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Cheng W, Xu J, Mu C, Jiang J, Cheng Z, Gao J. Conservation and Divergence of PEPC Gene Family in Different Ploidy Bamboos. PLANTS (BASEL, SWITZERLAND) 2024; 13:2426. [PMID: 39273910 PMCID: PMC11397392 DOI: 10.3390/plants13172426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 08/23/2024] [Accepted: 08/28/2024] [Indexed: 09/15/2024]
Abstract
Phosphoenolpyruvate carboxylase (PEPC), as a necessary enzyme for higher plants to participate in photosynthesis, plays a key role in photosynthetic carbon metabolism and the stress response. However, the molecular biology of the PEPC family of Bambusoideae has been poorly studied, and the function of its members in the growth and development of Bambusoideae is still unclear. Here, we identified a total of 62 PEPC family members in bamboo. All the PEPC genes in the bamboo subfamily were divided into twelve groups, each group typically containing significantly fewer PEPC members in Olyra latifolia than in Phyllostachys edulis, Dendrocalamus latiflorus and Dendrocalamus brandisii. The results of an intraspecific and interspecies collinearity analysis showed that fragment replication and whole genome replication were the main driving forces of bamboo PEPC members. Furthermore, the Ka/Ks values of collinear genes showed that bamboo PEPC experienced purification selection. In addition, the promoter region of PEPC genes contains cis-acting elements related to light response, plant hormone response and response to stress. An analysis of the expression levels of the PEPC family in different developmental stages and tissues of bamboo shoots has shown that PhePEPC7, PhePEPC9 and PhePEPC10 were highly expressed in the leaves of non-flowering plants and culms. Furthermore, PhePEPC6 was significantly upregulated in leaves after GA treatment. Further research has shown that PhePEPC6 was mainly localized in the cell membrane. This provides a solid bioinformatics foundation for further understanding the biological functions of the bamboo PEPC family.
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Affiliation(s)
- Wenlong Cheng
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, Beijing 100102, China
| | - Junlei Xu
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, Beijing 100102, China
| | - Changhong Mu
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, Beijing 100102, China
| | - Jutang Jiang
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, Beijing 100102, China
| | - Zhanchao Cheng
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, Beijing 100102, China
| | - Jian Gao
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, State Forestry and Grassland Administration, Beijing 100102, China
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2
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Cottenet G, Blancpain C, Holzwarth J. A digital PCR approach to assess the purity of oregano. Heliyon 2024; 10:e25985. [PMID: 38420487 PMCID: PMC10900423 DOI: 10.1016/j.heliyon.2024.e25985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 03/02/2024] Open
Abstract
Herbs and spices are food categories known to be at high risk of adulteration. Presence of undeclared foreign plant species has often been reported in oregano and may have a direct impact on its organoleptic quality and potentially the safety of this aromatic herb. A droplet digital PCR approach was developed to assess the purity of oregano by quantifying the DNA copies of oregano versus the total plant DNA copies. Nuclear single-copy genes were selected by targeting the terpene synthase 5 gene from oregano and the plant phosphoenolpyruvate carboxylase 2 gene. The reactions were specific to the Origanum genus and plant materials respectively, whereas trueness and precision data confirmed the reliability of the method to quantify oregano. The applicability of the method was further verified on proficiency test samples before being applied on commercial oregano samples.
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Affiliation(s)
- Geoffrey Cottenet
- Institute of Food Safety & Analytical Sciences, Nestlé Research, Vers-chez-les-Blanc, Lausanne, Switzerland
| | - Carine Blancpain
- Institute of Food Safety & Analytical Sciences, Nestlé Research, Vers-chez-les-Blanc, Lausanne, Switzerland
| | - James Holzwarth
- Institute of Food Safety & Analytical Sciences, Nestlé Research, Vers-chez-les-Blanc, Lausanne, Switzerland
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3
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Li R, Gao X, Wu Y, Wei C, Li MH, Liu DK, Liu ZJ. Identification and Analysis of PEPC Gene Family Reveals Functional Diversification in Orchidaceae and the Regulation of Bacterial-Type PEPC. Int J Mol Sci 2024; 25:2055. [PMID: 38396732 PMCID: PMC10888551 DOI: 10.3390/ijms25042055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/29/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Phosphoenolpyruvate carboxylase (PEPC) gene family plays a crucial role in both plant growth and response to abiotic stress. Approximately half of the Orchidaceae species are estimated to perform CAM pathway, and the availability of sequenced orchid genomes makes them ideal subjects for investigating the PEPC gene family in CAM plants. In this study, a total of 33 PEPC genes were identified across 15 orchids. Specifically, one PEPC gene was found in Cymbidium goeringii and Platanthera guangdongensis; two in Apostasia shenzhenica, Dendrobium chrysotoxum, D. huoshanense, Gastrodia elata, G. menghaiensis, Phalaenopsis aphrodite, Ph. equestris, and Pl. zijinensis; three in C. ensifolium, C. sinense, D. catenatum, D. nobile, and Vanilla planifolia. These PEPC genes were categorized into four subgroups, namely PEPC-i, PEPC-ii, and PEPC-iii (PTPC), and PEPC-iv (BTPC), supported by the comprehensive analyses of their physicochemical properties, motif, and gene structures. Remarkably, PEPC-iv contained a heretofore unreported orchid PEPC gene, identified as VpPEPC4. Differences in the number of PEPC homolog genes among these species were attributed to segmental duplication, whole-genome duplication (WGD), or gene loss events. Cis-elements identified in promoter regions were predominantly associated with light responsiveness, and circadian-related elements were observed in each PEPC-i and PEPC-ii gene. The expression levels of recruited BTPC, VpPEPC4, exhibited a lower expression level than other VpPEPCs in the tested tissues. The expression analyses and RT-qPCR results revealed diverse expression patterns in orchid PEPC genes. Duplicated genes exhibited distinct expression patterns, suggesting functional divergence. This study offered a comprehensive analysis to unveil the evolution and function of PEPC genes in Orchidaceae.
