Phylogenomics Of Populus And Speciation Of Populus Szechuanica Complex

Populus not only has significant economic and ecological values,but also serves as a model tree that is widely used in the basic research of tree growth,physiology,and genetics.Reconstructing the phylogeny and the speciation pattern of Populus contributes to the understanding of its origin,diversification mechanism and adaptive evolution.However,the interspecific relationships and biogeographical history of Populus were still lagged by the limited sequencing techniques and incomplete sampling.Moreover,gene flow would blur the boundaries between species and prevent the reconstruction of phylogeny.It also remains to seen how gene flow affect speciation of Populus.Thus,based on large-scale resequencing and whole-genome sequencing,we explored the phylogenetic relationships,biogeographic history of Populus and the speciation of Populus szechuanica complex through phylogenomic and population genomic methods.The main findings are as follows:(1)Based on the whole-genome resequencing data from 103 accessions of 53 Populus wild species,the robust phylogeny of Populus was reconstructed and suggested a foursubgeneric classification of this genus.The severe cytonuclear discordances were also discovered,which caused by the chloroplast capture and gene flow(recent hybridization).Ancient gene flow between clades and the hybrid origin of Populus pseudomaximowiczii and Populus szechuanica var.tibetica were also identified.(2)Based on the reliable nuclear genomic phylogeny,the crown age of Populus was estimated as 46.86 Ma.The reconstruction of chronogram and ancestral distributions suggested that North America was the original region of this genus.Both long-distance dispersal,and migrations via the Atlantic Road Bridge and Bering Land Bridge were contributed to the modern range of Populus.The diversification of Populus mainly occurred in East Asia in recent 15 Ma,possibly promoted by the uplift of the Tibetan Plateau.(3)Furthermore,we assembled a high-quality,chromosomal-level genome of Populus rockii with a size of 380.75 Mb,a completeness of 97.6%,and a contig N50 of 9.09 Mb.Both the reduction of gene families,and the constriction of protein-coding region led to the genome shrink of Populus rockii.Population genomic analysis proved the division of three lineages among Populus szechuanica complex,which were Populus szechuanica,Populus rockii and Populus xiangchengensis.Gene flow among these three species was continuous after speciation,which slowed down the degree of differentiation,but might contribute to the population expansion,and promoted the development of hybrid zone.The differential retention of alien introgression further promoted the genetic differentiation.The intraspecies genetic differentiation and alien introgression together facilitated the speciation among Populus szechuanica complex.In short,this study clarified the phylogenetic relationships among Populus species,and dissected its geographic migration history.Further genomic and population genomic analysis probed the effects of gene flow to the speciation of Populus species from different time and space.This study was contributed to the guidance significance for investigating the genetic differentiation and speciation of trees,and lay a foundation of poplar breeding.