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Groot Crego C, Hess J, Yardeni G, de La Harpe M, Priemer C, Beclin F, Saadain S, Cauz-Santos LA, Temsch EM, Weiss-Schneeweiss H, Barfuss MHJ, Till W, Weckwerth W, Heyduk K, Lexer C, Paun O, Leroy T. CAM evolution is associated with gene family expansion in an explosive bromeliad radiation. THE PLANT CELL 2024; 36:4109-4131. [PMID: 38686825 PMCID: PMC11449062 DOI: 10.1093/plcell/koae130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 04/04/2024] [Accepted: 04/07/2024] [Indexed: 05/02/2024]
Abstract
The subgenus Tillandsia (Bromeliaceae) belongs to one of the fastest radiating clades in the plant kingdom and is characterized by the repeated evolution of Crassulacean acid metabolism (CAM). Despite its complex genetic basis, this water-conserving trait has evolved independently across many plant families and is regarded as a key innovation trait and driver of ecological diversification in Bromeliaceae. By producing high-quality genome assemblies of a Tillandsia species pair displaying divergent photosynthetic phenotypes, and combining genome-wide investigations of synteny, transposable element (TE) dynamics, sequence evolution, gene family evolution, and temporal differential expression, we were able to pinpoint the genomic drivers of CAM evolution in Tillandsia. Several large-scale rearrangements associated with karyotype changes between the 2 genomes and a highly dynamic TE landscape shaped the genomes of Tillandsia. However, our analyses show that rewiring of photosynthetic metabolism is mainly obtained through regulatory evolution rather than coding sequence evolution, as CAM-related genes are differentially expressed across a 24-h cycle between the 2 species but are not candidates of positive selection. Gene orthology analyses reveal that CAM-related gene families manifesting differential expression underwent accelerated gene family expansion in the constitutive CAM species, further supporting the view of gene family evolution as a driver of CAM evolution.
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Affiliation(s)
- Clara Groot Crego
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Jaqueline Hess
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
- Cambrium GmbH, Max-Urich-Str. 3, 13055 Berlin, Germany
| | - Gil Yardeni
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
- Department of Biotechnology, Institute of Computational Biology, University of Life Sciences and Natural Resources (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Marylaure de La Harpe
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
- Office for Nature and Environment, Department of Education, Culture and Environmental protection, Canton of Grisons, 7001 Chur, Switzerland
| | - Clara Priemer
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MOSYS), University of Vienna, 1030 Vienna, Austria
| | - Francesca Beclin
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, 1030 Vienna, Austria
| | - Sarah Saadain
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Luiz A Cauz-Santos
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
| | - Eva M Temsch
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
| | | | - Michael H J Barfuss
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
| | - Walter Till
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
| | - Wolfram Weckwerth
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MOSYS), University of Vienna, 1030 Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, 1030 Vienna, Austria
| | - Karolina Heyduk
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
| | - Thibault Leroy
- Department of Botany and Biodiversity Research, University of Vienna, 1030 Vienna, Austria
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet Tolosan, France
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2
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Saunders TC, Larridon I, Baker WJ, Barrett RL, Forest F, Françoso E, Maurin O, Rokni S, Roalson EH. Tangled webs and spider-flowers: Phylogenomics, biogeography, and seed morphology inform the evolutionary history of Cleomaceae. AMERICAN JOURNAL OF BOTANY 2024:e16399. [PMID: 39206557 DOI: 10.1002/ajb2.16399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 06/07/2024] [Accepted: 06/09/2024] [Indexed: 09/04/2024]
Abstract
PREMISE Cleomaceae is an important model clade for studies of evolutionary processes including genome evolution, floral form diversification, and photosynthetic pathway evolution. Diversification and divergence patterns in Cleomaceae remain tangled as research has been restricted by its worldwide distribution, limited genetic sampling and species coverage, and a lack of definitive fossil calibration points. METHODS We used target sequence capture and the Angiosperms353 probe set to perform a phylogenetic study of Cleomaceae. We estimated divergence times and biogeographic analyses to explore the origin and diversification of the family. Seed morphology across extant taxa was documented with multifocal image-stacking techniques and morphological characters were extracted, analyzed, and compared to fossil records. RESULTS We recovered a well-supported and resolved phylogenetic tree of Cleomaceae generic relationships that includes 236 (~86%) species. We identified 11 principal clades and confidently placed Cleomella as sister to the rest of the family. Our analyses suggested that Cleomaceae and Brassicaceae diverged ~56 mya, and Cleomaceae began to diversify ~53 mya in the Palearctic and Africa. Multiple transatlantic disjunct distributions were identified. Seeds were imaged from 218 (~80%) species in the family and compared to all known fossil species. CONCLUSIONS Our results represent the most comprehensive phylogenetic study of Cleomaceae to date. We identified transatlantic disjunctions and proposed explanations for these patterns, most likely either long-distance dispersals or contractions in latitudinal distributions caused by climate change over geological timescales. We found that seed morphology varied considerably but mostly mirrored generic relationships.
