A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C4 photosynthesis

doi:10.1016/j.molp.2022.01.015

	A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C4 photosynthesis
	Huang, Weichen ; Zhang, Lin ; Columbus, J. Travis ; Hu, Yi ; Zhao, Yiyong ; Tang, Lin 5; Guo, Zhenhua ; Chen, Wenli 7; McKain, Michael 8; Bartlett, Madelaine 9; Huang, Chien-Hsun ; Li, De-Zhu ; Ge, Song7 ; Ma, Hong
	2022
发表期刊	MOLECULAR PLANT
ISSN	1674-2052
卷号	15 期号:4 页码:755-777
摘要	Poaceae (the grasses) includes rice, maize, wheat, and other crops, and is the most economically important angiosperm family. Poaceae is also one of the largest plant families, consisting of over 11 000 species with a global distribution that contributes to diverse ecosystems. Poaceae species are classified into 12 subfamilies, with generally strong phylogenetic support for their monophyly. However, many relationships within subfamilies, among tribes and/or subtribes, remain uncertain. To better resolve the Poaceae phylogeny, we generated 342 transcriptomic and seven genomic datasets; these were combined with other genomic and transcriptomic datasets to provide sequences for 357 Poaceae species in 231 genera, representing 45 tribes and all 12 subfamilies. Over 1200 low-copy nuclear genes were retrieved from these datasets, with several subsets obtained using additional criteria, and used for coalescent analyses to reconstruct a Poaceae phylogeny. Our results strongly support the monophyly of 11 subfamilies; however, the subfamily Puelioideae was separated into two non-sister clades, one for each of the two previously defined tribes, supporting a hypothesis that places each tribe in a separate subfamily. Molecular clock analyses estimated the crown age of Poaceae to be -101 million years old. Ancestral character reconstruction of C3/C4 photosynthesis supports the hypothesis of multiple independent origins of C4 photosynthesis. These origins are further supported by phylogenetic analysis of the ppc gene family that encodes the phosphoenolpyruvate carboxylase, which suggests that members of three paralogous subclades (ppc-aL1a, ppc-aL1b, and ppcB2) were recruited as functional C4 ppc genes. This study provides valuable resources and a robust phylogenetic framework for evolutionary analyses of the grass family.
关键词	Gramineae transcriptome nuclear phylogeny molecular clock C4 photosynthesis ppc gene evolution
学科领域	Biochemistry & Molecular Biology ; Plant Sciences
DOI	10.1016/j.molp.2022.01.015
收录类别	SCI
语种	英语
WOS关键词	GRASSES POACEAE ; PHOSPHOENOLPYRUVATE CARBOXYLASE ; DIVERSIFICATION ; CLASSIFICATION ; BAMBUSOIDEAE ; ORIGINS ; TREE ; CHLORIDOIDEAE ; DIVERGENCE ; SUBFAMILY
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000787043300004
出版者	CELL PRESS
文献子类	Article
出版地	CAMBRIDGE
EISSN	1752-9867
资助机构	Eberly College of Science ; Huck Institutes of the Life Sciences at the Pennsylvania State University ; National Natural Science Foundation of China [31770242, 31970224] ; Ministry of Education Key Laboratory of Biodiversity Science and Ecological Engineering ; State Key Laboratory of Genetic Engineering at Fudan University
作者邮箱	hxm16@psu.edu
作品OA属性	hybrid
引用统计	被引频次：37[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/28659
专题	系统与进化植物学国家重点实验室
作者单位	1.Penn State Univ, Dept Biol, Huck Inst Life Sci, 510 Mueller Lab, State Coll, PA 16802 USA 2.Fudan Univ, Minist Educ, Key Lab Biodivers Sci & Ecol Engn, 2005 Songhu Rd, Shanghai 200438, Peoples R China 3.Fudan Univ, State Key Lab Genet Engn, Inst Biodivers Sci, 2005 Songhu Rd, Shanghai 200438, Peoples R China 4.Fudan Univ, Inst Plant Biol, Sch Life Sci, 2005 Songhu Rd, Shanghai 200438, Peoples R China 5.Rancho Santa Ana Bot Garden & Claremont Grad Univ, 1500 North Coll Ave, Claremont, CA 91711 USA 6.Zhejiang Univ, Coll Life Sci, Hangzhou 310058, Zhejiang, Peoples R China 7.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Plant Germplasm & Genom Ctr, Kunming 650201, Yunnan, Peoples R China 8.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 9.Univ Alabama, Dept Biol Sci, 411 Mary Harmon Bryant Hall, Tuscaloosa, AL 35487 USA 10.Univ Massachusetts Amherst, Dept Biol, 611 North Pleasant St, Amherst, MA 01003 USA
推荐引用方式 GB/T 7714	Huang, Weichen,Zhang, Lin,Columbus, J. Travis,et al. A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C4 photosynthesis[J]. MOLECULAR PLANT,2022,15(4):755-777.
APA	Huang, Weichen.,Zhang, Lin.,Columbus, J. Travis.,Hu, Yi.,Zhao, Yiyong.,...&Ma, Hong.(2022).A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C4 photosynthesis.MOLECULAR PLANT,15(4),755-777.
MLA	Huang, Weichen,et al."A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C4 photosynthesis".MOLECULAR PLANT 15.4(2022):755-777.

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