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Affiliation(s)
- Ruyi Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
| | - Xuyong Gao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
| | - Yuwei Wu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
| | - Chunyi Wei
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
| | - Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ding-Kun Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at Landscape Architecture and Arts, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (R.L.); (X.G.); (Y.W.); (C.W.); (M.-H.L.)
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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4
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Yang Z, Yang Q, Liu Q, Li X, Wang L, Zhang Y, Ke Z, Lu Z, Shen H, Li J, Zhou W. A chromosome-level genome assembly of Agave hybrid NO.11648 provides insights into the CAM photosynthesis. HORTICULTURE RESEARCH 2024; 11:uhad269. [PMID: 38333731 PMCID: PMC10848310 DOI: 10.1093/hr/uhad269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 12/06/2023] [Indexed: 02/10/2024]
Abstract
The subfamily Agavoideae comprises crassulacean acid metabolism (CAM), C3, and C4 plants with a young age of speciation and slower mutation accumulation, making it a model crop for studying CAM evolution. However, the genetic mechanism underlying CAM evolution remains unclear because of lacking genomic information. This study assembled the genome of Agave hybrid NO.11648, a constitutive CAM plant belonging to subfamily Agavoideae, at the chromosome level using data generated from high-throughput chromosome conformation capture, Nanopore, and Illumina techniques, resulting in 30 pseudo-chromosomes with a size of 4.87 Gb and scaffold N50 of 186.42 Mb. The genome annotation revealed 58 841 protein-coding genes and 76.91% repetitive sequences, with the dominant repetitive sequences being the I-type repeats (Copia and Gypsy accounting for 18.34% and 13.5% of the genome, respectively). Our findings also provide support for a whole genome duplication event in the lineage leading to A. hybrid, which occurred after its divergence from subfamily Asparagoideae. Moreover, we identified a gene duplication event in the phosphoenolpyruvate carboxylase kinase (PEPCK) gene family and revealed that three PEPCK genes (PEPCK3, PEPCK5, and PEPCK12) were involved in the CAM pathway. More importantly, we identified transcription factors enriched in the circadian rhythm, MAPK signaling, and plant hormone signal pathway that regulate the PEPCK3 expression by analysing the transcriptome and using yeast one-hybrid assays. Our results shed light on CAM evolution and offer an essential resource for the molecular breeding program of Agave spp.
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Affiliation(s)
- Ziping Yang
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Qian Yang
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Qi Liu
- Wuhan Onemore-tech Co., Ltd, 430076 Wuhan, Hubei, China
| | - Xiaolong Li
- Biomarker Technologies Corporation, 101300 Beijing, China
| | - Luli Wang
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Yanmei Zhang
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Zhi Ke
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Zhiwei Lu
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Huibang Shen
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Junfeng Li
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Wenzhao Zhou
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
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Wang P, Cao H, Quan S, Wang Y, Li M, Wei P, Zhang M, Wang H, Ma H, Li X, Yang ZB. Nitrate improves aluminium resistance through SLAH-mediated citrate exudation from roots. PLANT, CELL & ENVIRONMENT 2023; 46:3518-3541. [PMID: 37574955 DOI: 10.1111/pce.14688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 07/17/2023] [Accepted: 08/01/2023] [Indexed: 08/15/2023]
Abstract
Aluminium (Al) toxicity is one of the major constraint for crop production in acidic soil, and the inappropriate utilization of nitrogen fertilizer can accelerate soil acidification. Despite previous studies investigating the regulation of nitrogen forms in Al toxicity of plants, the underlying mechanism, particularly at the molecular level, remains unclear. This study aims to uncover the potentially regulatory mechanism of nitrate (NO3 - ) in the Al resistance of maize and Arabidopsis. NO3 - conservatively improves Al resistance in maize and Arabidopsis, with nitrate-elevated citrate synthesis and exudation potentially playing critical roles in excluding Al from the root symplast. ZmSLAH2 in maize and AtSLAH1 in Arabidopsis are essential for the regulation of citrate exudation and NO3 - -promoted Al resistance, with ZmMYB81 directly targeting the ZmSLAH2 promoter to activate its activity. Additionally, NO3 - transport is necessary for NO3 - -promoted Al resistance, with ZmNRT1.1A and AtNRT1.1 potentially playing vital roles. The suppression of NO3 - transport in roots by ammonium (NH4 + ) may inhibit NO3 - -promoted Al resistance. This study provides novel insights into the understanding of the crucial role of NO3 - -mediated signalling in the Al resistance of plants and offers guidance for nitrogen fertilization on acid soils.
