Testing complete plastomes and nuclear ribosomal DNA sequences for species identification in a taxonomically difficult bamboo genus Fargesia

doi:10.1016/j.pld.2022.04.002

KIB OpenIR

	Testing complete plastomes and nuclear ribosomal DNA sequences for species identification in a taxonomically difficult bamboo genus Fargesia
	Lv,Shi-Yu; Ye,Xia-Ying; Li,Zhong-Hu; Ma,Peng-Fei; Li,De-Zhu
	2023
发表期刊	PLANT DIVERSITY
ISSN	2468-2659
卷号	45 期号:2 页码:147-155
摘要	Fargesia, the largest genus within the temperate bamboo tribe Arundinarieae, has more than 90 species mainly distributed in the mountains of Southwest China. The Fargesia bamboos are important components of the subalpine forest ecosystems that provide food and habitat for many endangered animals, including the giant panda. However, species-level identification of Fargesia is difficult. Moreover, the rapid radiation and slow molecular evolutionary rate of Fargesia pose a significant challenge to using DNA barcoding with standard plant barcodes (rbcL, matK, and ITS) in bamboos. With progress in the sequencing technologies, complete plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) sequences have been proposed as organelle barcodes for species identification; however, these have not been tested in bamboos. We collected 196 individuals representing 62 species of Fargesia to comprehensively evaluate the discriminatory power of plastomes and nrDNA sequences compared to standard barcodes. Our analysis indicates that complete plastomes have substantially higher discriminatory power (28.6%) than standard barcodes (5.7%), whereas nrDNA sequences show a moderate improvement (65.4%) compared to ITS (47.2%). We also found that nuclear markers performed better than plastid markers, and ITS alone had higher discriminatory power than complete plastomes. The study also demonstrated that plastomes and nrDNA sequences can contribute to intrageneric phylogenetic resolution in Fargesia. However, neither of these sequences were able to discriminate all the sampled species, and therefore, more nuclear markers need to be identified. Copyright (c) 2022 Kunming Institute of Botany, Chinese Academy of Sciences. Publishing services by Elsevier B.V. on behalf of KeAi Communications Co. Ltd.
关键词	Fargesia Genome-skimming DNA barcoding Plastome Ribosomal DNA WHOLE CHLOROPLAST GENOMES RNA-SEQ DATA ARUNDINARIEAE POACEAE BAMBUSOIDEAE TEMPERATE PLATFORM
学科领域	Plant Sciences
DOI	10.1016/j.pld.2022.04.002
WOS记录号	WOS:000976095300001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/74851
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Lv,Shi-Yu,Ye,Xia-Ying,Li,Zhong-Hu,et al. Testing complete plastomes and nuclear ribosomal DNA sequences for species identification in a taxonomically difficult bamboo genus Fargesia[J]. PLANT DIVERSITY,2023,45(2):147-155.
APA	Lv,Shi-Yu,Ye,Xia-Ying,Li,Zhong-Hu,Ma,Peng-Fei,&Li,De-Zhu.(2023).Testing complete plastomes and nuclear ribosomal DNA sequences for species identification in a taxonomically difficult bamboo genus Fargesia.PLANT DIVERSITY,45(2),147-155.
MLA	Lv,Shi-Yu,et al."Testing complete plastomes and nuclear ribosomal DNA sequences for species identification in a taxonomically difficult bamboo genus Fargesia".PLANT DIVERSITY 45.2(2023):147-155.

条目包含的文件		下载所有文件
文件名称/大小	文献类型	版本类型	开放类型	使用许可
10.1016_j.pld.2022.0（2234KB）	期刊论文	出版稿	开放获取	CC BY-NC-SA	浏览下载