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

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

扫码查看
原文链接
  • NETL
  • NSTL
  • 万方数据
Skmer approach improves species discrimination in taxonomically problematic genus Schima(Theaceae)
Genome skimming has dramatically extended DNA barcoding from short DNA fragments to next gen-eration barcodes in plants.However,conserved DNA barcoding markers,including complete plastid genome and nuclear ribosomal DNA(nrDNA)sequences,are inadequate for accurate species identifi-cation.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 0.5 × sequencing 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.

SchimaGenome skimmingSpecies discriminationSkmer

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

展开 >

CAS Key Laboratory for Plant Diversity and Biogeography of East Asia,Kunming Institute of Botany,Chinese Academy of Sciences,Kunming 650201,Yunnan,PR China

College of Forestry,Southwest Forestry University,Kunming 650224,Yunnan,PR China

Genomics and Genetic Engineering Laboratory of Ornamental Plants,College of Agriculture and Biotechnology,Zhejiang University,Hangzhou,Zhejiang,PR China

Germplasm Bank of Wild Species,Kunming Institute of Botany,Chinese Academy of Sciences,Kunming 650201,Yunnan,PR China

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

展开 >

Schima Genome skimming Species discrimination Skmer

2024

10.1016/j.pld.2024.06.003

植物多样性(英文)
中国科学院昆明植物研究所，中国植物学会

植物多样性(英文)

CSTPCD
影响因子：0.617
ISSN：2096-2703
年,卷(期)：2024.46(6)