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Affiliation(s)
- Theresa C Saunders
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164-4236, USA
| | | | | | - Russell L Barrett
- National Herbarium of New South Wales, Botanic Gardens of Sydney, Australian Botanic Garden, Locked Bag 6002, Mount Annan, 2567, New South Wales, Australia
- Evolution and Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales Sydney, Kensington, NSW 2052, Australia
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Elaine Françoso
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Centre for Ecology, Evolution and Behaviour, Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Saba Rokni
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Eric H Roalson
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164-4236, USA
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Chen BZ, Li DW, Luo KY, Jiu ST, Dong X, Wang WB, Li XZ, Hao TT, Lei YH, Guo DZ, Liu XT, Duan SC, Zhu YF, Chen W, Dong Y, Yu WB. Chromosome-level assembly of Lindenbergia philippensis and comparative genomic analyses shed light on genome evolution in Lamiales. FRONTIERS IN PLANT SCIENCE 2024; 15:1444234. [PMID: 39157518 PMCID: PMC11327160 DOI: 10.3389/fpls.2024.1444234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 07/16/2024] [Indexed: 08/20/2024]
Abstract
Lamiales, comprising over 23,755 species across 24 families, stands as a highly diverse and prolific plant group, playing a significant role in the cultivation of horticultural, ornamental, and medicinal plant varieties. Whole-genome duplication (WGD) and its subsequent post-polyploid diploidization (PPD) process represent the most drastic type of karyotype evolution, injecting significant potential for promoting the diversity of this lineage. However, polyploidization histories, as well as genome and subgenome fractionation following WGD events in Lamiales species, are still not well investigated. In this study, we constructed a chromosome-level genome assembly of Lindenbergia philippensis (Orobanchaceae) and conducted comparative genomic analyses with 14 other Lamiales species. L. philippensis is positioned closest to the parasitic lineage within Orobanchaceae and has a conserved karyotype. Through a combination of Ks analysis and syntenic depth analysis, we reconstructed and validated polyploidization histories of Lamiales species. Our results indicated that Primulina huaijiensis underwent three rounds of diploidization events following the γ-WGT event, rather than two rounds as reported. Besides, we reconfirmed that most Lamiales species shared a common diploidization event (L-WGD). Subsequently, we constructed the Lamiales Ancestral Karyotype (LAK), comprising 11 proto-chromosomes, and elucidated its evolutionary trajectory, highlighting the highly flexible reshuffling of the Lamiales paleogenome. We identified biased fractionation of subgenomes following the L-WGD event across eight species, and highlighted the positive impacts of non-WGD genes on gene family expansion. This study provides novel genomic resources and insights into polyploidy and karyotype remodeling of Lamiales species, essential for advancing our understanding of species diversification and genome evolution.
