Can plastid genome sequencing be used for species identification in Lauraceae?

doi:10.1093/botlinnean/boab018

KIB OpenIR

	Can plastid genome sequencing be used for species identification in Lauraceae?
	Liu,Zhi-Fang ; Ma,Hui ; Ci,Xiu-Qin ; Li,Lang ; Song,Yu; Liu,Bing ; Li,Hsi-Wen ; Wang,Shu-Li ; Qu,Xiao-Jian ; Hu,Jian-Lin ; Zhang,Xiao-Yan ; Conran,John G.; Twyford,Alex D.; Yang,Jun-Bo ; Hollingsworth,Peter M.; Li,Jie
	2021
发表期刊	BOTANICAL JOURNAL OF THE LINNEAN SOCIETY
ISSN	0024-4074
卷号	197 期号:1 页码:1-14
摘要	Using DNA barcoding for species identification remains challenging for many plant groups. New sequencing approaches such as complete plastid genome sequencing may provide some increased power and practical benefits for species identification beyond standard plant DNA barcodes. We undertook a case study comparing standard DNA barcoding to plastid genome sequencing for species discrimination in the ecologically and economically important family Lauraceae, using 191 plastid genomes for 131 species from 25 genera, representing the largest plastome data set for Lauraceae to date. We found that the plastome sequences were useful in correcting some identification errors and for finding new and cryptic species. However, plastome data overall were only able to discriminate c. 60% of the species in our sample, with this representing a modest improvement from 40 to 50% discrimination success with the standard plant DNA barcodes. Beyond species discrimination, the plastid genome sequences revealed complex relationships in the family, with 12/25 genera being non-monophyletic and with extensive incongruence relative to nuclear ribosomal DNA. These results highlight that although useful for improving phylogenetic resolution in the family and providing some species-level insights, plastome sequences only partially improve species discrimination, and this reinforces the need for large-scale nuclear data to improve discrimination among closely related species.
关键词	cytonuclear discordance DNA barcoding nrDNA phylogenetics plastomes CHLOROPLAST GENOME ALSEODAPHNOPSIS LAURACEAE GENE ORGANIZATION DNA BARCODES NUCLEAR EVOLUTION ALIGNMENT CLASSIFICATION DISCORDANCE CINNAMOMUM
DOI	10.1093/botlinnean/boab018
WOS记录号	WOS:000692321700001
引用统计	被引频次：41[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/73528
专题	中国科学院昆明植物研究所
作者单位	1.Chinese Acad Sci, Ctr Integrat Conservat, Xishuangbanna Trop Bot Garden, Plant Phylogenet & Conservat Grp, Kunming, Yunnan, Peoples R China 2.Univ Chinese Acad Sci, Beijing, Peoples R China 3.Chinese Acad Sci, Ctr Conservat Biol, Core Bot Gardens, Mengla, Peoples R China 4.Chinese Acad Sci, Ctr Integrat Conservat, Xishuangbanna Trop Bot Garden, Mengla, Peoples R China 5.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, Peoples R China 6.Chinese Acad Sci, Sino African Joint Res Ctr, Wuhan, Peoples R China 7.Chinese Acad Sci, Kunming Inst Bot, Herbarium KUN, Kunming, Yunnan, Peoples R China 8.Tibet Agr & Anim Husb Univ, Nyingchi, Peoples R China 9.Shandong Normal Univ, Coll Life Sci, Shandong Prov Key Lab Plant Stress Res, Jinan, Peoples R China 10.Conran, John G.] Univ Adelaide, Sch Biol Sci, Australian Ctr Evolutionary Biol & Biodivers, Adelaide, SA, Australia 11.Conran, John G.] Univ Adelaide, Sch Biol Sci, Sprigg Geobiol Ctr, Adelaide, SA, Australia 12.Twyford, Alex D.] Univ Edinburgh, Inst Evolutionary Biol, Ashworth Labs, Edinburgh, Midlothian, Scotland 13.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming, Yunnan, Peoples R China 14.Liu, Zhi-Fang; Hollingsworth, Peter M.] Royal Bot Garden Edinburgh, Genet & Conservat Sect, Edinburgh, Midlothian, Scotland
推荐引用方式 GB/T 7714	Liu,Zhi-Fang,Ma,Hui,Ci,Xiu-Qin,et al. Can plastid genome sequencing be used for species identification in Lauraceae?[J]. BOTANICAL JOURNAL OF THE LINNEAN SOCIETY,2021,197(1):1-14.
APA	Liu,Zhi-Fang.,Ma,Hui.,Ci,Xiu-Qin.,Li,Lang.,Song,Yu.,...&Li,Jie.(2021).Can plastid genome sequencing be used for species identification in Lauraceae?.BOTANICAL JOURNAL OF THE LINNEAN SOCIETY,197(1),1-14.
MLA	Liu,Zhi-Fang,et al."Can plastid genome sequencing be used for species identification in Lauraceae?".BOTANICAL JOURNAL OF THE LINNEAN SOCIETY 197.1(2021):1-14.