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Jeon D, Kim C. Polyploids of Brassicaceae: Genomic Insights and Assembly Strategies. PLANTS (BASEL, SWITZERLAND) 2024; 13:2087. [PMID: 39124204 PMCID: PMC11314605 DOI: 10.3390/plants13152087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 07/24/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024]
Abstract
The Brassicaceae family is distinguished by its inclusion of high-value crops such as cabbage, broccoli, mustard, and wasabi, all noted for their glucosinolates. In this family, many polyploidy species are distributed and shaped by numerous whole-genome duplications, independent genome doublings, and hybridization events. The evolutionary trajectory of the family is marked by enhanced diversification and lineage splitting after paleo- and meso-polyploidization, with discernible remnants of whole-genome duplications within their genomes. The recent neopolyploidization events notably increased the proportion of polyploid species within the family. Although sequencing efforts for the Brassicaceae genome have been robust, accurately distinguishing sub-genomes remains a significant challenge, frequently complicating the assembly process. Assembly strategies include comparative analyses with ancestral species and examining k-mers, long terminal repeat retrotransposons, and pollen sequencing. This review comprehensively explores the unique genomic characteristics of the Brassicaceae family, with a particular emphasis on polyploidization events and the latest strategies for sequencing and assembly. This review will significantly improve our understanding of polyploidy in the Brassicaceae family and assist in future genome assembly methods.
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Affiliation(s)
- Donghyun Jeon
- Department of Science in Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea;
| | - Changsoo Kim
- Department of Science in Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea;
- Department of Crop Science, Chungnam National University, Daejeon 34134, Republic of Korea
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2
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Malhotra B, Kumar P, Bisht NC. Defense versus growth trade-offs: Insights from glucosinolates and their catabolites. PLANT, CELL & ENVIRONMENT 2023; 46:2964-2984. [PMID: 36207995 DOI: 10.1111/pce.14462] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/14/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Specialized metabolites are a structurally diverse group of naturally occurring compounds that facilitate plant-environment interactions. Their synthesis and maintenance in plants is overall a resource-demanding process that occurs at the expense of growth and reproduction and typically incurs several costs. Evidence emerging on different specialized compounds suggests that they serve multiple auxiliary functions to influence and moderate primary metabolism in plants. These new functionalities enable them to mediate trade-offs from defenses to growth and also to offset their production and maintenance costs in plants. Recent research on glucosinolates (GSLs), which are specialized metabolites of Brassicales, demonstrates their emerging multifunctionalities to fine-tune plant growth and development under variable environments. Herein, we present findings from the septennium on individual GSLs and their catabolites (GHPs) per se, that work as mobile signals within plants to mediate precise regulations of their primary physiological functions. Both GSLs and GHPs calibrate growth-defense trade-off interactions either synergistically or directly when they function as storage compounds, abiotic stress alleviators, and one-to-one regulators of growth pathways in plants. We finally summarize the overall lessons learned from GSLs and GHPs as a model and raise the most pressing questions to address the molecular-genetic intricacies of specialized metabolite-based trade-offs in plants.
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Affiliation(s)
- Bhanu Malhotra
- National Institute of Plant Genome Research, New Delhi, India
| | - Pawan Kumar
- National Institute of Plant Genome Research, New Delhi, India
| | - Naveen C Bisht
- National Institute of Plant Genome Research, New Delhi, India
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3
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Poh WH, Ruhazat NS, Yang LK, Shivhare D, Lim PK, Kanagasundaram Y, Rice SA, Mutwil M. Transcriptomic and metabolomic characterization of antibacterial activity of Melastoma dodecandrum. FRONTIERS IN PLANT SCIENCE 2023; 14:1205725. [PMID: 37771487 PMCID: PMC10525717 DOI: 10.3389/fpls.2023.1205725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/21/2023] [Indexed: 09/30/2023]
Abstract
Antibacterial resistance poses a significant global threat, necessitating the discovery of new therapeutic agents. Plants are a valuable source of secondary metabolites with demonstrated anticancer and antibacterial properties. In this study, we reveal that Melastoma dodecandrum exhibits both bacteriostatic and bactericidal effects against Pseudomonas aeruginosa and Staphylococcus aureus. Treatment with plant extracts results in membrane damage and a reduction in P.aeruginosa swimming and swarming motility. A comparative analysis of bacterial transcriptomes exposed to M.dodecandrum extracts and four distinct antibiotics indicates that the extracts may trigger similar transcriptomic responses as triclosan, a fatty acid synthesis inhibitor. Activity-guided fractionation suggests that the antibacterial activity is not attributable to hydrolyzable tannins, but to unidentified minor compounds. Additionally, we identified 104 specialized metabolic pathways and demonstrated a high level of transcriptional coordination between these biosynthetic pathways and phytohormones, highlighting potential regulatory mechanisms of antibacterial metabolites in M.dodecandrum.
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Affiliation(s)
- Wee Han Poh
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nur Syahirah Ruhazat
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lay Kien Yang
- Shared Analytics, Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Devendra Shivhare
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- AAVACC PTE LTD, Singapore, Singapore
| | - Peng Ken Lim
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yoganathan Kanagasundaram
- Shared Analytics, Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Scott A. Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Agriculture and Food, Microbiomes for One Systems Health, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT, Australia
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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4
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Wang W, Li X, Fan S, He Y, Wei M, Wang J, Yin Y, Liu Y. Combined genomic and transcriptomic analysis reveals the contribution of tandem duplication genes to low-temperature adaptation in perennial ryegrass. FRONTIERS IN PLANT SCIENCE 2023; 14:1216048. [PMID: 37502702 PMCID: PMC10368995 DOI: 10.3389/fpls.2023.1216048] [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: 05/03/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023]
Abstract
Perennial ryegrass (Lolium perenne L.) is an agronomically important cool-season grass species that is widely used as forage for ruminant animal production and cultivated in temperate regions for the establishment of lawns. However, the underlying genetic mechanism of the response of L. perenne to low temperature is still unclear. In the present study, we performed a comprehensive study and identified 3,770 tandem duplication genes (TDGs) in L. perenne, and evolutionary analysis revealed that L. perenne might have undergone a duplication event approximately 7.69 Mya. GO and KEGG pathway functional analyses revealed that these TDGs were mainly enriched in photosynthesis, hormone-mediated signaling pathways and responses to various stresses, suggesting that TDGs contribute to the environmental adaptability of L. perenne. In addition, the expression profile analysis revealed that the expression levels of TDGs were highly conserved and significantly lower than those of all genes in different tissues, while the frequency of differentially expressed genes (DEGs) from TDGs was much higher than that of DEGs from all genes in response to low-temperature stress. Finally, in-depth analysis of the important and expanded gene family indicated that the members of the ELIP subfamily could rapidly respond to low temperature and persistently maintain higher expression levels during all low temperature stress time points, suggesting that ELIPs most likely mediate low temperature responses and help to facilitate adaptation to low temperature in L. perenne. Our results provide evidence for the genetic underpinning of low-temperature adaptation and valuable resources for practical application and genetic improvement for stress resistance in L. perenne.