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Affiliation(s)
- Bao-Zheng Chen
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Da-Wei Li
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Kai-Yong Luo
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Song-Tao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao Dong
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Wei-Bin Wang
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xu-Zhen Li
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Ting-Ting Hao
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Ya-Hui Lei
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Da-Zhong Guo
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xu-Tao Liu
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Sheng-Chang Duan
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yi-Fan Zhu
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Wei Chen
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yang Dong
- Yunnan Provincial Key Laboratory of Biological Big Data, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Wen-Bin Yu
- Center for Integrative Conservation and Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla, Yunnan, China
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Cheng X, Zheng Y, Liu X, Xu L, An S, Liu Y, Tan M, Wei Y, Shi H. Overexpression of cassava melatonin receptor PMTR1 plays dual roles in development under light and dark conditions in Arabidopsis. PLANT CELL REPORTS 2024; 43:153. [PMID: 38806727 DOI: 10.1007/s00299-024-03246-3] [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: 03/19/2024] [Revised: 05/08/2024] [Accepted: 05/24/2024] [Indexed: 05/30/2024]
Abstract
KEY MESSAGE MePMTR1 is involved in plant development and production as well as photosynthesis in plant. Melatonin is widely involved in plant growth and development as well as stress responses. Compared with the extending studies of melatonin in stress responses, the direct link between melatonin and plant development in the whole stages remains unclear. With the identification of phytomelatonin receptor PMTR1 in plants, melatonin signalling is becoming much clearer. However, the function of MePMTR1 in tropical crop cassava remains elusive. In this study, we found that overexpression of MePMTR1 showed larger biomass than wild type (WT), including higher number and area of leaves, weight, and accompanying with higher photosynthetic efficiency. Consistently, exogenous melatonin accelerated photosynthetic rate in Arabidopsis. In addition, MePMTR1-overexpressed plants exhibited more resistance to dark-induced senescence compared with WT, demonstrated by higher chlorophyll, lower hydrogen peroxide and superoxide content. In summary, this study illustrated that melatonin and its receptor regulate growth, development and senescence in plants, highlighting the potential application of melatonin and its receptor in improving crop yield and photosynthesis.
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Affiliation(s)
- Xiao Cheng
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, China
| | - Yu Zheng
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, China
| | - Xinyu Liu
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, China
| | - Lunhui Xu
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, China
| | - Shiqin An
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, China
| | - Yinghao Liu
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, China
| | - Mengting Tan
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, China
| | - Yunxie Wei
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, China.
| | - Haitao Shi
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan, China.
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5
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Mabry ME, Abrahams RS, Al-Shehbaz IA, Baker WJ, Barak S, Barker MS, Barrett RL, Beric A, Bhattacharya S, Carey SB, Conant GC, Conran JG, Dassanayake M, Edger PP, Hall JC, Hao Y, Hendriks KP, Hibberd JM, King GJ, Kliebenstein DJ, Koch MA, Leitch IJ, Lens F, Lysak MA, McAlvay AC, McKibben MTW, Mercati F, Moore RC, Mummenhoff K, Murphy DJ, Nikolov LA, Pisias M, Roalson EH, Schranz ME, Thomas SK, Yu Q, Yocca A, Pires JC, Harkess AE. Complementing model species with model clades. THE PLANT CELL 2024; 36:1205-1226. [PMID: 37824826 PMCID: PMC11062466 DOI: 10.1093/plcell/koad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/07/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023]
Abstract
Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a "model clade." These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis and the family Brassicaceae. We promote the utility of such a "model clade" and make suggestions for building global networks to support future studies in the model order Brassicales.
