Skmer approach improves species discrimination in taxonomically problematic genus Schima(Theaceae)  

作　　者：Han-Ning Duan Yin-Zi Jiang Jun-Bo Yang Jie Cai Jian-Li Zhao Lu Li Xiang-Qin Yu 

机构地区：[1]CAS Key Laboratory for Plant Diversity and Biogeography of East Asia,Kunming Institute of Botany,Chinese Academy of Sciences,Kunming 650201,Yunnan,PR China [2]College of Forestry,Southwest Forestry University,Kunming 650224,Yunnan,PR China [3]Genomics and Genetic Engineering Laboratory of Ornamental Plants,College of Agriculture and Biotechnology,Zhejiang University,Hangzhou,Zhejiang,PR China [4]Germplasm Bank of Wild Species,Kunming Institute of Botany,Chinese Academy of Sciences,Kunming 650201,Yunnan,PR China [5]Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology,Laboratory of Ecology and Evolutionary Biology,School of Ecology and Environmental Sciences,Yunnan University,Kunming 650500,Yunnan,PR China

出　　处：《Plant Diversity》2024年第6期713-722,共10页植物多样性（英文版）

基　　金：supported by National Natural Science Foundation of China(No.32070369);the Youth Innovation Promotion Association CAS of China(No.2021393);the Yunnan Revitalization Talent Support Program“Young Talent”Project,the Applied Fundamental Research Foundation of Yunnan Province(202301AT070308);the Fund of Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology(YNPRAEC-2023006).

摘　　要：Genome skimming has dramatically extended DNA barcoding from short DNA fragments to next generation barcodes in plants.However,conserved DNA barcoding markers,including complete plastid genome and nuclear ribosomal DNA(nrDNA)sequences,are inadequate for accurate species identification.Skmer,a recently proposed approach that estimates genetic distances among species based on unassembled genome skims,has been proposed to effectively improve species discrimination rate.In this study,we used Skmer to identify species based on genomic skims of 47 individuals representing 10 out of 13 species of Schima(Theaceae)from China.The unassembled reads identified six species,with a species identification rate of 60%,twice as high as previous efforts that used plastid genomes(27.27%).In addition,Skmer was able to identify Schima species with only 0.5sequencing depth,as six species were well-supported with unassembled data sizes as small as 0.5 Gb.These findings demonstrate the potential for Skmer approach in species identification,where nuclear genomic data plays a crucial role.For taxonomically difficult taxa such as Schima,which have diverged recently and have low levels of genetic variation,Skmer is a promising alternative to next generation barcodes.

关 键 词：SCHIMA Genome skimming Species discrimination Skmer 

分 类 号：Q949[生物学—植物学]