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Affiliation(s)
- Peng Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University (Qingdao), Qingdao, China
| | - Hongrui Cao
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University (Qingdao), Qingdao, China
| | - Shuxuan Quan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Mu Li
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Ping Wei
- Linyi Academy of Agricultural Sciences, Linyi, China
| | - Meng Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University (Qingdao), Qingdao, China
| | - Hui Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University (Qingdao), Qingdao, China
| | - Hongyu Ma
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University (Qingdao), Qingdao, China
| | - Xiaofeng Li
- College of Agronomy, Guangxi University, Nanning, China
| | - Zhong-Bao Yang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University (Qingdao), Qingdao, China
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6
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Fan W, He ZS, Zhe M, Feng JQ, Zhang L, Huang Y, Liu F, Huang JL, Ya JD, Zhang SB, Yang JB, Zhu A, Li DZ. High-quality Cymbidium mannii genome and multifaceted regulation of crassulacean acid metabolism in epiphytes. PLANT COMMUNICATIONS 2023; 4:100564. [PMID: 36809882 PMCID: PMC10504564 DOI: 10.1016/j.xplc.2023.100564] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/10/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Epiphytes with crassulacean acid metabolism (CAM) photosynthesis are widespread among vascular plants, and repeated evolution of CAM photosynthesis is a key innovation for micro-ecosystem adaptation. However, we lack a complete understanding of the molecular regulation of CAM photosynthesis in epiphytes. Here, we report a high-quality chromosome-level genome assembly of a CAM epiphyte, Cymbidium mannii (Orchidaceae). The 2.88-Gb orchid genome with a contig N50 of 22.7 Mb and 27 192 annotated genes was organized into 20 pseudochromosomes, 82.8% of which consisted of repetitive elements. Recent expansions of long terminal repeat retrotransposon families have made a major contribution to the evolution of genome size in Cymbidium orchids. We reveal a holistic scenario of molecular regulation of metabolic physiology using high-resolution transcriptomics, proteomics, and metabolomics data collected across a CAM diel cycle. Patterns of rhythmically oscillating metabolites, especially CAM-related products, reveal circadian rhythmicity in metabolite accumulation in epiphytes. Genome-wide analysis of transcript and protein level regulation revealed phase shifts during the multifaceted regulation of circadian metabolism. Notably, we observed diurnal expression of several core CAM genes (especially βCA and PPC) that may be involved in temporal fixation of carbon sources. Our study provides a valuable resource for investigating post-transcription and translation scenarios in C. mannii, an Orchidaceae model for understanding the evolution of innovative traits in epiphytes.
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Affiliation(s)
- Weishu Fan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Zheng-Shan He
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Mengqing Zhe
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jing-Qiu Feng
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Le Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yiwei Huang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Fang Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | | | - Ji-Dong Ya
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Shi-Bao Zhang
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Andan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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Zhang D, Zhao XW, Li YY, Ke SJ, Yin WL, Lan S, Liu ZJ. Advances and prospects of orchid research and industrialization. HORTICULTURE RESEARCH 2022; 9:uhac220. [PMID: 36479582 PMCID: PMC9720451 DOI: 10.1093/hr/uhac220] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/22/2022] [Indexed: 06/17/2023]
Abstract
Orchidaceae is one of the largest, most diverse families in angiosperms with significant ecological and economical values. Orchids have long fascinated scientists by their complex life histories, exquisite floral morphology and pollination syndromes that exhibit exclusive specializations, more than any other plants on Earth. These intrinsic factors together with human influences also make it a keystone group in biodiversity conservation. The advent of sequencing technologies and transgenic techniques represents a quantum leap in orchid research, enabling molecular approaches to be employed to resolve the historically interesting puzzles in orchid basic and applied biology. To date, 16 different orchid genomes covering four subfamilies (Apostasioideae, Vanilloideae, Epidendroideae, and Orchidoideae) have been released. These genome projects have given rise to massive data that greatly empowers the studies pertaining to key innovations and evolutionary mechanisms for the breadth of orchid species. The extensive exploration of transcriptomics, comparative genomics, and recent advances in gene engineering have linked important traits of orchids with a multiplicity of gene families and their regulating networks, providing great potential for genetic enhancement and improvement. In this review, we summarize the progress and achievement in fundamental research and industrialized application of orchids with a particular focus on molecular tools, and make future prospects of orchid molecular breeding and post-genomic research, providing a comprehensive assemblage of state of the art knowledge in orchid research and industrialization.
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Affiliation(s)
- Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xue-Wei Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan-Yuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shi-Jie Ke
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wei-Lun Yin
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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8
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Song C, Wang Y, Manzoor MA, Mao D, Wei P, Cao Y, Zhu F. In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing. FRONTIERS IN PLANT SCIENCE 2022; 13:1018029. [PMID: 36212315 PMCID: PMC9539832 DOI: 10.3389/fpls.2022.1018029] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/05/2022] [Indexed: 06/01/2023]
Abstract
High-throughput sequencing technology has been facilitated the development of new methodologies and approaches for studying the origin and evolution of plant genomes and subgenomes, population domestication, and functional genomics. Orchids have tens of thousands of members in nature. Many of them have promising application potential in the extension and conservation of the ecological chain, the horticultural use of ornamental blossoms, and the utilization of botanical medicines. However, a large-scale gene knockout mutant library and a sophisticated genetic transformation system are still lacking in the improvement of orchid germplasm resources. New gene editing tools, such as the favored CRISPR-Cas9 or some base editors, have not yet been widely applied in orchids. In addition to a large variety of orchid cultivars, the high-precision, high-throughput genome sequencing technology is also required for the mining of trait-related functional genes. Nowadays, the focus of orchid genomics research has been directed to the origin and classification of species, genome evolution and deletion, gene duplication and chromosomal polyploidy, and flower morphogenesis-related regulation. Here, the progressing achieved in orchid molecular biology and genomics over the past few decades have been discussed, including the evolution of genome size and polyploidization. The frequent incorporation of LTR retrotransposons play important role in the expansion and structural variation of the orchid genome. The large-scale gene duplication event of the nuclear genome generated plenty of recently tandem duplicated genes, which drove the evolution and functional divergency of new genes. The evolution and loss of the plastid genome, which mostly affected genes related to photosynthesis and autotrophy, demonstrated that orchids have experienced more separate transitions to heterotrophy than any other terrestrial plant. Moreover, large-scale resequencing provide useful SNP markers for constructing genetic maps, which will facilitate the breeding of novel orchid varieties. The significance of high-throughput sequencing and gene editing technologies in the identification and molecular breeding of the trait-related genes in orchids provides us with a representative trait-improving gene as well as some mechanisms worthy of further investigation. In addition, gene editing has promise for the improvement of orchid genetic transformation and the investigation of gene function. This knowledge may provide a scientific reference and theoretical basis for orchid genome studies.