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Affiliation(s)
- Wei Wang
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Xiaoning Li
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Shugao Fan
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Yang He
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Meng Wei
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Jiayi Wang
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Yanling Yin
- School of Resources and Environmental Engineering, Ludong University, Yantai, China
| | - Yanfeng Liu
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, Yantai, China
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5
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Hoang NV, Sogbohossou EOD, Xiong W, Simpson CJC, Singh P, Walden N, van den Bergh E, Becker FFM, Li Z, Zhu XG, Brautigam A, Weber APM, van Haarst JC, Schijlen EGWM, Hendre PS, Van Deynze A, Achigan-Dako EG, Hibberd JM, Schranz ME. The Gynandropsis gynandra genome provides insights into whole-genome duplications and the evolution of C4 photosynthesis in Cleomaceae. THE PLANT CELL 2023; 35:1334-1359. [PMID: 36691724 PMCID: PMC10118270 DOI: 10.1093/plcell/koad018] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
Gynandropsis gynandra (Cleomaceae) is a cosmopolitan leafy vegetable and medicinal plant, which has also been used as a model to study C4 photosynthesis due to its evolutionary proximity to C3 Arabidopsis (Arabidopsis thaliana). Here, we present the genome sequence of G. gynandra, anchored onto 17 main pseudomolecules with a total length of 740 Mb, an N50 of 42 Mb and 30,933 well-supported gene models. The G. gynandra genome and previously released genomes of C3 relatives in the Cleomaceae and Brassicaceae make an excellent model for studying the role of genome evolution in the transition from C3 to C4 photosynthesis. Our analyses revealed that G. gynandra and its C3 relative Tarenaya hassleriana shared a whole-genome duplication event (Gg-α), then an addition of a third genome (Th-α, +1×) took place in T. hassleriana but not in G. gynandra. Analysis of syntenic copy number of C4 photosynthesis-related gene families indicates that G. gynandra generally retained more duplicated copies of these genes than C3T. hassleriana, and also that the G. gynandra C4 genes might have been under positive selection pressure. Both whole-genome and single-gene duplication were found to contribute to the expansion of the aforementioned gene families in G. gynandra. Collectively, this study enhances our understanding of the polyploidy history, gene duplication and retention, as well as their impact on the evolution of C4 photosynthesis in Cleomaceae.
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Affiliation(s)
| | | | - Wei Xiong
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Conor J C Simpson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Pallavi Singh
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Nora Walden
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Erik van den Bergh
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Frank F M Becker
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Zheng Li
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Xin-Guang Zhu
- State Key Laboratory for Plant Molecular Genetics, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Andrea Brautigam
- Faculty of Biology, Bielefeld University, 33501 Bielefeld, Germany
| | - Andreas P M Weber
- Cluster of Excellence on Plant Science (CEPLAS), Institute of Plant Biochemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Jan C van Haarst
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Elio G W M Schijlen
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Prasad S Hendre
- African Orphan Crops Consortium (AOCC), World Agroforestry (ICRAF), Nairobi 00100, Kenya
| | - Allen Van Deynze
- African Orphan Crops Consortium (AOCC), World Agroforestry (ICRAF), Nairobi 00100, Kenya
- Seed Biotechnology Center, University of California, Davis, California 95616, USA
| | - Enoch G Achigan-Dako
- Laboratory of Genetics, Biotechnology and Seed Science (GbioS), Faculty of Agronomic Sciences, University of Abomey-Calavi, BP 2549 Abomey-Calavi, Republic of Benin
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
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Yang M, Chen J, Liu T, Xiang L, Zhou BF. Genome-Wide Identification and Expression Analysis of Calmodulin-Like Gene Family in Paspalums vaginatium Revealed Their Role in Response to Salt and Cold Stress. Curr Issues Mol Biol 2023; 45:1693-1711. [PMID: 36826054 PMCID: PMC9954852 DOI: 10.3390/cimb45020109] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/05/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
The calmodulin-like (CML) family is an important calcium (Ca2+) sensor in plants and plays a pivotal role in the response to abiotic and biotic stresses. As one of the most salt-tolerant grass species, Paspalums vaginatum is resistant to multiple abiotic stresses, such as salt, cold, and drought. However, investigations of PvCML proteins in P. vaginatum have been limited. Based on the recently published P. vaginatum genome, we identified forty-nine PvCMLs and performed a comprehensive bioinformatics analysis of PvCMLs. The main results showed that the PvCMLs were unevenly distributed on all chromosomes and that the expansion of PvCMLs was shaped by tandem and segmental duplications. In addition, cis-acting element analysis, expression profiles, and qRT-PCR analysis revealed that PvCMLs were involved in the response to salt and cold stress. Most interestingly, we found evidence of a tandem gene cluster that independently evolved in P. vaginatum and may participate in cold resistance. In summary, our work provides important insight into how grass species are resistant to abiotic stresses such as salt and cold and could be the basis of further gene function research on CMLs in P. vaginatum.
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Affiliation(s)
- Meizhen Yang
- Guangdong Engineering Research Center for Grassland Science, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Jingjin Chen
- Guangdong Engineering Research Center for Grassland Science, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Tingting Liu
- Guangdong Engineering Research Center for Grassland Science, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Leilei Xiang
- Guangdong Engineering Research Center for Grassland Science, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Biao-Feng Zhou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Correspondence: ; Tel.: +86-17665141041
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7
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Hu X, Hao J, Pan L, Xu T, Ren L, Chen Y, Tang M, Liao L, Wang Z. Genome-wide analysis of tandem duplicated genes and their expression under salt stress in seashore paspalum. FRONTIERS IN PLANT SCIENCE 2022; 13:971999. [PMID: 36247543 PMCID: PMC9562133 DOI: 10.3389/fpls.2022.971999] [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: 06/17/2022] [Accepted: 08/25/2022] [Indexed: 06/16/2023]
Abstract
Seashore paspalum (Paspalum vaginatum) is a halophytic, warm-season grass which is closely related to various grain crops. Gene duplication plays an important role in plant evolution, conferring significant plant adaptation at the genomic level. Here, we identified 2,542 tandem duplicated genes (TDGs) in the P. vaginatum genome and estimated the divergence time of pairs of TDGs based on synonymous substitution rates (Ks). Expression of P. vaginatum TDGs resulted in enrichment in many GO terms and KEGG pathways when compared to four other closely-related species. The GO terms included: "ion transmembrane transporter activity," "anion transmembrane transporter activity" and "cation transmembrane transport," and KEGG pathways included "ABC transport." RNA-seq analysis of TDGs showed tissue-specific expression under salt stress, and we speculated that P. vaginatum leaves became adapted to salt stress in the earlier whole-genome duplication (WGD; ~83.3 million years ago; Ma), whereas the entire P. vaginatum plant acquired a large number of TDGs related to salt stress in the second WGD (~23.3 Ma). These results can be used as a reference resource to accelerate salt-resistance research in other grasses and crops.