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Affiliation(s)
- Makenzie E Mabry
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - R Shawn Abrahams
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47906, USA
| | | | | | - Simon Barak
- Ben-Gurion University of the Negev, French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Midreshet Ben-Gurion, 8499000, Israel
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Botanic Garden, Locked Bag 6002, Mount Annan, NSW 2567, Australia
| | - Aleksandra Beric
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, St. Louis, MO 63108, USA
| | - Samik Bhattacharya
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Sarah B Carey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Gavin C Conant
- Department of Biological Sciences, Bioinformatics Research Center, Program in Genetics, North Carolina State University, Raleigh, NC 27695, USA
| | - John G Conran
- ACEBB and SGC, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48864, USA
| | - Jocelyn C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Yue Hao
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Kasper P Hendriks
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
- Functional Traits, Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | | | - Marcus A Koch
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Frederic Lens
- Functional Traits, Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands
- Institute of Biology Leiden, Plant Sciences, Leiden University, 2333 BE Leiden, the Netherlands
| | - Martin A Lysak
- CEITEC, and NCBR, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Alex C McAlvay
- Institute of Economic Botany, New York Botanical Garden, The Bronx, NY 10458, USA
| | - Michael T W McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Francesco Mercati
- National Research Council (CNR), Institute of Biosciences and Bioresource (IBBR), Palermo 90129, Italy
| | | | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Melbourne, VIC 3004, Australia
| | | | - Michael Pisias
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Eric H Roalson
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, 6708 PB Wageningen, the Netherlands
| | - Shawn K Thomas
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
- Bioinformatics and Analytics Core, University of Missouri, Columbia, MO 65211, USA
| | - Qingyi Yu
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Hilo, HI 96720, USA
| | - Alan Yocca
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - J Chris Pires
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523-1170, USA
| | - Alex E Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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Yang L, Zhang S, Chu D, Wang X. Exploring the evolution of CHS gene family in plants. Front Genet 2024; 15:1368358. [PMID: 38746055 PMCID: PMC11091334 DOI: 10.3389/fgene.2024.1368358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/04/2024] [Indexed: 05/16/2024] Open
Abstract
Chalcone synthase (CHS) is a key enzyme that catalyzes the first committed step of flavonoid biosynthetic pathway. It plays a vital role not only in maintaining plant growth and development, but also in regulating plant response to environmental hazards. However, the systematic phylogenomic analysis of CHS gene family in a wide range of plant species has not been reported yet. To fill this knowledge gap, a large-scale investigation of CHS genes was performed in 178 plant species covering green algae to dicotyledons. A total of 2,011 CHS and 293 CHS-like genes were identified and phylogenetically divided into four groups, respectively. Gene distribution patterns across the plant kingdom revealed the origin of CHS can be traced back to before the rise of algae. The gene length varied largely in different species, while the exon structure was relatively conserved. Selection pressure analysis also indicated the conserved features of CHS genes on evolutionary time scales. Moreover, our synteny analysis pinpointed that, besides genome-wide duplication and tandem duplication, lineage specific transposition events also occurred in the evolutionary trajectory of CHS gene family. This work provides novel insights into the evolution of CHS gene family and may facilitate further research to better understand the regulatory mechanism of traits relating to flavonoid biosynthesis in diverse plants.
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Affiliation(s)
- Li Yang
- Department of Gastroenterology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Shuai Zhang
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
| | - Dake Chu
- Department of Gastroenterology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Xumei Wang
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
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7
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Silva‐Alvim FAL, Alvim JC, Harvey A, Blatt MR. Speedy stomata of a C 4 plant correlate with enhanced K + channel gating. PLANT, CELL & ENVIRONMENT 2024; 47:817-831. [PMID: 38013592 PMCID: PMC10953386 DOI: 10.1111/pce.14775] [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: 07/04/2023] [Revised: 11/08/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023]
Abstract
Stomata are microscopic pores at the surface of plant leaves that facilitate gaseous diffusion to support photosynthesis. The guard cells around each stoma regulate the pore aperture. Plants that carry out C4 photosynthesis are usually more resilient than C3 plants to stress, and their stomata operate over a lower dynamic range of CO2 within the leaf. What makes guard cells of C4 plants more responsive than those of C3 plants? We used gas exchange and electrophysiology, comparing stomatal kinetics of the C4 plant Gynandropsis gynandra and the phylogenetically related C3 plant Arabidopsis thaliana. We found, with varying CO2 and light, that Gynandropsis showed faster changes in stomata conductance and greater water use efficiency when compared with Arabidopsis. Electrophysiological analysis of the dominant K+ channels showed that the outward-rectifying channels, responsible for K+ loss during stomatal closing, were characterised by a greater maximum conductance and substantial negative shift in the voltage dependence of gating, indicating a reduced inhibition by extracellular K+ and enhanced capacity for K+ flux. These differences correlated with the accelerated stomata kinetics of Gynandropsis, suggesting that subtle changes in the biophysical properties of a key transporter may prove a target for future efforts to engineer C4 stomatal kinetics.