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Affiliation(s)
- Cheng Song
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Yan Wang
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | | | - Di Mao
- Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Peipei Wei
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Yunpeng Cao
- Chinese Academy of Sciences (CAS) Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Fucheng Zhu
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
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9
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Heyduk K, McAssey EV, Leebens‐Mack J. Differential timing of gene expression and recruitment in independent origins of CAM in the Agavoideae (Asparagaceae). THE NEW PHYTOLOGIST 2022; 235:2111-2126. [PMID: 35596719 PMCID: PMC9796715 DOI: 10.1111/nph.18267] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Crassulacean acid metabolism (CAM) photosynthesis has evolved repeatedly across the plant tree of life, however our understanding of the genetic convergence across independent origins remains hampered by the lack of comparative studies. Here, we explore gene expression profiles in eight species from the Agavoideae (Asparagaceae) encompassing three independent origins of CAM. Using comparative physiology and transcriptomics, we examined the variable modes of CAM in this subfamily and the changes in gene expression across time of day and between well watered and drought-stressed treatments. We further assessed gene expression and the molecular evolution of genes encoding phosphoenolpyruvate carboxylase (PPC), an enzyme required for primary carbon fixation in CAM. Most time-of-day expression profiles are largely conserved across all eight species and suggest that large perturbations to the central clock are not required for CAM evolution. By contrast, transcriptional response to drought is highly lineage specific. Yucca and Beschorneria have CAM-like expression of PPC2, a copy of PPC that has never been shown to be recruited for CAM in angiosperms. Together the physiological and transcriptomic comparison of closely related C3 and CAM species reveals similar gene expression profiles, with the notable exception of differential recruitment of carboxylase enzymes for CAM function.
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Affiliation(s)
- Karolina Heyduk
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHI96822USA
- Department of Plant BiologyUniversity of GeorgiaAthensGA30602USA
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCT06520USA
| | - Edward V. McAssey
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHI96822USA
| | - Jim Leebens‐Mack
- Department of Plant BiologyUniversity of GeorgiaAthensGA30602USA
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10
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Yamamoto N, Tong W, Lv B, Peng Z, Yang Z. The Original Form of C 4-Photosynthetic Phospho enolpyruvate Carboxylase Is Retained in Pooids but Lost in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:905894. [PMID: 35958195 PMCID: PMC9358456 DOI: 10.3389/fpls.2022.905894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Poaceae is the most prominent monocot family that contains the primary cereal crops wheat, rice, and maize. These cereal species exhibit physiological diversity, such as different photosynthetic systems and environmental stress tolerance. Phosphoenolpyruvate carboxylase (PEPC) in Poaceae is encoded by a small multigene family and plays a central role in C4-photosynthesis and dicarboxylic acid metabolism. Here, to better understand the molecular basis of the cereal species diversity, we analyzed the PEPC gene family in wheat together with other grass species. We could designate seven plant-type and one bacterial-type grass PEPC groups, ppc1a, ppc1b, ppc2a, ppc2b, ppc3, ppc4, ppcC4, and ppc-b, respectively, among which ppc1b is an uncharacterized type of PEPC. Evolutionary inference revealed that these PEPCs were derived from five types of ancient PEPCs (ppc1, ppc2, ppc3, ppc4, and ppc-b) in three chromosomal blocks of the ancestral Poaceae genome. C4-photosynthetic PEPC (ppcC4 ) had evolved from ppc1b, which seemed to be arisen by a chromosomal duplication event. We observed that ppc1b was lost in many Oryza species but preserved in Pooideae after natural selection. In silico analysis of cereal RNA-Seq data highlighted the preferential expression of ppc1b in upper ground organs, selective up-regulation of ppc1b under osmotic stress conditions, and nitrogen response of ppc1b. Characterization of wheat ppc1b showed high levels of gene expression in young leaves, transcriptional responses under nitrogen and abiotic stress, and the presence of a Dof1 binding site, similar to ppcC4 in maize. Our results indicate the evolving status of Poaceae PEPCs and suggest the functional association of ppc1-derivatives with adaptation to environmental changes.
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Affiliation(s)
- Naoki Yamamoto
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, China
| | - Wurina Tong
- College of Environmental Science and Engineering, China West Normal University, Nanchong, China
| | - Bingbing Lv
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, China
| | - Zhengsong Peng
- School of Agricultural Science, Xichang College, Xichang, China
| | - Zaijun Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, China
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11
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Shu JP, Yan YH, Wang RJ. Convergent molecular evolution of phosphoenolpyruvate carboxylase gene family in C 4 and crassulacean acid metabolism plants. PeerJ 2022; 10:e12828. [PMID: 35116203 PMCID: PMC8784020 DOI: 10.7717/peerj.12828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 01/03/2022] [Indexed: 01/10/2023] Open
Abstract
Phosphoenolpyruvate carboxylase (PEPC), as the key enzyme in initial carbon fixation of C4and crassulacean acid mechanism (CAM) pathways, was thought to undergo convergent adaptive changes resulting in the convergent evolution of C4 and CAM photosynthesis in vascular plants. However, the integral evolutionary history and convergence of PEPC in plants remain poorly understood. In the present study, we identified the members of PEPC gene family across green plants with seventeen genomic datasets, found ten conserved motifs and modeled three-dimensional protein structures of 90 plant-type PEPC genes. After reconstructing PEPC gene family tree and reconciled with species tree, we found PEPC genes underwent 71 gene duplication events and 16 gene loss events, which might result from whole-genome duplication events in plants. Based on the phylogenetic tree of the PEPC gene family, we detected four convergent evolution sites of PEPC in C4 species but none in CAM species. The PEPC gene family was ubiquitous and highly conservative in green plants. After originating from gene duplication of ancestral C3-PEPC, C4-PEPC isoforms underwent convergent molecular substitution that might facilitate the convergent evolution of C4 photosynthesis in Angiosperms. However, there was no evidence for convergent molecular evolution of PEPC genes between CAM plants. Our findings help to understand the origin and convergent evolution of C4 and CAM plants and shed light on the adaptation of plants in dry, hot environments.
