Evolutionary history of PEPC genes in green plants: Implications for the evolution of CAM in orchids.
The phosphoenolpyruvate carboxylase (PEPC) gene is the key enzyme in CAM and C4 photosynthesis. A detailed phylogenetic analysis of the PEPC family was performed using sequences from 60 available published plant genomes, the Phalaenopsis equestris genome and RNA-Seq of 15 additional orchid species. The PEPC family consists of three distinct subfamilies, PPC-1, PPC-2, and PPC-3, all of which share a recent common ancestor in chlorophyte algae. The eudicot PPC-1 lineage separated into two clades due to whole genome duplication (WGD). Similarly, the monocot PPC-1 lineage also divided into PPC-1M1 and PPC-1M2 through an ancient duplication event. The monocot CAM- or C4-related PEPC originated from the clade PPC-1M1. WGD may not be the major driver for the performance of CAM function by PEPC, although it increased the number of copies of the PEPC gene. CAM may have evolved early in monocots, as the CAM-related PEPC of orchids originated from the monocot ancient duplication, and the earliest CAM-related PEPC may have evolved immediately after the diversification of monocots, with CAM developing prior to C4. Our results represent the most complete evolutionary history of PEPC genes in green plants to date and particularly elucidate the origin of PEPC in orchids.
State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Forestry Policy and Information, Chinese Academy of Forestry, Beijing 100091, China.
Hua
H
Deng
Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China.
Liang-Sheng
LS
Zhang
Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China.
Guo-Qiang
GQ
Zhang
State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
Bao-Qiang
BQ
Zheng
Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China; The Center for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua University, Shenzhen, China; College of Forestry, South China Agricultural University, Guangzhou, China. Electronic address: liuzj@sinicaorchid.org.
Zhong-Jian
ZJ
Liu
State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China. Electronic address: chwy8915@sina.com.
Yan
Y
Wang
D005075:Biological Evolution; D029595:Orchidaceae / Q000201:enzymology / Q000235:genetics*; D010730:Phosphoenolpyruvate Carboxylase / Q000235:genetics*; D010788:Photosynthesis / Q000235:genetics*; D010802:Phylogeny
D010730:Phosphoenolpyruvate Carboxylase
Crassulacean acid metabolism (CAM); Orchidaceae; Phosphoenolpyruvate carboxylase (PEPC); Phylogeny; RNA-Seq sequences