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Affiliation(s)
- Xu Hu
- College of Tropical Crops, Hainan University, Haikou, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, China
| | - Jiangshan Hao
- College of Tropical Crops, Hainan University, Haikou, China
- School of Agriculture, Jinhua Polytechnic, Jinhua, China
| | - Ling Pan
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, China
| | - Tao Xu
- College of Tropical Crops, Hainan University, Haikou, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, China
| | - Longzhou Ren
- College of Tropical Crops, Hainan University, Haikou, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, China
| | - Yu Chen
- College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Minqiang Tang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, China
| | - Li Liao
- College of Tropical Crops, Hainan University, Haikou, China
| | - Zhiyong Wang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, China
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Angelovici R, Kliebenstein D. A plant balancing act: Meshing new and existing metabolic pathways towards an optimized system. CURRENT OPINION IN PLANT BIOLOGY 2022; 66:102173. [PMID: 35144143 DOI: 10.1016/j.pbi.2022.102173] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/17/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Specialized metabolic pathways evolve from existing pathways, creating new functionality potentially boosting fitness. However, how these pathways are integrated into a pre-existing working and well-balanced metabolic system is unclear. They could be integrated to the system as a functional appendage, or they could be fully embedded into primary metabolism by establishing new biochemical and regulatory connections. A full integration into the primary metabolic system requires substantial system re-wiring and because of this complexity, the latter is often not experimentally pursued. New studies provide evidence that some specialized metabolic pathways are fully embedded in primary metabolism with extensive new regulatory and biochemical connections. This suggests, that we should consider whether other specialized metabolic pathways could be fully integrated rather than being simple appendages. In this mini review, we survey compelling evidence supporting that some specialized metabolic pathways are fully integrated and ask if these metabolites now act as de-facto primary metabolites?
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Affiliation(s)
- Ruthie Angelovici
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
| | - Dan Kliebenstein
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA; DynaMo Center of Excellence, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark.
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9
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Zhou X, Liu Z. Unlocking plant metabolic diversity: A (pan)-genomic view. PLANT COMMUNICATIONS 2022; 3:100300. [PMID: 35529944 PMCID: PMC9073316 DOI: 10.1016/j.xplc.2022.100300] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/12/2021] [Accepted: 01/13/2022] [Indexed: 05/28/2023]
Abstract
Plants produce a remarkable diversity of structurally and functionally diverse natural chemicals that serve as adaptive compounds throughout their life cycles. However, unlocking this metabolic diversity is significantly impeded by the size, complexity, and abundant repetitive elements of typical plant genomes. As genome sequencing becomes routine, we anticipate that links between metabolic diversity and genetic variation will be strengthened. In addition, an ever-increasing number of plant genomes have revealed that biosynthetic gene clusters are not only a hallmark of microbes and fungi; gene clusters for various classes of compounds have also been found in plants, and many are associated with important agronomic traits. We present recent examples of plant metabolic diversification that have been discovered through the exploration and exploitation of various genomic and pan-genomic data. We also draw attention to the fundamental genomic and pan-genomic basis of plant chemodiversity and discuss challenges and future perspectives for investigating metabolic diversity in the coming pan-genomics era.
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Affiliation(s)
- Xuan Zhou
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhenhua Liu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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10
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Zhang T, Liu R, Zheng J, Wang Z, Gao T, Qin M, Hu X, Wang Y, Yang S, Li T. Insights into glucosinolate accumulation and metabolic pathways in Isatis indigotica Fort. BMC PLANT BIOLOGY 2022; 22:78. [PMID: 35193497 PMCID: PMC8862337 DOI: 10.1186/s12870-022-03455-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 02/03/2022] [Indexed: 05/19/2023]
Abstract
BACKGROUND Glucosinolates (GSLs) play important roles in defending against exogenous damage and regulating physiological activities in plants. However, GSL accumulation patterns and molecular regulation mechanisms are largely unknown in Isatis indigotica Fort. RESULTS Ten GSLs were identified in I. indigotica, and the dominant GSLs were epiprogoitrin (EPI) and indole-3-methyl GSL (I3M), followed by progoitrin (PRO) and gluconapin (GNA). The total GSL content was highest (over 20 μmol/g) in reproductive organs, lowest (less than 1.0 μmol/g) in mature organs, and medium in fresh leaves (2.6 μmol/g) and stems (1.5 μmol/g). In the seed germination process, the total GSL content decreased from 27.2 μmol/g (of seeds) to 2.7 μmol/g (on the 120th day) and then increased to 4.0 μmol/g (180th day). However, the content of indole GSL increased rapidly in the first week after germination and fluctuated between 1.13 μmol/g (28th day) and 2.82 μmol/g (150th day). Under the different elicitor treatments, the total GSL content increased significantly, ranging from 2.9-fold (mechanical damage, 3 h) to 10.7-fold (MeJA, 6 h). Moreover, 132 genes were involved in GSL metabolic pathways. Among them, no homologs of AtCYP79F2 and AtMAM3 were identified, leading to a distinctive GSL profile in I. indigotica. Furthermore, most genes involved in the GSL metabolic pathway were derived from tandem duplication, followed by dispersed duplication and segmental duplication. Purifying selection was observed, although some genes underwent relaxed selection. In addition, three tandem-arrayed GSL-OH genes showed different expression patterns, suggesting possible subfunctionalization during evolution. CONCLUSIONS Ten different GSLs with their accumulation patterns and 132 genes involved in the GSL metabolic pathway were explored, which laid a foundation for the study of GSL metabolism and regulatory mechanisms in I. indigotica.
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Affiliation(s)
- Tianyi Zhang
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, Xi'an, Shaanxi, 710119, People's Republic of China
| | - Rui Liu
- National Engineering Laboratory for Resources Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, 710119, People's Republic of China
| | - Jinyu Zheng
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, Xi'an, Shaanxi, 710119, People's Republic of China
| | - Zirong Wang
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, Xi'an, Shaanxi, 710119, People's Republic of China
| | - Tian'e Gao
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, Xi'an, Shaanxi, 710119, People's Republic of China
| | - Miaomiao Qin
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, Xi'an, Shaanxi, 710119, People's Republic of China
| | - Xiangyang Hu
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, Xi'an, Shaanxi, 710119, People's Republic of China
| | - Yuanyuan Wang
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, Xi'an, Shaanxi, 710119, People's Republic of China
| | - Shu Yang
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi'an, Shaanxi, 710000, People's Republic of China
| | - Tao Li
- Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), The Ministry of Education, Xi'an, Shaanxi, 710119, People's Republic of China.
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11
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Agrawal AA, Zhang X. The evolution of coevolution in the study of species interactions. Evolution 2021; 75:1594-1606. [PMID: 34166533 DOI: 10.1111/evo.14293] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/31/2021] [Accepted: 06/06/2021] [Indexed: 01/05/2023]
Abstract
The study of reciprocal adaptation in interacting species has been an active and inspiring area of evolutionary research for nearly 60 years. Perhaps owing to its great natural history and potential consequences spanning population divergence to species diversification, coevolution continues to capture the imagination of biologists. Here we trace developments following Ehrlich and Raven's classic paper, with a particular focus on the modern influence of two studies by Dr. May Berenbaum in the 1980s. This series of classic work presented a compelling example exhibiting the macroevolutionary patterns predicted by Ehrlich and Raven and also formalized a microevolutionary approach to measuring selection, functional traits, and understanding reciprocal adaptation between plants and their herbivores. Following this breakthrough was a wave of research focusing on diversifying macroevolutionary patterns, mechanistic chemical ecology, and natural selection on populations within and across community types. Accordingly, we breakdown coevolutionary theory into specific hypotheses at different scales: reciprocal adaptation between populations within a community, differential coevolution among communities, lineage divergence, and phylogenetic patterns. We highlight progress as well as persistent gaps, especially the link between reciprocal adaptation and diversification.
