Phylogeny Analyses In Genus Populus Based On Chloroplast Genome

The genus Populus species,wind pollination of tall deciduous trees with strong vitality and reproductive ability,are widely distributed in the world,especially grown in many climatic types of the northern hemisphere.Based on traditionally morphological characters,the genus Populus were divided into five sections,but the phylogenetic relationships among these sections remained uncertain.Due to a long history of cultivation in many regions,there are a wide range of hybridization among natural intraspecific species,natural interspecific species,and hybrid species in genus Populus,and this is a big challenge to research the evolutionary relationship and taxonomy.Up to now,some researchers have reconstructed the phylogenetic relationship in the family and the genus level of flora,and obtained some achievement.However,at the present stage of phylogenetic studies,the DNA sequence of the chloroplast coding region,such as matK,rbcL,and trnH-psbA,and the nuclear gene,like ITS,were used,but these fragments were almost unable to ascertain their genetic relationship in the study of topological structure under the level of section.Therefore,we intend to explore the phylogenetic relationship of genus Populus using chloroplast genome sequence,and this is first study that attempts to ascertain phylogenetic relationship of different sections under the genus.In this study,we selected two species in this genus,Populus lasiocarpa and P.yunnanensis,to sequence,and de novo assemble complete chloroplast genome,and obtained seven chloroplast genome sequences from GeneBank database.The selected nine species covered five sections in Populus.We studied the phylogenetic relationships of the genus Populus in the branch of maternal inheritance through the whole chloroplast genome sequence of these species.In this paper,the whole chloroplast genome sequences were used in partitioning schemes,and then to construct the dendrogram respectively.Comparing with each other,all these phylogenetic trees were analyzed.Partitioning schemes are various subsets of data,including coding sequences,noncoding sequences,and different districts of the genome.The results of this research can summarize the fllowing:(1)Based on complete chloroplast genomes of Populus,we obtained 14 phylogenetic trees constructed by large regions,77 phylogenetic trees by each genes,and 141 phylogenetic trees by intergenic genes.We obtained a series of phylogenetic trees with high bootstrap support values after analyzing and comparing with each other;(2)Sect.Tacamahaca can be divided into two clades based on maternally inherited loci,i.e.clade?,distributed in North America and northeast China,and clade?,distributed in southwest China;(3)SSC-noncoding regions revealed an inconsistent topology,which is different form other regions,with high bootstrap support values,indicating that this distinction may be resulted from incomplete lineage sorting between species of Populus;(4)It issuperior reliability that phylogenetic relationship is constructed using all non-coding sequences of chloroplast genome.This study could provide a new approach to study the phylogenetic relationship of genus Populusand a new method to explore phylogenetic system at low taxonomic levels for future researchers.