Resequencing of 284 genomes reveals evolutionary history and hotspot of genetic diversity of the giant bamboos

doi:10.1016/j.pld.2025.12.018

Plant Diversity ›› 2026, Vol. 48 ›› Issue (03): 460-473.DOI: 10.1016/j.pld.2025.12.018

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Resequencing of 284 genomes reveals evolutionary history and hotspot of genetic diversity of the giant bamboos

May Zin Win^a,b, Shuang-Xiu Xu^a,b, Shu-Yang Gao^a,b,c, Jing-Xia Liu^a, Zu-Chang Xu^a,b, Cen Guo^d, Yun-Long Liu^c, Peng-Fei Ma^a, De-Zhu Li^a,b,c

a Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
b Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
c Center for Interdisciplinary Biodiversity Research & College of Forestry, Shandong Agricultural University, Tai'an 271018, Shandong, China;
d Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, Yunnan, China

Received:2025-11-28 Revised:2025-12-26 Online:2026-06-10 Published:2026-05-25
Contact: May Zin Win,E-mail:mayzinwin@mail.kib.ac.cn;Shuang-Xiu Xu,E-mail:xushuangxiu@mail.kib.ac.cn;Shu-Yang Gao,E-mail:gaoshuyang@mail.kib.ac.cn;Jing-Xia Liu,E-mail:liujingxia@mail.kib.ac.cn;Zu-Chang Xu,E-mail:xuzuchang@mail.kib.ac.cn;Cen Guo,E-mail:guocen@xtbg.ac.cn;Yun-Long Liu,E-mail:liuyunlong@sdau.edu.cn;Peng-Fei Ma,E-mail:mapengfei@mail.kib.ac.cn;De-Zhu Li,E-mail:dzl@mail.kib.ac.cn
Supported by:
This study was supported by the National Natural Science Foundation of China (32120103003), Yunnan Fundamental Research Projects (202401AS070082 and 202101AT070175), and a grant for Reserve Talents for Young and Middle-aged Academic and Technological Leaders in Yunnan Province, China (202105AC160022).

Resequencing of 284 genomes reveals evolutionary history and hotspot of genetic diversity of the giant bamboos

May Zin Win^a,b, Shuang-Xiu Xu^a,b, Shu-Yang Gao^a,b,c, Jing-Xia Liu^a, Zu-Chang Xu^a,b, Cen Guo^d, Yun-Long Liu^c, Peng-Fei Ma^a, De-Zhu Li^a,b,c

a Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
b Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650201, Yunnan, China;
c Center for Interdisciplinary Biodiversity Research & College of Forestry, Shandong Agricultural University, Tai'an 271018, Shandong, China;
d Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, Yunnan, China

通讯作者: May Zin Win,E-mail:mayzinwin@mail.kib.ac.cn;Shuang-Xiu Xu,E-mail:xushuangxiu@mail.kib.ac.cn;Shu-Yang Gao,E-mail:gaoshuyang@mail.kib.ac.cn;Jing-Xia Liu,E-mail:liujingxia@mail.kib.ac.cn;Zu-Chang Xu,E-mail:xuzuchang@mail.kib.ac.cn;Cen Guo,E-mail:guocen@xtbg.ac.cn;Yun-Long Liu,E-mail:liuyunlong@sdau.edu.cn;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 study was supported by the National Natural Science Foundation of China (32120103003), Yunnan Fundamental Research Projects (202401AS070082 and 202101AT070175), and a grant for Reserve Talents for Young and Middle-aged Academic and Technological Leaders in Yunnan Province, China (202105AC160022).

Abstract

Abstract: The Dendrocalamus giganteus complex comprises D. giganteus, D. calostachyus and D. sinicus, being the largest known, iconic bamboo species and is economically, ecologically and culturally significant in Southeast Asia, serving as a pillar of daily life of indigenous people. However, lack of understanding of its genetic diversity pattern and population history has hindered effective germplasm conservation and development as sustainable non-timber forest resources. Here, we present a population genomic study of the giant bamboos with whole-genome resequencing of 284 accessions of three closely related species across their potentially native geographical ranges in Myanmar and Yunnan Province, China. We identified seven highly supported phylogenetic clades for the populations of the D. giganteus complex, and all populations exhibit low levels of genetic diversity while a high degree of genetic differentiation among them. One of them in the remote northern and northwestern Myanmar was found as the hotspot of genetic diversity of the giant bamboos. Tajima's D value and demographic history inference suggested the occurrence of population bottleneck, leading to a sharp decline in Ne during the last glacial period. Strikingly, D. sinicus displayed the lowest genetic diversity in the complex likely due to predominance of selfing or inbreeding. Overall, our study provides valuable insights into the evolutionary history and population genetics of the D. giganteus complex, serving as an important foundation for developing effective conservation strategies for the giant bamboos in Southeast Asia.

Key words: Dendrocalamus, Whole-genome resequencing, Genetic differentiation, Linkage disequilibrium, Demographic history, Southeast Asia

摘要： The Dendrocalamus giganteus complex comprises D. giganteus, D. calostachyus and D. sinicus, being the largest known, iconic bamboo species and is economically, ecologically and culturally significant in Southeast Asia, serving as a pillar of daily life of indigenous people. However, lack of understanding of its genetic diversity pattern and population history has hindered effective germplasm conservation and development as sustainable non-timber forest resources. Here, we present a population genomic study of the giant bamboos with whole-genome resequencing of 284 accessions of three closely related species across their potentially native geographical ranges in Myanmar and Yunnan Province, China. We identified seven highly supported phylogenetic clades for the populations of the D. giganteus complex, and all populations exhibit low levels of genetic diversity while a high degree of genetic differentiation among them. One of them in the remote northern and northwestern Myanmar was found as the hotspot of genetic diversity of the giant bamboos. Tajima's D value and demographic history inference suggested the occurrence of population bottleneck, leading to a sharp decline in Ne during the last glacial period. Strikingly, D. sinicus displayed the lowest genetic diversity in the complex likely due to predominance of selfing or inbreeding. Overall, our study provides valuable insights into the evolutionary history and population genetics of the D. giganteus complex, serving as an important foundation for developing effective conservation strategies for the giant bamboos in Southeast Asia.

关键词: Dendrocalamus, Whole-genome resequencing, Genetic differentiation, Linkage disequilibrium, Demographic history, Southeast Asia

May Zin Win, Shuang-Xiu Xu, Shu-Yang Gao, Jing-Xia Liu, Zu-Chang Xu, Cen Guo, Yun-Long Liu, Peng-Fei Ma, De-Zhu Li. Resequencing of 284 genomes reveals evolutionary history and hotspot of genetic diversity of the giant bamboos[J]. Plant Diversity, 2026, 48(03): 460-473.

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Resequencing of 284 genomes reveals evolutionary history and hotspot of genetic diversity of the giant bamboos

Resequencing of 284 genomes reveals evolutionary history and hotspot of genetic diversity of the giant bamboos

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