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Affiliation(s)
- Anurag A Agrawal
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853
| | - Xuening Zhang
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853
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12
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Neequaye M, Stavnstrup S, Harwood W, Lawrenson T, Hundleby P, Irwin J, Troncoso-Rey P, Saha S, Traka MH, Mithen R, Østergaard L. CRISPR-Cas9-Mediated Gene Editing of MYB28 Genes Impair Glucoraphanin Accumulation of Brassica oleracea in the Field. CRISPR J 2021; 4:416-426. [PMID: 34152214 DOI: 10.1089/crispr.2021.0007] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Discoveries in model plants grown under optimal conditions can provide important directions for crop improvement. However, it is important to verify whether results can be translated to crop plants grown in the field. In this study, we sought to study the role of MYB28 in the regulation of aliphatic glucosinolate (A-GSL) biosynthesis and associated sulfur metabolism in field-grown Brassica oleracea with the use of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 gene-editing technology. We describe the first myb28 knockout mutant in B. oleracea, and the first CRISPR field trial in the United Kingdom approved and regulated by the UK Department for Environment, Food & Rural Affairs after the reclassification of gene-edited crops as genetically modified organisms by the European Court of Justice on July 25, 2018. We report that knocking out myb28 results in downregulation of A-GSL biosynthesis genes and reduction in accumulation of the methionine-derived glucosinolate, glucoraphanin, in leaves and florets of field-grown myb28 mutant broccoli plants, whereas accumulation of sulfate, S-methyl cysteine sulfoxide, and indole glucosinolate in leaf and floret tissues remained unchanged. These results demonstrate the potential of gene-editing approaches to translate discoveries in fundamental biological processes for improved crop performance.
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Affiliation(s)
- Mikhaela Neequaye
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom and Norwich Research Park, Norwich, United Kingdom.,Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Sophia Stavnstrup
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom and Norwich Research Park, Norwich, United Kingdom
| | - Wendy Harwood
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom and Norwich Research Park, Norwich, United Kingdom
| | - Tom Lawrenson
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom and Norwich Research Park, Norwich, United Kingdom
| | - Penny Hundleby
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom and Norwich Research Park, Norwich, United Kingdom
| | - Judith Irwin
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom and Norwich Research Park, Norwich, United Kingdom
| | - Perla Troncoso-Rey
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Shikha Saha
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Maria H Traka
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Richard Mithen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Lars Østergaard
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom and Norwich Research Park, Norwich, United Kingdom
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13
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Agerbirk N, Hansen CC, Kiefer C, Hauser TP, Ørgaard M, Asmussen Lange CB, Cipollini D, Koch MA. Comparison of glucosinolate diversity in the crucifer tribe Cardamineae and the remaining order Brassicales highlights repetitive evolutionary loss and gain of biosynthetic steps. PHYTOCHEMISTRY 2021; 185:112668. [PMID: 33743499 DOI: 10.1016/j.phytochem.2021.112668] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 01/05/2021] [Accepted: 01/09/2021] [Indexed: 06/12/2023]
Abstract
We review glucosinolate (GSL) diversity and analyze phylogeny in the crucifer tribe Cardamineae as well as selected species from Brassicaceae (tribe Brassiceae) and Resedaceae. Some GSLs occur widely, while there is a scattered distribution of many less common GSLs, tentatively sorted into three classes: ancient, intermediate and more recently evolved. The number of conclusively identified GSLs in the tribe (53 GSLs) constitute 60% of all GSLs known with certainty from any plant (89 GSLs) and apparently unique GSLs in the tribe constitute 10 of those GSLs conclusively identified (19%). Intraspecific, qualitative GSL polymorphism is known from at least four species in the tribe. The most ancient GSL biosynthesis in Brassicales probably involved biosynthesis from Phe, Val, Leu, Ile and possibly Trp, and hydroxylation at the β-position. From a broad comparison of families in Brassicales and tribes in Brassicaceae, we estimate that a common ancestor of the tribe Cardamineae and the family Brassicaceae exhibited GSL biosynthesis from Phe, Val, Ile, Leu, possibly Tyr, Trp and homoPhe (ancient GSLs), as well as homologs of Met and possibly homoIle (intermediate age GSLs). From the comparison of phylogeny and GSL diversity, we also suggest that hydroxylation and subsequent methylation of indole GSLs and usual modifications of Met-derived GSLs (formation of sulfinyls, sulfonyls and alkenyls) occur due to conserved biochemical mechanisms and was present in a common ancestor of the family. Apparent loss of homologs of Met as biosynthetic precursors was deduced in the entire genus Barbarea and was frequent in Cardamine (e.g. C. pratensis, C. diphylla, C. concatenata, possibly C. amara). The loss was often associated with appearance of significant levels of unique or rare GSLs as well as recapitulation of ancient types of GSLs. Biosynthetic traits interpreted as de novo evolution included hydroxylation at rare positions, acylation at the thioglucose and use of dihomoIle and possibly homoIle as biosynthetic precursors. Biochemical aspects of the deduced evolution are discussed and testable hypotheses proposed. Biosyntheses from Val, Leu, Ile, Phe, Trp, homoPhe and homologs of Met are increasingly well understood, while GSL biosynthesis from mono- and dihomoIle is poorly understood. Overall, interpretation of known diversity suggests that evolution of GSL biosynthesis often seems to recapitulate ancient biosynthesis. In contrast, unprecedented GSL biosynthetic innovation seems to be rare.
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Affiliation(s)
- Niels Agerbirk
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
| | - Cecilie Cetti Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Christiane Kiefer
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies, Heidelberg University, 69120, Heidelberg, Germany
| | - Thure P Hauser
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Marian Ørgaard
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Conny Bruun Asmussen Lange
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Don Cipollini
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Highway, Dayton, OH, 45435, USA
| | - Marcus A Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies, Heidelberg University, 69120, Heidelberg, Germany
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14
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Wipf HML, Coleman-Derr D. Evaluating domestication and ploidy effects on the assembly of the wheat bacterial microbiome. PLoS One 2021; 16:e0248030. [PMID: 33735198 PMCID: PMC7971525 DOI: 10.1371/journal.pone.0248030] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/17/2021] [Indexed: 02/01/2023] Open
Abstract
While numerous studies implicate the microbiome in host fitness, contributions of host evolution to microbial recruitment remain largely uncharacterized. Past work has shown that plant polyploidy and domestication can influence plant biotic and abiotic interactions, yet impacts on broader microbiome assembly are still unknown for many crop species. In this study, we utilized three approaches-two field studies and one greenhouse-based experiment-to determine the degree to which patterns in bacterial community assembly in wheat (Triticum sp.) roots and rhizospheres are attributable to the host factors of ploidy level (2n, 4n, 6n) and domestication status (cultivated vs. wild). Profiling belowground bacterial communities with 16S rRNA gene amplicon sequencing, we analyzed patterns in diversity and composition. From our initial analyses of a subsetted dataset, we observed that host ploidy level was statistically significant in explaining variation in alpha and beta diversity for rhizosphere microbiomes, as well as correlated with distinct phylum-level shifts in composition, in the field. Using a reduced complexity field soil inoculum and controlled greenhouse conditions, we found some evidence suggesting that genomic lineage and ploidy level influence root alpha and beta diversity (p-value<0.05). However, in a follow-up field experiment using an expanded set of Triticum genomes that included both wild and domesticated varieties, we did not find a strong signal for either diploid genome lineages, domestication status, or ploidy level in shaping rhizosphere bacterial communities. Taken together, these results suggest that while host ploidy and domestication may have some minor influence on microbial assembly, these impacts are subtle and difficult to assess in belowground compartments for wheat varieties. By improving our understanding of the degree to which host ploidy and cultivation factors shape the plant microbiome, this research informs perspectives on what key driving forces may underlie microbiome structuring, as well as where future efforts may be best directed towards fortifying plant growth by microbial means. The greatest influence of the host on the wheat microbiome appeared to occur in the rhizosphere compartment, and we suggest that future work focuses on this environment to further characterize how host genomic and phenotypic changes influence plant-microbe communications.