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Affiliation(s)
| | - Jonas Chaves Alvim
- Laboratory of Plant Physiology and Biophysics, Bower BuildingUniversity of GlasgowGlasgowUK
| | - Andy Harvey
- Physics & AstronomyUniversity of GlasgowGlasgowUK
| | - Michael R. Blatt
- Laboratory of Plant Physiology and Biophysics, Bower BuildingUniversity of GlasgowGlasgowUK
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8
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Zou Z, Zhang L, Zhao Y. Integrative Analysis of Oleosin Genes Provides Insights into Lineage-Specific Family Evolution in Brassicales. PLANTS (BASEL, SWITZERLAND) 2024; 13:280. [PMID: 38256833 PMCID: PMC10820149 DOI: 10.3390/plants13020280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024]
Abstract
Oleosins (OLEs) are a class of small but abundant structural proteins that play essential roles in the formation and stabilization of lipid droplets (LDs) in seeds of oil crops. Despite the proposal of five oleosin clades (i.e., U, SL, SH, T, and M) in angiosperms, their evolution in eudicots has not been well-established. In this study, we employed Brassicales, an economically important order of flowering plants possessing the lineage-specific T clade, as an example to address this issue. Three to 10 members were identified from 10 species representing eight plant families, which include Caricaceae, Moringaceae, Akaniaceae, Capparaceae, and Cleomaceae. Evolutionary and reciprocal best hit-based homologous analyses assigned 98 oleosin genes into six clades (i.e., U, SL, SH, M, N, and T) and nine orthogroups (i.e., U1, U2, SL, SH1, SH2, SH3, M, N, and T). The newly identified N clade represents an ancient group that has already appeared in the basal angiosperm Amborella trichopoda, which are constitutively expressed in the tree fruit crop Carica papaya, including pulp and seeds of the fruit. Moreover, similar to Clade N, the previously defined M clade is actually not Lauraceae-specific but an ancient and widely distributed group that diverged before the radiation of angiosperm. Compared with A. trichopoda, lineage-specific expansion of the family in Brassicales was largely contributed by recent whole-genome duplications (WGDs) as well as the ancient γ event shared by all core eudicots. In contrast to the flower-preferential expression of Clade T, transcript profiling revealed an apparent seed/embryo/endosperm-predominant expression pattern of most oleosin genes in Arabidopsis thaliana and C. papaya. Moreover, the structure and expression divergence of paralogous pairs was frequently observed, and a good example is the lineage-specific gain of an intron. These findings provide insights into lineage-specific family evolution in Brassicales, which facilitates further functional studies in nonmodel plants such as C. papaya.