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Affiliation(s)
- Jiang-Ping Shu
- Key laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China,Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China,Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China,University of Chinese Academy of Sciences, Beijing, China
| | - Yue-Hong Yan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China,Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Centre of China and The Orchid Conservation and Research Centre of Shenzhen, Shenzhen, China,University of Chinese Academy of Sciences, Beijing, China
| | - Rui-Jiang Wang
- Key laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China,University of Chinese Academy of Sciences, Beijing, China
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12
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Wickell D, Kuo LY, Yang HP, Dhabalia Ashok A, Irisarri I, Dadras A, de Vries S, de Vries J, Huang YM, Li Z, Barker MS, Hartwick NT, Michael TP, Li FW. Underwater CAM photosynthesis elucidated by Isoetes genome. Nat Commun 2021; 12:6348. [PMID: 34732722 PMCID: PMC8566536 DOI: 10.1038/s41467-021-26644-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/12/2021] [Indexed: 12/13/2022] Open
Abstract
To conserve water in arid environments, numerous plant lineages have independently evolved Crassulacean Acid Metabolism (CAM). Interestingly, Isoetes, an aquatic lycophyte, can also perform CAM as an adaptation to low CO2 availability underwater. However, little is known about the evolution of CAM in aquatic plants and the lack of genomic data has hindered comparison between aquatic and terrestrial CAM. Here, we investigate underwater CAM in Isoetes taiwanensis by generating a high-quality genome assembly and RNA-seq time course. Despite broad similarities between CAM in Isoetes and terrestrial angiosperms, we identify several key differences. Notably, Isoetes may have recruited the lesser-known 'bacterial-type' PEPC, along with the 'plant-type' exclusively used in other CAM and C4 plants for carboxylation of PEP. Furthermore, we find that circadian control of key CAM pathway genes has diverged considerably in Isoetes relative to flowering plants. This suggests the existence of more evolutionary paths to CAM than previously recognized.
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Affiliation(s)
- David Wickell
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Li-Yaung Kuo
- Institute of Molecular & Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | | | - Amra Dhabalia Ashok
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Iker Irisarri
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany
| | - Armin Dadras
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Sophie de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
- Campus Institute Data Science, University of Goettingen, Goettingen, Germany
- Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences, University of Goettingen, Goettingen, Germany
| | | | - Zheng Li
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Nolan T Hartwick
- The Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Todd P Michael
- The Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Fay-Wei Li
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
- Boyce Thompson Institute, Ithaca, NY, USA.
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13
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Genome-wide identification and molecular evolution analysis of the heat shock transcription factor (HSF) gene family in four diploid and two allopolyploid Gossypium species. Genomics 2021; 113:3112-3127. [PMID: 34246694 DOI: 10.1016/j.ygeno.2021.07.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 06/21/2021] [Accepted: 07/06/2021] [Indexed: 11/23/2022]
Abstract
Heat shock transcription factors (HSFs) can regulate plant development and stress response. The comprehensive evolutionary history of the HSF family remains elusive in cotton. In this study, each cotton species had 78 members in Gossypium barbadense and Gossypium hirsutum. The diploid species had 39 GaHSFs in Gossypium arboreum, 31 GrHSFs in Gossypium raimondii, 34 GtHSFs in Gossypium turneri, and 34 GlHSFs in Gossypium longicalyx. The HSF family in cotton can be classified into three subfamilies, with seven groups in subfamily A and five groups in subfamily B. Different groups exhibited distinct gene proportions, conserved motifs, gene structures, expansion rates, gene loss rates, and cis-regulatory elements. The paleohexaploidization event led to the expansion of the HSF family in cotton, and the gene duplication events in six Gossypium species were inherited from their common ancestor. The HSF family in diploid species had a divergent evolutionary history, whereas two cultivated tetraploids presented a highly conserved evolution of the HSF family. The HSF members in At and Dt subgenomes of the cultivated tetraploids showed a different evolution from their corresponding diploid donors. Some HSF members were regarded as key candidates for regulating cotton development and stress response. This study provided the comprehensive information on the evolutionary history of the HSF family in cotton.
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14
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Phansopa C, Dunning LT, Reid JD, Christin PA. Lateral Gene Transfer Acts As an Evolutionary Shortcut to Efficient C4 Biochemistry. Mol Biol Evol 2021; 37:3094-3104. [PMID: 32521019 PMCID: PMC7751175 DOI: 10.1093/molbev/msaa143] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The adaptation of proteins for novel functions often requires changes in their kinetics via amino acid replacement. This process can require multiple mutations, and therefore extended periods of selection. The transfer of genes among distinct species might speed up the process, by providing proteins already adapted for the novel function. However, this hypothesis remains untested in multicellular eukaryotes. The grass Alloteropsis is an ideal system to test this hypothesis due to its diversity of genes encoding phosphoenolpyruvate carboxylase, an enzyme that catalyzes one of the key reactions in the C4 pathway. Different accessions of Alloteropsis either use native isoforms relatively recently co-opted from other functions or isoforms that were laterally acquired from distantly related species that evolved the C4 trait much earlier. By comparing the enzyme kinetics, we show that native isoforms with few amino acid replacements have substrate KM values similar to the non-C4 ancestral form, but exhibit marked increases in catalytic efficiency. The co-option of native isoforms was therefore followed by rapid catalytic improvements, which appear to rely on standing genetic variation observed within one species. Native C4 isoforms with more amino acid replacements exhibit additional changes in affinities, suggesting that the initial catalytic improvements are followed by gradual modifications. Finally, laterally acquired genes show both strong increases in catalytic efficiency and important changes in substrate handling. We conclude that the transfer of genes among distant species sharing the same physiological novelty creates an evolutionary shortcut toward more efficient enzymes, effectively accelerating evolution.