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Affiliation(s)
- Heidi M. L. Wipf
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Plant Gene Expression Center, USDA-ARS, Albany, California, United States of America
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15
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Mitreiter S, Gigolashvili T. Regulation of glucosinolate biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:70-91. [PMID: 33313802 DOI: 10.1093/jxb/eraa479] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 05/18/2023]
Abstract
Glucosinolates are secondary defense metabolites produced by plants of the order Brassicales, which includes the model species Arabidopsis and many crop species. In the past 13 years, the regulation of glucosinolate synthesis in plants has been intensively studied, with recent research revealing complex molecular mechanisms that connect glucosinolate production with responses to other central pathways. In this review, we discuss how the regulation of glucosinolate biosynthesis is ecologically relevant for plants, how it is controlled by transcription factors, and how this transcriptional machinery interacts with hormonal, environmental, and epigenetic mechanisms. We present the central players in glucosinolate regulation, MYB and basic helix-loop-helix transcription factors, as well as the plant hormone jasmonate, which together with other hormones and environmental signals allow the coordinated and rapid regulation of glucosinolate genes. Furthermore, we highlight the regulatory connections between glucosinolates, auxin, and sulfur metabolism and discuss emerging insights and open questions on the regulation of glucosinolate biosynthesis.
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Affiliation(s)
- Simon Mitreiter
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Tamara Gigolashvili
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
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16
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Paszek J, Tiuryn J, Górecki P. Minimizing genomic duplication episodes. Comput Biol Chem 2020; 89:107260. [PMID: 33038778 DOI: 10.1016/j.compbiolchem.2020.107260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 04/02/2020] [Indexed: 11/17/2022]
Abstract
BACKGROUND The genomic duplication study is fundamental to understand the process of evolution. In evolutionary molecular biology, many approaches focus on discovering the occurrences of gene duplications and multiple gene duplication episodes and their locations in the Tree of Life. To reconstruct such episodes, one can cluster single gene duplications inferred by reconciling a set of gene trees with a species tree. RESULTS We propose an efficient quadratic time algorithm to solve the problem of genomic duplication clustering, in which input gene trees are rooted, episode locations are restricted to preserve the minimal number of single gene duplications, clustering rules are described by minimum episodes method, and the goal is based on the recently introduced new approach to minimize the maximal number of duplication episodes on a single path, called here the MP score. Based on our theoretical results, we show new algorithmic relationships between the MP score and the minimum episodes (ME) score, defined as the minimal number of duplication episodes. CONCLUSIONS Our evaluation analysis on three empirical datasets demonstrates, that under the model in which the minimal number of duplications is preserved, the duplication clusterings with minimal MP score support the clusterings with the minimal total number of duplication episodes. AVAILABILITY The software is available at https://bitbucket.org/pgor17/rmp.
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Affiliation(s)
- Jarosław Paszek
- Warsaw University, Faculty of Mathematics, Informatics and Mechanics, Banacha 2, 02-097 Warsaw, Poland.
| | - Jerzy Tiuryn
- Warsaw University, Faculty of Mathematics, Informatics and Mechanics, Banacha 2, 02-097 Warsaw, Poland.
| | - Paweł Górecki
- Warsaw University, Faculty of Mathematics, Informatics and Mechanics, Banacha 2, 02-097 Warsaw, Poland.
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17
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Yin L, Zhu Z, Luo X, Huang L, Li Y, Mason AS, Yang J, Ge X, Long Y, Wang J, Zou Q, Tao L, Kang Z, Tang R, Wang M, Fu S. Genome-Wide Duplication of Allotetraploid Brassica napus Produces Novel Characteristics and Extensive Ploidy Variation in Self-Pollinated Progeny. G3 (BETHESDA, MD.) 2020; 10:3687-3699. [PMID: 32753368 PMCID: PMC7534442 DOI: 10.1534/g3.120.401493] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/01/2020] [Indexed: 01/27/2023]
Abstract
Whole genome duplications (WGDs) have played a major role in angiosperm species evolution. Polyploid plants have undergone multiple cycles of ancient WGD events during their evolutionary history. However, little attention has been paid to the additional WGD of the existing allopolyploids. In this study, we explored the influences of additional WGD on the allopolyploid Brassica napus Compared to tetraploid B. napus, octoploid B. napus (AAAACCCC, 2n = 8x =76) showed significant differences in phenotype, reproductive ability and the ploidy of self-pollinated progeny. Genome duplication also altered a key reproductive organ feature in B. napus, that is, increased the number of pollen apertures. Unlike autopolyploids produced from the diploid Brassica species, the octoploid B. napus produced from allotetraploid B. napus had a relatively stable meiotic process, high pollen viability and moderate fertility under self-pollination conditions, indicating that sub-genomic interactions may be important for the successful establishment of higher-order polyploids. Doubling the genome of B. napus provided us with an opportunity to gain insight into the flexibility of the Brassica genomes. The genome size of self-pollinated progeny of octoploid B. napus varied greatly, and was accompanied by extensive genomic instability, such as aneuploidy, mixed-ploidy and mitotic abnormality. The octoploid B. napus could go through any of genome reduction, equilibrium or expansion in the short-term, thus providing a novel karyotype library for the Brassica genus. Our results reveal the short-term evolutionary consequences of recurrent polyploidization events, and help to deepen our understanding of polyploid plant evolution.
