gene Families Analysis Of Populus Based On Phylogenomics

Poplar is the general name of the species of Salicaceae in the genus Populus.It is difficult to define the species of Poplar because the reproductive isolation of poplar is not strict and it is easy to produce natural hybridization and its own variation is abundant.How to scientifically use high quality genome or transcriptome data to solve biological problems is worth exploring.The emergence of phylogenomics provides a new way to explore the evolutionary relationships of plants.In order to solve the difficult problems in the phylogenetic framework of Populus,we used 12 transcriptome data as materials,including8 species of populus transcriptome,to obtain high quality transcripts using three different strategies: Trinity nonparametric assembly,String Tie parametric assembly,and Trinity guided nonparametric assembly.Phylogenetic relationships of Populus were reconstructed from genome-wide and transcriptome levels using phylogenetic genomics.As a tree model species,poplar disease resistance research has always been a hot spot in stress resistance breeding.NLR(Nucleotide-binding domain and Leucine-rich Repeat)resistance genes are the largest family of resistance genes evolved by plants.It plays a key role in plant disease and pest control.Based on the construction of poplar phylogeny,BLAST and HMMER software were used to identify the members of poplar NLR gene family,and bioinformatics method was used to analyze the NLR gene family of Poplar species.The main research results are as follows1.The transcriptome of 8 poplar species,including P.lasiocarpa,P.koreana,P.laurifoli,P.qiongdaoensis,were sequenced by second-generation high-throughput sequencing technique.A total of 80.84 G of high quality data was obtained,and the utilization rate reached 97.75%.The average base number was 6.74 Gbp.An average of96,717 transcripts were obtained from each species,including at least 35,839 unigene transcripts.The average transcript length and N50 were 1562 bp and 2220 bp,respectively.In addition to P.lasiocarpa and P.adenopoda,more than 90% integrity and comparison rate were obtained.2.A total of 928 single-copy lineal homologous gene sets were identified,and the phylogenetic relationships of Populus were constructed by STAG algorithm using ML,BI,NJ and MP.Populus was monophyletic in origin,separated from Salix purpurea at about44.95MYA(95% HPD 36.67-51.34MYA).The Sect.Turanga is at the base and forms sister branches with the common ancestor of other poplars.The Sect.Populus can be further divided into Albidae Dode and Trepidae Dode.The Sect.Aigeiros 、 Sect.Tacamahaca and Sect.Leucoides cluster into ATL Clade and form sister groups with other poplar groups.The Sect.Aigeiros and Sect.Tacamahaca originated from multiple lineages.Due to the gene introgression,the relationship between Sect.Aigeiros and Sect.Tacamahaca evolved into a network.Similar phenomena also occurred in poplars.3.Twenty-three of the 51 single-copy homologous genes in 26 plants had positive selection sites.Nearly one third of the positive selected genes are related to hydrolase activity,including metabolic pathways,Biosynthesis of secondary metabolites、Terpenoid backbone biosynthesis.These genes play very important roles in RNA metabolism,plant disease resistance,hydrolysis and synthesis of glycoconjugates and sugars.4.The NLR genes of Salix purpurea and Populus are derived from the common ancestor.Due to mutation,natural selection or other reasons,NLR gene families have differentiated and expanded to varying degrees during evolution,with specific replication in different plants.During evolution,NLR proteins acquire new functions by integrating new domains,accompanied by frequent loss of N-terminal and C-terminal domains.RNL and CNL genes are independent of each other and form sister relationship,which is in relative basal position.The repetition types of NLR genes were mainly tandem repeats(50.71%)and dispersed repeats(40.36%),which were distributed unevenly on chromosomes in the form of gene clusters,and the physicochemical properties of NLR proteins encoded by them were significantly different.In the collinear genes of Populus deltoides,the remaining NLR genes except Podel.19G104000,Podel.19G115600,Podel.05G031900 and Podel.05G036300 underwent purification selections during their evolutionary process.Phylogeny is a basic problem in biology.In this study,the phylogenetic relationship of Populus was reconstructed through phylogenomics,and the research results can provide references for the phylogeny of Populus.The study of Populus NLR gene can provide reference for the cultivation of poplar resistant varieties.