Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron

doi:10.1111/1755-0998.13479

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	Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron
	Fu,Chao-Nan ; Mo,Zhi-Qiong ; Yang,Jun-Bo ; Cai,Jie ; Ye,Lin-Jiang ; Zou,Jia-Yun ; Qin,Han-Tao ; Zheng,Wei ; Hollingsworth,Peter M.; Li,De-Zhu; Gao,Lian-Ming
	2022
发表期刊	MOLECULAR ECOLOGY RESOURCES
ISSN	1755-098X
卷号	22 期号:1 页码:404-414
摘要	Standard plant DNA barcodes based on 2-3 plastid regions, and nrDNA ITS show variable levels of resolution, and fail to discriminate among species in many plant groups. Genome skimming to recover complete plastid genome sequences and nrDNA arrays has been proposed as a solution to address these resolution limitations. However, few studies have empirically tested what gains are achieved in practice. Of particular interest is whether adding substantially more plastid and nrDNA characters will lead to an increase in discriminatory power, or whether the resolution limitations of standard plant barcodes are fundamentally due to plastid genomes and nrDNA not tracking species boundaries. To address this, we used genome skimming to recover near-complete plastid genomes and nuclear ribosomal DNA from Rhododendron species and compared discrimination success with standard plant barcodes. We sampled 218 individuals representing 145 species of this species-rich and taxonomically difficult genus, focusing on the global biodiversity hotspots of the Himalaya-Hengduan Mountains. Only 33% of species were distinguished using ITS+matK+rbcL+trnH-psbA. In contrast, 55% of species were distinguished using plastid genome and nrDNA sequences. The vast majority of this increase is due to the additional plastid characters. Thus, despite previous studies showing an asymptote in discrimination success beyond 3-4 plastid regions, these results show that a demonstrable increase in discriminatory power is possible with extensive plastid genome data. However, despite these gains, many species remain unresolved, and these results also reinforce the need to access multiple unlinked nuclear loci to obtain transformative gains in species discrimination in plants.
关键词	Himalaya-Hengduan Mountains infrageneric phylogenetic resolution next generation DNA barcoding Rhododendron species discrimination PHYLOGENETIC-RELATIONSHIPS SECTIONAL RELATIONSHIPS CHLOROPLAST GENOME DNA BARCODES ERICACEAE HYBRIDIZATION YUNNAN DIVERSITY PATTERNS AGASTUM
DOI	10.1111/1755-0998.13479
WOS记录号	WOS:000682983700001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/73538
专题	中国科学院昆明植物研究所
作者单位	1.[Fu, Chao-Nan 2.Mo, Zhi-Qiong 3.Ye, Lin-Jiang 4.Zou, Jia-Yun 5.Qin, Han-Tao 6.Zheng, Wei 7.Li, De-Zhu 8.Chinese Acad Sci, Kunming Inst Bot, CAS Key Lab Plant Divers & Biogeog East Asia, Kunming 650201, Yunnan, Peoples R China 9.Yang, Jun-Bo 10.Cai, Jie 11.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming, Yunnan, Peoples R China 12.[Mo, Zhi-Qiong 13.Univ Chinese Acad Sci, Beijing, Peoples R China 14.[Hollingsworth, Peter M.] Royal Bot Garden Edinburgh, Edinburgh EH3 5LR, Midlothian, Scotland 15.Chinese Acad Sci, Kunming Inst Bot, Lijiang Forest Ecosyst Natl Observat & Res Stn, Lijiang, Yunnan, Peoples R China
推荐引用方式 GB/T 7714	Fu,Chao-Nan,Mo,Zhi-Qiong,Yang,Jun-Bo,et al. Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron[J]. MOLECULAR ECOLOGY RESOURCES,2022,22(1):404-414.
APA	Fu,Chao-Nan.,Mo,Zhi-Qiong.,Yang,Jun-Bo.,Cai,Jie.,Ye,Lin-Jiang.,...&Gao,Lian-Ming.(2022).Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron.MOLECULAR ECOLOGY RESOURCES,22(1),404-414.
MLA	Fu,Chao-Nan,et al."Testing genome skimming for species discrimination in the large and taxonomically difficult genus Rhododendron".MOLECULAR ECOLOGY RESOURCES 22.1(2022):404-414.

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