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Affiliation(s)
- Chatchawal Phansopa
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom.,Department of Chemistry, University of Sheffield, Sheffield, United Kingdom
| | - Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - James D Reid
- Department of Chemistry, University of Sheffield, Sheffield, United Kingdom
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15
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Zhang L, Wu S, Chang X, Wang X, Zhao Y, Xia Y, Trigiano RN, Jiao Y, Chen F. The ancient wave of polyploidization events in flowering plants and their facilitated adaptation to environmental stress. PLANT, CELL & ENVIRONMENT 2020; 43:2847-2856. [PMID: 33001478 DOI: 10.1111/pce.13898] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/22/2020] [Accepted: 09/26/2020] [Indexed: 05/24/2023]
Abstract
Flowering plants, or angiosperms, consist of more than 300,000 species, far more than any other land plant lineages. The accumulated evidence indicates that multiple ancient polyploidy events occurred around 100 to 120 million years ago during the Cretaceous and drove the early diversification of four major clades of angiosperms: gamma whole-genome triplication in the common ancestor of core eudicots, tau whole-genome duplication during the early diversification of monocots, lambda whole-genome duplication during the early diversification of magnoliids, and pi whole-genome duplication in the Nymphaeales lineage. These four polyploidy events have played essential roles in the adaptive evolution and diversification of major clades of flowering plants. Here, we specifically review the current understanding of this wave of ancient whole-genome duplications and their evolutionary significance. Notably, although these ancient whole-genome duplications occurred independently, they have contributed to the expansion of many stress-related genes (e.g., heat shock transcription factors and Arabidopsis response regulators),and these genes could have been selected for by global environmental changes in the Cretaceous. Therefore, this ancient wave of paleopolyploidy events could have significantly contributed to the adaptation of angiosperms to environmental changes, and potentially promoted the wide diversification of flowering plants.
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Affiliation(s)
- Liangsheng Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shengdan Wu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Xiaojun Chang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiuyun Wang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yunpeng Zhao
- Laboratory of Systematic & Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yiping Xia
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Robert N Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee, USA
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
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16
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A Tale of Two Families: Whole Genome and Segmental Duplications Underlie Glutamine Synthetase and Phosphoenolpyruvate Carboxylase Diversity in Narrow-Leafed Lupin ( Lupinus angustifolius L.). Int J Mol Sci 2020; 21:ijms21072580. [PMID: 32276381 PMCID: PMC7177731 DOI: 10.3390/ijms21072580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/04/2020] [Accepted: 04/06/2020] [Indexed: 01/04/2023] Open
Abstract
Narrow-leafed lupin (Lupinus angustifolius L.) has recently been supplied with advanced genomic resources and, as such, has become a well-known model for molecular evolutionary studies within the legume family—a group of plants able to fix nitrogen from the atmosphere. The phylogenetic position of lupins in Papilionoideae and their evolutionary distance to other higher plants facilitates the use of this model species to improve our knowledge on genes involved in nitrogen assimilation and primary metabolism, providing novel contributions to our understanding of the evolutionary history of legumes. In this study, we present a complex characterization of two narrow-leafed lupin gene families—glutamine synthetase (GS) and phosphoenolpyruvate carboxylase (PEPC). We combine a comparative analysis of gene structures and a synteny-based approach with phylogenetic reconstruction and reconciliation of the gene family and species history in order to examine events underlying the extant diversity of both families. Employing the available evidence, we show the impact of duplications on the initial complement of the analyzed gene families within the genistoid clade and posit that the function of duplicates has been largely retained. In terms of a broader perspective, our results concerning GS and PEPC gene families corroborate earlier findings pointing to key whole genome duplication/triplication event(s) affecting the genistoid lineage.
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18
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RNA-seq transcriptomic profiling of crassulacean acid metabolism pathway in Dendrobium catenatum. Sci Data 2018; 5:180252. [PMID: 30422119 PMCID: PMC6233253 DOI: 10.1038/sdata.2018.252] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 09/26/2018] [Indexed: 11/09/2022] Open
Abstract
The regulation of crassulacean acid metabolism (CAM) pathway has recently become a topic of intensive research and has been explored in terms of several aspects, including phylogenetics, genomics, and transcriptomics. Orchidaceae, which contains approximately 9,000 CAM species, is one of the largest lineages using this special photosynthetic pathway. However, no comprehensive transcriptomic profiling focused on CAM regulation in orchid species had previously been performed. In this report, we present two Illumina RNA-seq datasets, including a total of 24 mature leaf samples with 844.4 million reads, from Dendrobium catenatum (Orchidaceae), a facultative CAM species. The first dataset was generated from a time-course experiment based on the typical CAM phases in a diel. The second was derived from an experiment on drought stress and stress removal. A series of quality assessments were conducted to verify the reliability of the datasets. These transcriptomic profiling datasets will be useful to explore and understand the essence of CAM regulation.
