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
AbstractStandard 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.
KeywordHimalaya-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
WOS IDWOS:000682983700001
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Document Type期刊论文
Affiliation1.[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
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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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