Deep genome skimming reveals the hybrid origin of Pseudosasa gracilis (Poaceae: Bambusoideae)

doi:10.1016/j.pld.2023.06.001

Plant Diversity ›› 2024, Vol. 46 ›› Issue (03): 344-352.DOI: 10.1016/j.pld.2023.06.001

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Deep genome skimming reveals the hybrid origin of Pseudosasa gracilis (Poaceae: Bambusoideae)

Xiang-Zhou Hu^a,b, Cen Guo^a, Sheng-Yuan Qin^a,b, De-Zhu Li^a,b, Zhen-Hua Guo^a,b

a. Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China;
b. University of Chinese Academy of Sciences, Beijing 100049, China

Received:2023-02-07 Revised:2023-05-24 Online:2024-05-20 Published:2024-05-25
Contact: Xiang-Zhou Hu,E-mail:huxiangzhou@mail.kib.ac.cn;Cen Guo,E-mail:guocen@mail.kib.ac.cn;Sheng-Yuan Qin,E-mail:qinshengyuan@mail.kib.ac.cn;De-Zhu Li,E-mail:DZL@mail.kib.ac.cn;Zhen-Hua Guo,E-mail:guozhenhua@mail.kib.ac.cn
Supported by:
We thank Ms. Liang-Min Liu, Ms. Shuang-Xiu Xu (all from Kunming Institute of Botany, Chinese Academy of Sciences) for assistance in analytical processes. We are also grateful to Jun Chen, De-Sheng Chen (Mangshan National Nature Reserve Administration, Hunan Province), Zhang-Ping You (Nanling National Nature Reserve, Guangdong Province), and Hua-Ge Deng (Luofu Mountain Provincial Nature Reserve, Guangdong Province) for logistic support for sampling, and to the iFlora High Performance Computing Center of Germplasm Bank of Wild Species (iFlora HPC Center of GBOWS, KIB, CAS) for computation. This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB31000000) and the National Natural Science Foundation of China (32200193).

Deep genome skimming reveals the hybrid origin of Pseudosasa gracilis (Poaceae: Bambusoideae)

Xiang-Zhou Hu^a,b, Cen Guo^a, Sheng-Yuan Qin^a,b, De-Zhu Li^a,b, Zhen-Hua Guo^a,b

a. Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China;
b. University of Chinese Academy of Sciences, Beijing 100049, China

通讯作者: Xiang-Zhou Hu,E-mail:huxiangzhou@mail.kib.ac.cn;Cen Guo,E-mail:guocen@mail.kib.ac.cn;Sheng-Yuan Qin,E-mail:qinshengyuan@mail.kib.ac.cn;De-Zhu Li,E-mail:DZL@mail.kib.ac.cn;Zhen-Hua Guo,E-mail:guozhenhua@mail.kib.ac.cn
基金资助:
We thank Ms. Liang-Min Liu, Ms. Shuang-Xiu Xu (all from Kunming Institute of Botany, Chinese Academy of Sciences) for assistance in analytical processes. We are also grateful to Jun Chen, De-Sheng Chen (Mangshan National Nature Reserve Administration, Hunan Province), Zhang-Ping You (Nanling National Nature Reserve, Guangdong Province), and Hua-Ge Deng (Luofu Mountain Provincial Nature Reserve, Guangdong Province) for logistic support for sampling, and to the iFlora High Performance Computing Center of Germplasm Bank of Wild Species (iFlora HPC Center of GBOWS, KIB, CAS) for computation. This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB31000000) and the National Natural Science Foundation of China (32200193).

Abstract

Abstract: Pseudosasa gracilis (Poaceae:Bambusoideae) is a temperate woody bamboo species endemic to South-central China with a narrow distribution. Previous phylogenetic studies revealed an unexpected, isolated phylogenetic position of Ps. gracilis. Here we conducted phylogenomic analysis by sampling populations of Ps. gracilis and its sympatric species Ps. nanunica and Sinosasa polytricha reflecting different genomic signals, by deep genome skimming. Integrating molecular evidence from chloroplast genes and genome-wide SNPs, we deciphered the phylogenetic relationships of Ps. gracilis. Both plastid and nuclear data indicate that Ps. gracilis is more closely related to Sinosasa, which is discordant with the taxonomic treatment. To further explore this molecular-morphological conflict, we screened 411 "perfect-copy" syntenic genes to reconstruct phylogenies using both the concatenation and coalescent methods. We observed extensive discordance between gene trees and the putative species tree. A significant hybridization event was detected based on 411 genes from the D subgenome, showing Ps. gracilis was a hybrid descendant between Sinosasa longiligulata and Ps. nanunica, with 63.56% and 36.44% inheritance probabilities of each parent. Moreover, introgression events were detected in the C subgenome between Ps. gracilis and S. polytricha in the same distribution region. Our findings suggest that sympatric hybridization and introgression play a crucial role in the origin of Ps. gracilis. By providing an empirical example of bamboo of hybrid origin using comprehensive analyses based on genomic data from different inheritance systems and morphological characters, our study represents a step forward in understanding of reticulate evolution of bamboos.

Key words: Phylogenomics, Hybridization, Introgression, Pseudosasa gracilis, Pseudosasa, Sinosasa

摘要： Pseudosasa gracilis (Poaceae:Bambusoideae) is a temperate woody bamboo species endemic to South-central China with a narrow distribution. Previous phylogenetic studies revealed an unexpected, isolated phylogenetic position of Ps. gracilis. Here we conducted phylogenomic analysis by sampling populations of Ps. gracilis and its sympatric species Ps. nanunica and Sinosasa polytricha reflecting different genomic signals, by deep genome skimming. Integrating molecular evidence from chloroplast genes and genome-wide SNPs, we deciphered the phylogenetic relationships of Ps. gracilis. Both plastid and nuclear data indicate that Ps. gracilis is more closely related to Sinosasa, which is discordant with the taxonomic treatment. To further explore this molecular-morphological conflict, we screened 411 "perfect-copy" syntenic genes to reconstruct phylogenies using both the concatenation and coalescent methods. We observed extensive discordance between gene trees and the putative species tree. A significant hybridization event was detected based on 411 genes from the D subgenome, showing Ps. gracilis was a hybrid descendant between Sinosasa longiligulata and Ps. nanunica, with 63.56% and 36.44% inheritance probabilities of each parent. Moreover, introgression events were detected in the C subgenome between Ps. gracilis and S. polytricha in the same distribution region. Our findings suggest that sympatric hybridization and introgression play a crucial role in the origin of Ps. gracilis. By providing an empirical example of bamboo of hybrid origin using comprehensive analyses based on genomic data from different inheritance systems and morphological characters, our study represents a step forward in understanding of reticulate evolution of bamboos.

关键词: Phylogenomics, Hybridization, Introgression, Pseudosasa gracilis, Pseudosasa, Sinosasa

Xiang-Zhou Hu, Cen Guo, Sheng-Yuan Qin, De-Zhu Li, Zhen-Hua Guo. Deep genome skimming reveals the hybrid origin of Pseudosasa gracilis (Poaceae: Bambusoideae)[J]. Plant Diversity, 2024, 46(03): 344-352.

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Deep genome skimming reveals the hybrid origin of Pseudosasa gracilis (Poaceae: Bambusoideae)

Deep genome skimming reveals the hybrid origin of Pseudosasa gracilis (Poaceae: Bambusoideae)

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