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19
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Ping CY, Chen FC, Cheng TC, Lin HL, Lin TS, Yang WJ, Lee YI. Expression Profiles of Phosphoenolpyruvate Carboxylase and Phosphoenolpyruvate Carboxylase Kinase Genes in Phalaenopsis, Implications for Regulating the Performance of Crassulacean Acid Metabolism. FRONTIERS IN PLANT SCIENCE 2018; 9:1587. [PMID: 30425727 PMCID: PMC6218735 DOI: 10.3389/fpls.2018.01587] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 10/12/2018] [Indexed: 05/26/2023]
Abstract
Phalaenopsis is one of the most important potted plants in the ornamental market of the world. Previous reports implied that crassulacean acid metabolism (CAM) orchids at their young seedling stages might perform C3 or weak CAM photosynthetic pathways, but the detailed molecular evidence is still lacking. In this study, we used a key species in white Phalaenopsis breeding line, Phalaenopsis aphrodite subsp. formosana, to study the ontogenetical changes of CAM performance in Phalaenopsis. Based on the investigations of rhythms of day/night CO2 exchange, malate contents and phosphoenolpyruvate carboxylase (PEPC) activities, it is suggested that a progressive shift from C3 to CAM occurred as the protocorms differentiated the first leaf. To understand the role of phosphoenolpyruvate carboxylase kinase (PEPC kinase) in relation to its target PEPC in CAM performance in Phalaenopsis, the expression profiles of the genes encoding PEPC (PPC) and PEPC kinase (PPCK) were measured in different developmental stages. In Phalaenopsis, two PPC isogenes were constitutively expressed over a 24-h cycle similar to the housekeeping genes in all stages, whereas the significant day/night difference in PaPPCK expression corresponds to the day/night fluctuations in PEPC activity and malate level. These results suggest that the PaPPCK gene product is most likely involved in regulation of CAM performance in different developmental stages of Phalaenopsis seedlings.
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Affiliation(s)
- Chia-Yun Ping
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Fure-Chyi Chen
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Teen-Chi Cheng
- Department of Plant Industry, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Huey-Ling Lin
- Department of Horticulture, National Chung Hsing University, Taichung, Taiwan
| | - Tzong-Shyan Lin
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Wen-Ju Yang
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Yung-I Lee
- Department of Biology, National Museum of Natural Science, Taichung, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
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20
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Comparative transcriptomics provides insight into the molecular basis of species diversification of section Trigonopedia (Cypripedium) on the Qinghai-Tibetan Plateau. Sci Rep 2018; 8:11640. [PMID: 30076357 PMCID: PMC6076244 DOI: 10.1038/s41598-018-30147-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 07/24/2018] [Indexed: 11/15/2022] Open
Abstract
Deceptive pollination is key to the species richness of Orchidaceae. However, the genetic basis of species diversification is still under study. Section Trigonopedia is a monophyletic clade of genus Cypripedium distributed in the southwest of China. The species of this section are pollinated by different flies. Pollinator differentiation makes section Trigonopedia an ideal group for studying the genetic basis underlying species diversification. Here, we sequenced the transcriptomes of eight species of the genus Cypripedium, including six co-flowering species of section Trigonopedia and two species outside this section as an outgroup. We reconstructed the phylogeny of the section with the combined 1572 single-copy genes extracted from the eight species and produced a highly resolved tree of the section. Furthermore, we combined substitution rate estimation and differential expression analysis to identify candidate genes, including genes related to floral scent synthesis and environmental adaptation, involved in species differentiation. Field investigations showed that these species have adapted to different habitats. We propose that the species diversification in this section is initiated by floral scent differentiation, followed by habitat differentiation, finally leading to speciation. This study sheds novel light on the diversification of closely related orchid species in the Qinghai-Tibetan region.
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Zhao Y, Huang Y, Wang Y, Cui Y, Liu Z, Hua J. RNA interference of GhPEPC2 enhanced seed oil accumulation and salt tolerance in Upland cotton. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 271:52-61. [PMID: 29650157 DOI: 10.1016/j.plantsci.2018.03.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 03/02/2018] [Accepted: 03/13/2018] [Indexed: 05/14/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPCase) mainly produces oxaloacetic acid for tricarboxylic acid (TCA) cycle. Here we reported that GhPEPC2 silencing with PEPC2-RNAi vector could regulate oil and protein accumulation in cottonseeds. In GhPEPC2 transgenic plants, PEPCase activities in immature embryos were significantly reduced, and the oil content in seed kernel was increased 7.3 percentages, whereas total proteins decreased 5.65 percentages. Compared to wild type, agronomical traits of transgenic plant were obviously unaffected. Furthermore, gene expression profile of GhPEPC2 transgenic seeds were investigated using RNA-seq, most lipid synthesis related genes were up-regulated, but amino acid metabolic related genes were down-regulated. In addition, the GhPEPC2 transgenic cotton seedlings were stressed using sodium salts at seedling stage, and the salt tolerance was significantly enhanced. Our observations of GhPEPC2 in cotton would shade light on understanding the regulation of oil content, protein accumulation and salt tolerance enhancement in other plants.