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Affiliation(s)
- Zhi Zou
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Biosciences and Biotechnology/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
| | - Li Zhang
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Biosciences and Biotechnology/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
- Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Science, South-Central University for Nationalities, Wuhan 430074, China
| | - Yongguo Zhao
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Biosciences and Biotechnology/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming 525011, China
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Huang CF, Liu WY, Yu CP, Wu SH, Ku MSB, Li WH. C 4 leaf development and evolution. CURRENT OPINION IN PLANT BIOLOGY 2023; 76:102454. [PMID: 37743123 DOI: 10.1016/j.pbi.2023.102454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 07/30/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023]
Abstract
C4 photosynthesis is more efficient than C3 photosynthesis for two reasons. First, C4 plants have evolved efficient C4 enzymes to suppress wasteful photorespiration and enhance CO2 fixation. Second, C4 leaves have Kranz anatomy in which the veins are surrounded by one layer of bundle sheath (BS) cells and one layer of mesophyll (M) cells. The BS and M cells are functionally well differentiated and also well coordinated for rapid assimilation of atmospheric CO2 and transport of photo-assimilates between the two types of cells. Recent comparative transcriptomics of developing M and BS cells in young maize embryonic leaves revealed not only potential regulators of BS and M cell differentiation but also rapid early BS cell differentiation whereas slower, more prolonged M cell differentiation, contrary to the traditional view of a far simpler process of M cell development. Moreover, new upstream regulators of Kranz anatomy development have been identified and a number of gene co-expression modules for early vascular development have been inferred. Also, a candidate gene regulatory network associated with Kranz anatomy and vascular development has been constructed. Additionally, how whole genome duplication (WGD) may facilitate C4 evolution has been studied and the reasons for why the same WGD event led to successful C4 evolution in Gynandropsis gynandra but not in the sister species Tarenaya hassleriana have been proposed. Finally, new future research directions are suggested.
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Affiliation(s)
- Chi-Fa Huang
- Biodiversity Research Center, Academia Sinica, 115 Taipei, Taiwan
| | - Wen-Yu Liu
- Biodiversity Research Center, Academia Sinica, 115 Taipei, Taiwan
| | - Chun-Ping Yu
- Biodiversity Research Center, Academia Sinica, 115 Taipei, Taiwan
| | - Shu-Hsing Wu
- Institute of Plant and Microbial Biology, Academia Sinica, 115 Taipei, Taiwan
| | - Maurice S B Ku
- Institute of Bioagricultural Science, National Chiayi University, 600 Chiayi, Taiwan.
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, 115 Taipei, Taiwan; Department of Ecology and Evolution, University of Chicago, Chicago 60637, USA.
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Guerreiro R, Bonthala VS, Schlüter U, Hoang NV, Triesch S, Schranz ME, Weber APM, Stich B. A genomic panel for studying C3-C4 intermediate photosynthesis in the Brassiceae tribe. PLANT, CELL & ENVIRONMENT 2023; 46:3611-3627. [PMID: 37431820 DOI: 10.1111/pce.14662] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/18/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023]
Abstract
Research on C4 and C3-C4 photosynthesis has attracted significant attention because the understanding of the genetic underpinnings of these traits will support the introduction of its characteristics into commercially relevant crop species. We used a panel of 19 taxa of 18 Brassiceae species with different photosynthesis characteristics (C3 and C3-C4) with the following objectives: (i) create draft genome assemblies and annotations, (ii) quantify orthology levels using synteny maps between all pairs of taxa, (iii) describe the phylogenetic relatedness across all the species, and (iv) track the evolution of C3-C4 intermediate photosynthesis in the Brassiceae tribe. Our results indicate that the draft de novo genome assemblies are of high quality and cover at least 90% of the gene space. Therewith we more than doubled the sampling depth of genomes of the Brassiceae tribe that comprises commercially important as well as biologically interesting species. The gene annotation generated high-quality gene models, and for most genes extensive upstream sequences are available for all taxa, yielding potential to explore variants in regulatory sequences. The genome-based phylogenetic tree of the Brassiceae contained two main clades and indicated that the C3-C4 intermediate photosynthesis has evolved five times independently. Furthermore, our study provides the first genomic support of the hypothesis that Diplotaxis muralis is a natural hybrid of D. tenuifolia and D. viminea. Altogether, the de novo genome assemblies and the annotations reported in this study are a valuable resource for research on the evolution of C3-C4 intermediate photosynthesis.