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Affiliation(s)
- Liqin Yin
- College of Life Sciences, Sichuan University, 29 Wangjiang Road, Chengdu, China
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Zhendong Zhu
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Xuan Luo
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
- Agricultural College, Sichuan Agricultural University, 211 Huimin Road, Chengdu, China
| | - Liangjun Huang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
- Agricultural College, Sichuan Agricultural University, 211 Huimin Road, Chengdu, China
| | - Yu Li
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Annaliese S Mason
- Plant Breeding Department, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35396 Giessen, Germany
| | - Jin Yang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yan Long
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, China
| | - Jisheng Wang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Qiong Zou
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Lanrong Tao
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Zeming Kang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Rong Tang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Maolin Wang
- College of Life Sciences, Sichuan University, 29 Wangjiang Road, Chengdu, China
| | - Shaohong Fu
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
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18
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Liu Z, Suarez Duran HG, Harnvanichvech Y, Stephenson MJ, Schranz ME, Nelson D, Medema MH, Osbourn A. Drivers of metabolic diversification: how dynamic genomic neighbourhoods generate new biosynthetic pathways in the Brassicaceae. THE NEW PHYTOLOGIST 2020; 227:1109-1123. [PMID: 31769874 PMCID: PMC7383575 DOI: 10.1111/nph.16338] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/17/2019] [Indexed: 05/11/2023]
Abstract
Plants produce an array of specialized metabolites with important ecological functions. The mechanisms underpinning the evolution of new biosynthetic pathways are not well-understood. Here, we exploit available genome sequence resources to investigate triterpene biosynthesis across the Brassicaceae. Oxidosqualene cyclases (OSCs) catalyze the first committed step in triterpene biosynthesis. Systematic analysis of 13 sequenced Brassicaceae genomes was performed to identify all OSC genes. The genome neighbourhoods (GNs) around a total of 163 OSC genes were investigated to identify Pfam domains significantly enriched in these regions. All-vs-all comparisons of OSC neighbourhoods and phylogenomic analysis were used to investigate the sequence similarity and evolutionary relationships of the numerous candidate triterpene biosynthetic gene clusters (BGCs) observed. Functional analysis of three representative BGCs was carried out and their triterpene pathway products were elucidated. Our results indicate that plant genomes are remarkably plastic, and that dynamic GNs generate new biosynthetic pathways in different Brassicaceae lineages by shuffling the genes encoding a core palette of triterpene-diversifying enzymes, presumably in response to strong environmental selection pressure. These results illuminate a genomic basis for diversification of plant-specialized metabolism through natural combinatorics of enzyme families, which can be mimicked using synthetic biology to engineer diverse bioactive molecules.
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Affiliation(s)
- Zhenhua Liu
- Department of Metabolic BiologyJohn Innes CentreNorwich Research Park, Colney LaneNorwichNR4 7UHUK
| | | | - Yosapol Harnvanichvech
- Bioinformatics GroupWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Michael J. Stephenson
- Department of Metabolic BiologyJohn Innes CentreNorwich Research Park, Colney LaneNorwichNR4 7UHUK
| | - M. Eric Schranz
- Biosystematics GroupWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - David Nelson
- Department of Microbiology, Immunology and BiochemistryUniversity of Tennessee858 Madison Avenue, Suite G01MemphisTN38163USA
| | - Marnix H. Medema
- Bioinformatics GroupWageningen UniversityDroevendaalsesteeg 16708PBWageningenthe Netherlands
| | - Anne Osbourn
- Department of Metabolic BiologyJohn Innes CentreNorwich Research Park, Colney LaneNorwichNR4 7UHUK
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Walden N, Nguyen TP, Mandáková T, Lysak MA, Schranz ME. Genomic Blocks in Aethionema arabicum Support Arabideae as Next Diverging Clade in Brassicaceae. FRONTIERS IN PLANT SCIENCE 2020; 11:719. [PMID: 32582250 PMCID: PMC7286309 DOI: 10.3389/fpls.2020.00719] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/06/2020] [Indexed: 05/22/2023]
Abstract
The tribe Aethionemeae is sister to all other crucifers, making it a crucial group for unraveling genome evolution and phylogenetic relationships within the crown group Brassicaceae. In this study, we extend the analysis of Brassicaceae genomic blocks (GBs) to Aethionema whereby we identified unique block boundaries shared only with the tribe Arabideae. This was achieved using bioinformatic methods to analyze synteny between the recently updated genome sequence of Aethionema arabicum and other high-quality Brassicaceae genome sequences. We show that compared to the largely conserved genomic structure of most non-polyploid Brassicaceae lineages, GBs are highly rearranged in Aethionema. Furthermore, we detected similarities between the genomes of Aethionema and Arabis alpina, in which also a high number of genomic rearrangements compared to those of other Brassicaceae was found. These similarities suggest that tribe Arabideae, a clade showing conflicting phylogenetic position between studies, may have diverged before diversification of the other major lineages, and highlight the potential of synteny information for phylogenetic inference.
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Affiliation(s)
- Nora Walden
- Biosystematics Group, Wageningen University, Wageningen, Netherlands
| | - Thu-Phuong Nguyen
- Biosystematics Group, Wageningen University, Wageningen, Netherlands
| | - Terezie Mandáková
- Central European Institute of Technology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Martin A. Lysak
- Central European Institute of Technology, Faculty of Science, Masaryk University, Brno, Czechia
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20
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Huang XC, German DA, Koch MA. Temporal patterns of diversification in Brassicaceae demonstrate decoupling of rate shifts and mesopolyploidization events. ANNALS OF BOTANY 2020; 125:29-47. [PMID: 31314080 PMCID: PMC6948214 DOI: 10.1093/aob/mcz123] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/16/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Whole-genome duplication (WGD) events are considered important driving forces of diversification. At least 11 out of 52 Brassicaceae tribes had independent mesopolyploid WGDs followed by diploidization processes. However, the association between mesopolyploidy and subsequent diversification is equivocal. Herein we show the results from a family-wide diversification analysis on Brassicaceae, and elaborate on the hypothesis that polyploidization per se is a fundamental driver in Brassicaceae evolution. METHODS We established a time-calibrated chronogram based on whole plastid genomes comprising representative Brassicaceae taxa and published data spanning the entire Rosidae clade. This allowed us to set multiple calibration points and anchored various Brassicaceae taxa for subsequent downstream analyses. All major splits among Brassicaceae lineages were used in BEAST analyses of 48 individually analysed tribes comprising 2101 taxa in total using the internal transcribed spacers of nuclear ribosomal DNA. Diversification patterns were investigated on these tribe-wide chronograms using BAMM and were compared with family-wide data on genome size variation and species richness. KEY RESULTS Brassicaceae diverged 29.9 million years ago (Mya) during the Oligocene, and the majority of tribes started diversification in the Miocene with an average crown group age of about 12.5 Mya. This matches the cooling phase right after the Mid Miocene climatic optimum. Significant rate shifts were detected in 12 out of 52 tribes during the Mio- and Pliocene, decoupled from preceding mesopolyploid WGDs. Among the various factors analysed, the combined effect of tribal crown group age and net diversification rate (speciation minus extinction) is likely to explain sufficiently species richness across Brassicaceae tribes. CONCLUSIONS The onset of the evolutionary splits among tribes took place under cooler and drier conditions. Pleistocene glacial cycles may have contributed to the maintenance of high diversification rates. Rate shifts are not consistently associated with mesopolyploid WGD. We propose, therefore, that WGDs in general serve as a constant 'pump' for continuous and high species diversification.
