Phylogenetic Relationships and Next-Generation Barcodes in the Genus Torreya Reveal a High Proportion of Misidentified Cultivated Plants

doi:10.3390/ijms241713216

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	Phylogenetic Relationships and Next-Generation Barcodes in the Genus Torreya Reveal a High Proportion of Misidentified Cultivated Plants
	Mo,Zhi-Qiong; Wang,Jie; Moller,Michael; Yang,Jun-Bo; Gao,Lian-Ming
	2023
发表期刊	INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
ISSN	1422-0067
卷号	24 期号:17 页码:13216
摘要	Accurate species identification is key to conservation and phylogenetic inference. Living plant collections from botanical gardens/arboretum are important resources for the purpose of scientific research, but the proportion of cultivated plant misidentification are un-tested using DNA barcodes. Here, we assembled the next-generation barcode (complete plastid genome and complete nrDNA cistron) and mitochondrial genes from genome skimming data of Torreya species with multiple accessions for each species to test the species discrimination and the misidentification proportion of cultivated plants used in Torreya studies. A total of 38 accessions were included for analyses, representing all nine recognized species of genus Torreya. The plastid phylogeny showed that all 21 wild samples formed species-specific clades, except T. jiulongshanensis. Disregarding this putative hybrid, seven recognized species sampled here were successfully discriminated by the plastid genome. Only the T. nucifera accessions grouped into two grades. The species identification rate of the nrDNA cistron was 62.5%. The Skmer analysis based on nuclear reads from genome skims showed promise for species identification with seven species discriminated. The proportion of misidentified cultivated plants from arboreta/botanical gardens was relatively high with four accessions (23.5%) representing three species. Interspecific relationships within Torreya were fully resolved with maximum support by plastomes, where Torreya jackii was on the earliest diverging branch, though sister to T. grandis in the nrDNA cistron tree, suggesting that this is likely a hybrid species between T. grandis and an extinct Torreya ancestor lineage. The findings here provide quantitative insights into the usage of cultivated samples for phylogenetic study.
关键词	Torreya genome skimming species identification phylogeny COMPLETE CHLOROPLAST GENOME SEQUENCE TAXACEAE CEPHALOTAXACEAE DIVERSIFICATION PHYLOGENOMICS INFERENCE ALIGNMENT ZHEJIANG ACCURATE
DOI	10.3390/ijms241713216
WOS记录号	WOS:001064139300001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/75017
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Mo,Zhi-Qiong,Wang,Jie,Moller,Michael,et al. Phylogenetic Relationships and Next-Generation Barcodes in the Genus Torreya Reveal a High Proportion of Misidentified Cultivated Plants[J]. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,2023,24(17):13216.
APA	Mo,Zhi-Qiong,Wang,Jie,Moller,Michael,Yang,Jun-Bo,&Gao,Lian-Ming.(2023).Phylogenetic Relationships and Next-Generation Barcodes in the Genus Torreya Reveal a High Proportion of Misidentified Cultivated Plants.INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,24(17),13216.
MLA	Mo,Zhi-Qiong,et al."Phylogenetic Relationships and Next-Generation Barcodes in the Genus Torreya Reveal a High Proportion of Misidentified Cultivated Plants".INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 24.17(2023):13216.

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