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Affiliation(s)
- Yanpeng Zhao
- Laboratory of Cotton Genetics, Genomics and Breeding/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Yi Huang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
| | - Yumei Wang
- Research Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China.
| | - Yupeng Cui
- Laboratory of Cotton Genetics, Genomics and Breeding/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Zhengjie Liu
- Laboratory of Cotton Genetics, Genomics and Breeding/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding/Beijing Key Laboratory of Crop Genetic Improvement/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
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Heyduk K, Ray JN, Ayyampalayam S, Leebens-Mack J. Shifts in gene expression profiles are associated with weak and strong Crassulacean acid metabolism. AMERICAN JOURNAL OF BOTANY 2018; 105:587-601. [PMID: 29746718 DOI: 10.1002/ajb2.1017] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/19/2017] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY The relative ease of high throughput sequencing is facilitating comprehensive phylogenomic and gene expression studies, even for nonmodel groups. To date, however, these two approaches have not been merged; while phylogenomic methods might use transcriptome sequences to resolve relationships, assessment of gene expression patterns in a phylogenetic context is less common. Here we analyzed both carbon assimilation and gene expression patterns of closely related species within the Agavoideae (Asparagaceae) to elucidate changes in gene expression across weak and strong phenotypes for Crassulacean acid metabolism (CAM). METHODS Gene expression patterns were compared across four genera: Agave (CAM), which is paraphyletic with Polianthes (weak CAM) and Manfreda (CAM), and Beschorneria (weak CAM). RNA-sequencing was paired with measures of gas exchange and titratable acidity. Climate niche space was compared across the four lineages to examine abiotic factors and their correlation to CAM. KEY RESULTS Expression of homologous genes showed both shared and variable patterns in weak and strong CAM species. Network analysis highlights that despite shared expression patterns, highly connected genes differ between weak and strong CAM, implicating shifts in regulatory gene function as key for the evolution of CAM. Variation in carbohydrate metabolism between weak and strong CAM supports the importance of sugar turnovers for CAM physiology. CONCLUSIONS Integration of phylogenetics and RNA-sequencing provides a powerful tool to study the evolution of CAM photosynthesis across closely related but photosynthetically variable species. Our findings regarding shared or shifted gene expression and regulation of CAM via carbohydrate metabolism have important implications for efforts to engineer the CAM pathway into C3 food and biofuel crops.
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Affiliation(s)
- Karolina Heyduk
- Miller Plant Sciences, University of Georgia, 120 Carlton Street, 2502, Athens, Georgia, 30602, USA
| | - Jeremy N Ray
- Miller Plant Sciences, University of Georgia, 120 Carlton Street, 2502, Athens, Georgia, 30602, USA
| | | | - James Leebens-Mack
- Miller Plant Sciences, University of Georgia, 120 Carlton Street, 2502, Athens, Georgia, 30602, USA
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Functional Anatomical Traits of the Photosynthetic Organs of Plants with Crassulacean Acid Metabolism. THE LEAF: A PLATFORM FOR PERFORMING PHOTOSYNTHESIS 2018. [DOI: 10.1007/978-3-319-93594-2_10] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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24
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Tsai WC, Dievart A, Hsu CC, Hsiao YY, Chiou SY, Huang H, Chen HH. Post genomics era for orchid research. BOTANICAL STUDIES 2017; 58:61. [PMID: 29234904 PMCID: PMC5727007 DOI: 10.1186/s40529-017-0213-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/01/2017] [Indexed: 05/05/2023]
Abstract
Among 300,000 species in angiosperms, Orchidaceae containing 30,000 species is one of the largest families. Almost every habitats on earth have orchid plants successfully colonized, and it indicates that orchids are among the plants with significant ecological and evolutionary importance. So far, four orchid genomes have been sequenced, including Phalaenopsis equestris, Dendrobium catenatum, Dendrobium officinale, and Apostaceae shengen. Here, we review the current progress and the direction of orchid research in the post genomics era. These include the orchid genome evolution, genome mapping (genome-wide association analysis, genetic map, physical map), comparative genomics (especially receptor-like kinase and terpene synthase), secondary metabolomics, and genome editing.
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Affiliation(s)
- Wen-Chieh Tsai
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Anne Dievart
- CIRAD, UMR AGAP, TA A 108/03, Avenue Agropolis, 34398 Montpellier, France
- Present Address: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Life Sciences Building, Room 3-117, Shanghai, 200240 People’s Republic of China
| | - Chia-Chi Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Shang-Yi Chiou
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hsin Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hong-Hwa Chen
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
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25
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Zhang L, Chen F, Zhang GQ, Zhang YQ, Niu S, Xiong JS, Lin Z, Cheng ZMM, Liu ZJ. Origin and mechanism of crassulacean acid metabolism in orchids as implied by comparative transcriptomics and genomics of the carbon fixation pathway. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:175-85. [PMID: 26959080 DOI: 10.1111/tpj.13159] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 03/03/2016] [Accepted: 03/04/2016] [Indexed: 05/20/2023]
Abstract
Crassulacean acid metabolism (CAM) is a CO2 fixation pathway that maximizes water-use efficiency (WUE), compared with the C3/C4 CO2 pathway, which permits CAM plants to adapt to arid environments. The CAM pathway provides excellent opportunities to genetically design plants, especially bioenergy crops, with a high WUE and better photosynthetic performance than C3/C4 in arid environments. The information available on the origin and evolution of CAM is scant, however. Here, we analyzed transcriptomes from 13 orchid species and two existing orchid genomes, covering CAM and C3 plants, with an emphasis on comparing 13 gene families involved in the complete carbon fixation pathway. The dosage of the core photosynthesis-related genes plays no substantial role in the evolution of CAM in orchids; however, CAM may have evolved primarily by changes at the transcription level of key carbon fixation pathway genes. We proposed that in both dark and light, CO2 is primarily fixed and then released through two metabolic pathways via known genes, such as PPC1, PPDK and PPCK. This study reports a comprehensive comparison of carbon fixation pathway genes across different photosynthetic plants, and reveals the importance of the level of expression of key genes in the origin and evolution of CAM.
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Affiliation(s)
- Liangsheng Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Fei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Plant Sciences, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Yong-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Shance Niu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Jin-Song Xiong
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Plant Sciences, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St Louis, MO, 63103, USA
| | - Zong-Ming Max Cheng
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Plant Sciences, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Zhong-Jian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
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