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Affiliation(s)
- Xiao-Chen Huang
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany
| | - Dmitry A German
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany
| | - Marcus A Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany
- For correspondence. E-mail
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21
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Abrahams RS, Pires JC, Schranz ME. Genomic Origin and Diversification of the Glucosinolate MAM Locus. FRONTIERS IN PLANT SCIENCE 2020; 11:711. [PMID: 32582245 PMCID: PMC7289053 DOI: 10.3389/fpls.2020.00711] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/05/2020] [Indexed: 05/06/2023]
Abstract
Glucosinolates are a diverse group of plant metabolites that characterize the order Brassicales. The MAM locus is one of the most significant QTLs for glucosinolate diversity. However, most of what we understand about evolution at the locus is focused on only a few species and not within a phylogenetic context. In this study, we utilize a micro-synteny network and phylogenetic inference to investigate the origin and diversification of the MAM/IPMS gene family. We uncover unique MAM-like genes found at the orthologous locus in the Cleomaceae that shed light on the transition from IPMS to MAM. In the Brassicaceae, we identify six distinct MAM clades across Lineages I, II, and III. We characterize the evolutionary impact and consequences of local duplications, transpositions, whole genome duplications, and gene fusion events, generating several new hypothesizes on the function and diversity of the MAM locus.
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Affiliation(s)
- R. Shawn Abrahams
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
- Biosystematics Group, Wageningen University, Wageningen, Netherlands
| | - J. Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - M. Eric Schranz
- Biosystematics Group, Wageningen University, Wageningen, Netherlands
- *Correspondence: M. Eric Schranz,
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22
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Genome Improvement and Genetic Map Construction for Aethionema arabicum, the First Divergent Branch in the Brassicaceae Family. G3-GENES GENOMES GENETICS 2019; 9:3521-3530. [PMID: 31554715 PMCID: PMC6829135 DOI: 10.1534/g3.119.400657] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The genus Aethionema is a sister-group to the core-group of the Brassicaceae family that includes Arabidopsis thaliana and the Brassica crops. Thus, Aethionema is phylogenetically well-placed for the investigation and understanding of genome and trait evolution across the family. We aimed to improve the quality of the reference genome draft version of the annual species Aethionema arabicum. Second, we constructed the first Ae. arabicum genetic map. The improved reference genome and genetic map enabled the development of each other. We started with the initially published genome (version 2.5). PacBio and MinION sequencing together with genetic map v2.5 were incorporated to produce the new reference genome v3.0. The improved genome contains 203 MB of sequence, with approximately 94% of the assembly made up of called (non-gap) bases, assembled into 2,883 scaffolds (with only 6% of the genome made up of non-called bases (Ns)). The N50 (10.3 MB) represents an 80-fold increase over the initial genome release. We generated a Recombinant Inbred Line (RIL) population that was derived from two ecotypes: Cyprus and Turkey (the reference genotype. Using a Genotyping by Sequencing (GBS) approach, we generated a high-density genetic map with 749 (v2.5) and then 632 SNPs (v3.0) was generated. The genetic map and reference genome were integrated, thus greatly improving the scaffolding of the reference genome into 11 linkage groups. We show that long-read sequencing data and genetics are complementary, resulting in an improved genome assembly in Ae. arabicum. They will facilitate comparative genetic mapping work for the Brassicaceae family and are also valuable resources to investigate wide range of life history traits in Aethionema.
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23
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Colle M, Leisner CP, Wai CM, Ou S, Bird KA, Wang J, Wisecaver JH, Yocca AE, Alger EI, Tang H, Xiong Z, Callow P, Ben-Zvi G, Brodt A, Baruch K, Swale T, Shiue L, Song GQ, Childs KL, Schilmiller A, Vorsa N, Buell CR, VanBuren R, Jiang N, Edger PP. Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry. Gigascience 2019; 8:5304886. [PMID: 30715294 PMCID: PMC6423372 DOI: 10.1093/gigascience/giz012] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 12/18/2018] [Accepted: 01/18/2019] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Highbush blueberry (Vaccinium corymbosum) has long been consumed for its unique flavor and composition of health-promoting phytonutrients. However, breeding efforts to improve fruit quality in blueberry have been greatly hampered by the lack of adequate genomic resources and a limited understanding of the underlying genetics encoding key traits. The genome of highbush blueberry has been particularly challenging to assemble due, in large part, to its polyploid nature and genome size. FINDINGS Here, we present a chromosome-scale and haplotype-phased genome assembly of the cultivar "Draper," which has the highest antioxidant levels among a diversity panel of 71 cultivars and 13 wild Vaccinium species. We leveraged this genome, combined with gene expression and metabolite data measured across fruit development, to identify candidate genes involved in the biosynthesis of important phytonutrients among other metabolites associated with superior fruit quality. Genome-wide analyses revealed that both polyploidy and tandem gene duplications modified various pathways involved in the biosynthesis of key phytonutrients. Furthermore, gene expression analyses hint at the presence of a spatial-temporal specific dominantly expressed subgenome including during fruit development. CONCLUSIONS These findings and the reference genome will serve as a valuable resource to guide future genome-enabled breeding of important agronomic traits in highbush blueberry.
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Affiliation(s)
- Marivi Colle
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.,MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI, 48824, USA
| | - Courtney P Leisner
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA
| | - Ching Man Wai
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
| | - Shujun Ou
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| | - Kevin A Bird
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| | - Jie Wang
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA.,Center for Genomics Enabled Plant Science, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA
| | - Jennifer H Wisecaver
- Department of Biochemistry, Purdue University, 175 South University Street, West Lafayette, IN, 47907, USA.,Purdue Center for Plant Biology, Purdue University, 610 Purdue Mall, West Lafayette, IN, 47907, USA
| | - Alan E Yocca
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.,Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA
| | - Elizabeth I Alger
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
| | - Haibao Tang
- Human Longevity Inc., 4570 Executive Drive, San Diego, CA 92121, USA
| | - Zhiyong Xiong
- Key Laboratory of Herbage and Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, 221 Aimin Road, Hohhot, 010070, China
| | - Pete Callow
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
| | - Gil Ben-Zvi
- NRGene, 5 Golda Meir Street, Ness Ziona, 7403648, Israel
| | - Avital Brodt
- NRGene, 5 Golda Meir Street, Ness Ziona, 7403648, Israel
| | - Kobi Baruch
- NRGene, 5 Golda Meir Street, Ness Ziona, 7403648, Israel
| | - Thomas Swale
- Dovetail Genomics, 100 Enterprise Way, Scotts Valley, CA, 95066, USA
| | - Lily Shiue
- Dovetail Genomics, 100 Enterprise Way, Scotts Valley, CA, 95066, USA
| | - Guo-Qing Song
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA.,Center for Genomics Enabled Plant Science, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA
| | - Anthony Schilmiller
- Mass Spectrometry & Metabolomics Core Facility, Michigan State University, 603 Wilson Road, East Lansing, MI, 48824, USA
| | - Nicholi Vorsa
- Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, NJ, 08901, USA.,Philip E. Marucci Center for Blueberry and Cranberry Research and Extension, Rutgers University, 125A Lake Oswego Road, Chatsworth, NJ, 08019, USA
| | - C Robin Buell
- MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI, 48824, USA.,Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA.,Plant Resilience Institute, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.,Plant Resilience Institute, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824 USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824, USA.,MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI, 48824, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, 293 Farm Lane, East Lansing, MI, 48824, USA
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24
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Ouassou M, Mukhaimar M, El Amrani A, Kroymann J, Chauveau O. [Biosynthesis of indole glucosinolates and ecological role of secondary modification pathways]. C R Biol 2019; 342:58-80. [PMID: 31088733 DOI: 10.1016/j.crvi.2019.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 11/26/2022]
Abstract
Indole glucosinolates are plant secondary metabolites derived from the amino acid tryptophan. They are part of a large group of sulfur-containing molecules almost exclusively found among Brassicales, which include the mustard family (Brassicaceae) with many edible plant species of major nutritional importance. These compounds mediate numerous interactions between these plants and their natural enemies and are therefore of major biological and economical interest. This literature review aims at taking stock of recent advances of our knowledge about the biosynthetic pathways of indole glucosinolates, but also about the defense strategies and ecological processes involving these metabolites.