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Affiliation(s)
- Ricardo Guerreiro
- Institute of Quantitative Genetics and Genomics of Plants, Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
| | - Venkata Suresh Bonthala
- Institute of Quantitative Genetics and Genomics of Plants, Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
| | - Urte Schlüter
- Institute of Plant Biochemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Nam V Hoang
- Biosystematics Group, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Sebastian Triesch
- Institute of Plant Biochemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - M Eric Schranz
- Biosystematics Group, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Benjamin Stich
- Institute of Quantitative Genetics and Genomics of Plants, Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, Köln, Germany
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Paterlini A. A year at the forefront of plasmodesmal biology. Biol Open 2023; 12:bio060123. [PMID: 37874138 PMCID: PMC10618598 DOI: 10.1242/bio.060123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023] Open
Abstract
Cell-cell communication is a central feature of multicellular organisms, enabling division of labour and coordinated responses. Plasmodesmata are membrane-lined pores that provide regulated cytoplasmic continuity between plant cells, facilitating signalling and transport across neighboring cells. Plant development and survival profoundly depend on the existence and functioning of these structures, bringing them to the spotlight for both fundamental and applied research. Despite the rich conceptual and translational rewards in sight, however, the study of plasmodesmata poses significant challenges. This Review will mostly focus on research published between May 2022 and May 2023 and intends to provide a short overview of recent discoveries, innovations, community resources and hypotheses.
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Affiliation(s)
- Andrea Paterlini
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
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12
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Zhao W, Li J, Sun X, Zheng Q, Liu J, Hua W, Liu J. Integrated global analysis in spider flowers illuminates features underlying the evolution and maintenance of C 4 photosynthesis. HORTICULTURE RESEARCH 2023; 10:uhad129. [PMID: 37560018 PMCID: PMC10407600 DOI: 10.1093/hr/uhad129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/11/2023] [Indexed: 08/11/2023]
Abstract
The carbon concentrating mechanism-C4 photosynthesis-represents a classic example of convergent evolution, but how this important trait originated and evolved remains largely enigmatic. The spider flower Gynandropsis gynandra is a valuable leafy vegetable crop and medicinal plant that has also been recognized as a C4 model species. Here we present a high-quality chromosome-scale annotated genome assembly of G. gynandra through a combination of Oxford Nanopore Technology (ONT), HiFi and Hi-C technology. The 17 super-scaffolds cover 98.66% of the estimated genome (997.61 Mb), with a contig N50 of 11.43 Mb and a scaffold N50 of 51.02 Mb. Repetitive elements occupy up to 71.91% of its genome, and over half are long terminal repeat retrotransposons (LTR-RTs) derived from recent bursts, contributing to genome size expansion. Strikingly, LTR-RT explosion also played a critical role in C4 evolution by altering expression features of photosynthesis-associated genes via preferential insertion in promoters. Integrated multiomics analyses of G. gynandra and the ornamental horticulture C3 relative Tarenaya hassleriana reveal that species-specific whole-genome duplication, gene family expansion, recent LTR-RT amplification, and more recent tandem duplication events have all facilitated the evolution of C4 photosynthesis, revealing uniqueness of C4 evolution in the Cleome genus. Moreover, high leaf vein density and heat stress resilience are associated with shifted gene expression patterns. The mode of C3-to-C4 transition found here yields new insights into evolutionary convergence of a complex plant trait. The availability of this reference-grade genomic resource makes G. gynandra an ideal model system facilitating efforts toward C4-aimed crop engineering.
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Affiliation(s)
- Wei Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jun Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Xingchao Sun
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Qiwei Zheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jing Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Wei Hua
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jun Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
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Molla KA. A C4 orphan crop, Gynandropsis gynandra, joins the genome club. THE PLANT CELL 2023; 35:1288-1289. [PMID: 36794693 PMCID: PMC10118257 DOI: 10.1093/plcell/koad043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
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