Phylogenomic analyses reveal reticulate evolution between Neomicrocalamus and Temochloa (Poaceae: Bambusoideae)

Zhuo-Yu Cai; Zheng-Yang Niu; You-Yuan Zhang; Yi-Hua Tong; Tien Chinh Vu; Wei Lim Goh; Sarawood Sungkaew; Atchara Teerawatananon; Nian-He Xia

doi:10.3389/fpls.2023.1274337

Phylogenomic analyses reveal reticulate evolution between Neomicrocalamus and Temochloa (Poaceae: Bambusoideae)

Front Plant Sci. 2023 Dec 4:14:1274337. doi: 10.3389/fpls.2023.1274337. eCollection 2023.

Authors

Zhuo-Yu Cai^{1

2

3}, Zheng-Yang Niu^{1

2

3}, You-Yuan Zhang^{1

4}, Yi-Hua Tong^{1

3

5}, Tien Chinh Vu^{6

7}, Wei Lim Goh⁸, Sarawood Sungkaew⁹, Atchara Teerawatananon¹⁰, Nian-He Xia^{1

3}

Affiliations

¹ Key Laboratory of Plant Resources, Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Digital Botanical Garden, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
² College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
³ South China National Botanical Garden, Guangzhou, China.
⁴ Quality Management Office, Guiyang Vocational and Technical College, Guiyang, China.
⁵ State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
⁶ Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
⁷ Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
⁸ Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Kampar, Perak, Malaysia.
⁹ Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok, Thailand.
¹⁰ Natural History Museum of Thailand, National Science Museum, Pathum Thani, Thailand.

Abstract

Neomicrocalamus and Temochloa are closely related to bamboo genera. However, when considered with newly discovered and morphologically similar material from China and Vietnam, the phylogenetic relationship among these three groups was ambiguous in the analyses based on DNA regions. Here, as a means of investigating the relationships among the three bamboo groups and exploring potential sources of genomic conflicts, we present a phylogenomic examination based on the whole plastome, single-nucleotide polymorphism (SNP), and single-copy nuclear (SCN) gene datasets. Three different phylogenetic hypotheses were found. The inconsistency is attributed to the combination of incomplete lineage sorting and introgression. The origin of newly discovered bamboos is from introgressive hybridization between Temochloa liliana (which contributed 80.7% of the genome) and Neomicrocalamus prainii (19.3%), indicating that the newly discovered bamboos are closer to T. liliana in genetics. The more similar morphology and closer distribution elevation also imply a closer relationship between Temochloa and newly discovered bamboos.

Keywords: incomplete lineage sorting; introgression; phylogenetic incongruence; single-copy nuclear gene; single-nucleotide polymorphism.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This study was supported by the National Natural Science Foundation of China (Grant No. 32270227), the Regional International Cooperation Project of Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences (Grant No. 2016CASSEABRIQG008), and the China Scholarship Council (File No. 202104910377).