Comparative plastid genomics of Pinus species:Insights into sequence variations and phylogenetic relationships  

作　　者：Umar Zeb Wan-Lin Dong Ting-Ting Zhang Ruo-Nan Wang Khurram Shahzad Xiong-Feng Ma Zhong-Hu Li 

机构地区：[1]Key Laboratory of Resource Biology and Biotechnology in Western China,Ministry of Education,College of Life Sciences,Northwest University,Xi'an 710069,China [2]Zhengzhou Research Base,Zhengzhou University,Zhengzhou 450001,China

出　　处：《Journal of Systematics and Evolution》2020年第2期118-132,共15页植物分类学报（英文版）

基　　金：This work was supported by grants from the National Natural Science Foundation of China(41101058);the Shaanxi Provincial Key Laboratory Project of Department of Education(Grant No.17JS135);the Shaanxi Science and Technology Innovation Team(2019TD-012);the Graduate Student Independent Innovation Project of Northwest University(YZZ17166);the Open Foundation of Key Laboratory of Resource Biology and Biotechnology in Western China(Ministry of Education)(Numbers ZSK2017007 and ZSK2019008).

摘　　要：Pinus L.is the largest genus of conifers and provides a classical model for studying species divergence and phylogenetic evolution by gymnosperms.However,our poor understanding of sequence divergence in the whole plastid genomes of Pinus species severely hinders studies of their evolution and phylogeny.Thus,we analyzed the sequences of 97 Pinus plastid genomes,including four newly sequenced genomes and 93 previously published plastomes,to explore the evolution and phylogenetic relationships in the genus Pinus.The complete chloroplast genomes of Pinus species ranged in size from 109640 bp(P.cembra L.)to 121976 bp(P.glabra Walter),and these genomes comprised circular DNA molecules in a similar manner to those of most gymnosperms.We identified 9108 repeats where most of the repeats comprised the dispersed type with 3983(44%),followed by tandem repeats with 2999(33%),and then palindromic repeats with 2126(23%).Sixteen divergence hotspot regions were identified in Pinus plastid genomes,which could be useful molecular markers for future population genetics studies.Phylogenetic analysis showed that Pinus species could be divided into two diverged clades comprising the subgenera Strobus(single needle section)and Pinus(double needles section).Molecular dating suggested that the genus Pinus originated approximately 130.38 Mya during the late Cretaceous.The two subgenera subsequently split 85.86 Mya,which was largely consistent with the other molecular results based on partial DNA markers.These findings provide important insights into the sequence variations and phylogenetic evolution of Pinus plastid genomes.

关 键 词：DIVERGENCE time molecular evolution PHYLOGENETIC relationship PINUS PLASTID genome 

分 类 号：Q94[生物学—植物学]