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

Plant Diversity ›› 2023, Vol. 45 ›› Issue (02): 147-155.DOI: 10.1016/j.pld.2022.04.002

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

Shi-Yu Lv^a,b, Xia-Ying Ye^c, Zhong-Hu Li^a, Peng-Fei Ma^b, De-Zhu Li^b,d

a. School of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China;
b. Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China;
c. Agronomy and Life Science Department, Zhaotong University, Zhaotong, Yunnan, 657000, China;
d. Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650201, China

收稿日期:2022-03-24 修回日期:2022-04-05 出版日期:2023-03-25 发布日期:2023-06-13
通讯作者: Peng-Fei Ma,E-mail:mapengfei@mail.kib.ac.cn;De-Zhu Li,E-mail:dzl@mail.kib.ac.cn
基金资助:
This work was supported by grants from CAS’ Large-scale Scientific Facilities (Grant No. 2017-LSF-GBOWS-02), the Key R&D Program of Yunnan Province, China (Grant No. 202103AC100003), and Ten Thousand Talent Program of Yunnan Province (Grant No. YNWR-QNBJ-2020-297).

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

Shi-Yu Lv^a,b, Xia-Ying Ye^c, Zhong-Hu Li^a, Peng-Fei Ma^b, De-Zhu Li^b,d

a. School of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China;
b. Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China;
c. Agronomy and Life Science Department, Zhaotong University, Zhaotong, Yunnan, 657000, China;
d. Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650201, China

Received:2022-03-24 Revised:2022-04-05 Online:2023-03-25 Published:2023-06-13
Contact: Peng-Fei Ma,E-mail:mapengfei@mail.kib.ac.cn;De-Zhu Li,E-mail:dzl@mail.kib.ac.cn
Supported by:
This work was supported by grants from CAS’ Large-scale Scientific Facilities (Grant No. 2017-LSF-GBOWS-02), the Key R&D Program of Yunnan Province, China (Grant No. 202103AC100003), and Ten Thousand Talent Program of Yunnan Province (Grant No. YNWR-QNBJ-2020-297).

摘要/Abstract

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.

关键词: Fargesia, Genome-skimming, DNA barcoding, Plastome, Ribosomal DNA

Abstract: 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.

Key words: Fargesia, Genome-skimming, DNA barcoding, Plastome, Ribosomal DNA

Shi-Yu Lv, Xia-Ying Ye, Zhong-Hu Li, Peng-Fei Ma, De-Zhu Li. Testing complete plastomes and nuclear ribosomal DNA sequences for species identification in a taxonomically difficult bamboo genus Fargesia[J]. Plant Diversity, 2023, 45(02): 147-155.

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

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

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