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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
Source PublicationPLANT DIVERSITY
ISSN2468-2659
Volume45Issue:2Pages:147-155
AbstractFargesia, 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.
KeywordFargesia Genome-skimming DNA barcoding Plastome Ribosomal DNA WHOLE CHLOROPLAST GENOMES RNA-SEQ DATA ARUNDINARIEAE POACEAE BAMBUSOIDEAE TEMPERATE PLATFORM
Subject AreaPlant Sciences
DOI10.1016/j.pld.2022.04.002
WOS IDWOS:000976095300001
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Document Type期刊论文
Identifierhttp://ir.kib.ac.cn/handle/151853/74851
Collection中国科学院昆明植物研究所
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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.
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