Reassessing the phylogenetic relationships of Pseudosorghum and Saccharinae (Poaceae) using plastome and nuclear ribosomal sequences

doi:10.1016/j.pld.2025.03.002

Plant Diversity ›› 2025, Vol. 47 ›› Issue (03): 382-393.DOI: 10.1016/j.pld.2025.03.002

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Reassessing the phylogenetic relationships of Pseudosorghum and Saccharinae (Poaceae) using plastome and nuclear ribosomal sequences

Kai Chen^a,b,c, Yan-Chun Liu^d,e, Yue Huang^a,b,c, Xu-Kun Wu^a,b,c, Hai-Ying Ma^f, Hua Peng^g, De-Zhu Li^b, Peng-Fei Ma^a,b

a. State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China;
b. Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China;
c. University of Chinese Academy of Sciences, Beijing 100049, China;
d. Shanghai Botanical Garden, Shanghai 200030, China;
e. Shanghai Engineering Research Center of Sustainable Plant Innovation, Shanghai 200231, China;
f. School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan 650504, China;
g. CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China

Received:2024-10-23 Revised:2025-02-25 Online:2025-05-21 Published:2025-05-25
Contact: Hua Peng,E-mail:hpeng@mail.kib.ac.cn;De-Zhu Li,E-mail:dzl@mail.kib.ac.cn;Peng-Fei Ma,E-mail:mapengfei@mail.kib.ac.cn
Supported by:
This work was supported by Yunnan Fundamental Research Project (202401BC070001), a research project of the Germplasm Bank of Wild Species, Kunming Institute of Botany, CAS, and the Project of Science and Technology Commission of Shanghai Municipality (23DZ1204601).

Reassessing the phylogenetic relationships of Pseudosorghum and Saccharinae (Poaceae) using plastome and nuclear ribosomal sequences

Kai Chen^a,b,c, Yan-Chun Liu^d,e, Yue Huang^a,b,c, Xu-Kun Wu^a,b,c, Hai-Ying Ma^f, Hua Peng^g, De-Zhu Li^b, Peng-Fei Ma^a,b

a. State Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China;
b. Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China;
c. University of Chinese Academy of Sciences, Beijing 100049, China;
d. Shanghai Botanical Garden, Shanghai 200030, China;
e. Shanghai Engineering Research Center of Sustainable Plant Innovation, Shanghai 200231, China;
f. School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan 650504, China;
g. CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China

通讯作者: Hua Peng,E-mail:hpeng@mail.kib.ac.cn;De-Zhu Li,E-mail:dzl@mail.kib.ac.cn;Peng-Fei Ma,E-mail:mapengfei@mail.kib.ac.cn
基金资助:
This work was supported by Yunnan Fundamental Research Project (202401BC070001), a research project of the Germplasm Bank of Wild Species, Kunming Institute of Botany, CAS, and the Project of Science and Technology Commission of Shanghai Municipality (23DZ1204601).

Abstract

Abstract: The sugarcane subtribe Saccharinae (Andropogoneae, Poaceae) was established in 1846, but its delimitation has long been debated. Moreover, the relationships among the genera of Saccharinae remain unclear, and there is no consensus on whether Pseudosorghum, a small genus in tropical Asia with only two species, should be included. Here, we performed phylogenomic analyses using whole plastomes (69 of them newly sequenced) from 132 individuals, representing 65 species in 19 related genera. We also built trees with nuclear ribosomal DNA sequences. Our results justify the inclusion of Pseudosorghum, likely also the Eulalia Clade III, in Saccharinae. Furthermore, both morphological and molecular analyses support merging the two Pseudosorghum species. The backbone relationships of the Saccharinae phylogeny were highly supported with four polyphyletic clades of Miscanthus and the inclusion of Narenga and Tripidium rufipilum in Saccharum. Pseudosorghum is moderately supported as sister to the Miscanthus Clade I, while the remaining Tripidium species could be excluded from the subtribe. Saccharinae is estimated to have originated ~3.73 million years ago in East Asia, followed by intercontinental dispersals. Our study provides a comprehensive phylogenetic framework for future taxonomic revisions of this economically important subtribe.

Key words: Phylogenomics, Saccharinae, Pseudosorghum, Plastome, nrDNA, Biogeography

摘要： The sugarcane subtribe Saccharinae (Andropogoneae, Poaceae) was established in 1846, but its delimitation has long been debated. Moreover, the relationships among the genera of Saccharinae remain unclear, and there is no consensus on whether Pseudosorghum, a small genus in tropical Asia with only two species, should be included. Here, we performed phylogenomic analyses using whole plastomes (69 of them newly sequenced) from 132 individuals, representing 65 species in 19 related genera. We also built trees with nuclear ribosomal DNA sequences. Our results justify the inclusion of Pseudosorghum, likely also the Eulalia Clade III, in Saccharinae. Furthermore, both morphological and molecular analyses support merging the two Pseudosorghum species. The backbone relationships of the Saccharinae phylogeny were highly supported with four polyphyletic clades of Miscanthus and the inclusion of Narenga and Tripidium rufipilum in Saccharum. Pseudosorghum is moderately supported as sister to the Miscanthus Clade I, while the remaining Tripidium species could be excluded from the subtribe. Saccharinae is estimated to have originated ~3.73 million years ago in East Asia, followed by intercontinental dispersals. Our study provides a comprehensive phylogenetic framework for future taxonomic revisions of this economically important subtribe.

关键词: Phylogenomics, Saccharinae, Pseudosorghum, Plastome, nrDNA, Biogeography

Kai Chen, Yan-Chun Liu, Yue Huang, Xu-Kun Wu, Hai-Ying Ma, Hua Peng, De-Zhu Li, Peng-Fei Ma. Reassessing the phylogenetic relationships of Pseudosorghum and Saccharinae (Poaceae) using plastome and nuclear ribosomal sequences[J]. Plant Diversity, 2025, 47(03): 382-393.

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Reassessing the phylogenetic relationships of Pseudosorghum and Saccharinae (Poaceae) using plastome and nuclear ribosomal sequences

Reassessing the phylogenetic relationships of Pseudosorghum and Saccharinae (Poaceae) using plastome and nuclear ribosomal sequences

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