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Affiliation(s)
- Malika Ouassou
- Unité « Écologie, systématique et évolution », UMR 8079, université Paris-Sud, CNRS, AgroParisTech, université Paris-Saclay, 91405 Orsay, France; Laboratory of Biochemistry and Molecular Genetics, Department of Biology, Faculty of Science and Technics, Abdelmalek Essaadi University, Tangier, Maroc
| | - Maisara Mukhaimar
- National Agricultural Research Center (NARC)-Jenin/Gaza, Ministry of Agriculture, Jenin, Palestine
| | - Amal El Amrani
- Laboratory of Biochemistry and Molecular Genetics, Department of Biology, Faculty of Science and Technics, Abdelmalek Essaadi University, Tangier, Maroc
| | - Juergen Kroymann
- Unité « Écologie, systématique et évolution », UMR 8079, université Paris-Sud, CNRS, AgroParisTech, université Paris-Saclay, 91405 Orsay, France
| | - Olivier Chauveau
- Unité « Écologie, systématique et évolution », UMR 8079, université Paris-Sud, CNRS, AgroParisTech, université Paris-Saclay, 91405 Orsay, France.
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25
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Okamura Y, Sato A, Tsuzuki N, Sawada Y, Hirai MY, Heidel-Fischer H, Reichelt M, Murakami M, Vogel H. Differential regulation of host plant adaptive genes in Pieris butterflies exposed to a range of glucosinolate profiles in their host plants. Sci Rep 2019; 9:7256. [PMID: 31076616 PMCID: PMC6510735 DOI: 10.1038/s41598-019-43703-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/27/2019] [Indexed: 11/15/2022] Open
Abstract
Specialist herbivores have often evolved highly sophisticated mechanisms to counteract defenses mediated by major plant secondary-metabolites. Plant species of the herbivore host range often display high chemical diversity and it is not well understood how specialist herbivores respond to this chemical diversity. Pieris larvae overcome toxic products from glucosinolate hydrolysis, the major chemical defense of their Brassicaceae hosts, by expressing nitrile-specifier proteins (NSP) in their gut. Furthermore, Pieris butterflies possess so-called major allergen (MA) proteins, which are multi-domain variants of a single domain major allergen (SDMA) protein expressed in the guts of Lepidopteran larvae. Here we show that Pieris larvae fine-tune NSP and MA gene expression depending on the glucosinolate profiles of their Brassicaceae hosts. Although the role of MA is not yet fully understood, the expression levels of NSP and MA in larvae that fed on plants whose glucosinolate composition varied was dramatically changed, whereas levels of SDMA expression remained unchanged. In addition, we found a similar regulation pattern among these genes in larvae feeding on Arabidopsis mutants with different glucosinolate profiles. Our results demonstrate that Pieris larvae appear to use different host plant adaptive genes to overcome a wide range of glucosinolate profiles in their host plants.
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Affiliation(s)
- Yu Okamura
- Community Ecology Lab., Faculty of Science, Chiba University, 263-8522, Chiba, Japan.
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany.
| | - Ai Sato
- Community Ecology Lab., Faculty of Science, Chiba University, 263-8522, Chiba, Japan
| | - Natsumi Tsuzuki
- Community Ecology Lab., Faculty of Science, Chiba University, 263-8522, Chiba, Japan
| | - Yuji Sawada
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Hanna Heidel-Fischer
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI), Beutenberg-Str. 11a, 07745, Jena, Germany
| | - Michael Reichelt
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany
| | - Masashi Murakami
- Community Ecology Lab., Faculty of Science, Chiba University, 263-8522, Chiba, Japan
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany
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26
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Barco B, Clay NK. Evolution of Glucosinolate Diversity via Whole-Genome Duplications, Gene Rearrangements, and Substrate Promiscuity. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:585-604. [PMID: 31035830 DOI: 10.1146/annurev-arplant-050718-100152] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Over several decades, glucosinolates have become a model system for the study of specialized metabolic diversity in plants. The near-complete identification of biosynthetic enzymes, regulators, and transporters has provided support for the role of gene duplication and subsequent changes in gene expression, protein function, and substrate specificity as the evolutionary bases of glucosinolate diversity. Here, we provide examples of how whole-genome duplications, gene rearrangements, and substrate promiscuity potentiated the evolution of glucosinolate biosynthetic enzymes, regulators, and transporters by natural selection. This in turn may have led to the repeated evolution of glucosinolate metabolism and diversity in higher plants.
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Affiliation(s)
- Brenden Barco
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, Connecticut 06511, USA; ,
| | - Nicole K Clay
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, Connecticut 06511, USA; ,
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27
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Abstract
Specialized metabolites are critical for plant–environment interactions, e.g., attracting pollinators or defending against herbivores, and are important sources of plant-based pharmaceuticals. However, it is unclear what proportion of enzyme-encoding genes play a role in specialized metabolism (SM) as opposed to general metabolism (GM) in any plant species. This is because of the diversity of specialized metabolites and the considerable number of incompletely characterized pathways responsible for their production. In addition, SM gene ancestors frequently played roles in GM. We evaluate features distinguishing SM and GM genes and build a computational model that accurately predicts SM genes. Our predictions provide candidates for experimental studies, and our modeling approach can be applied to other species that produce medicinally or industrially useful compounds. Plant specialized metabolism (SM) enzymes produce lineage-specific metabolites with important ecological, evolutionary, and biotechnological implications. Using Arabidopsis thaliana as a model, we identified distinguishing characteristics of SM and GM (general metabolism, traditionally referred to as primary metabolism) genes through a detailed study of features including duplication pattern, sequence conservation, transcription, protein domain content, and gene network properties. Analysis of multiple sets of benchmark genes revealed that SM genes tend to be tandemly duplicated, coexpressed with their paralogs, narrowly expressed at lower levels, less conserved, and less well connected in gene networks relative to GM genes. Although the values of each of these features significantly differed between SM and GM genes, any single feature was ineffective at predicting SM from GM genes. Using machine learning methods to integrate all features, a prediction model was established with a true positive rate of 87% and a true negative rate of 71%. In addition, 86% of known SM genes not used to create the machine learning model were predicted. We also demonstrated that the model could be further improved when we distinguished between SM, GM, and junction genes responsible for reactions shared by SM and GM pathways, indicating that topological considerations may further improve the SM prediction model. Application of the prediction model led to the identification of 1,220 A. thaliana genes with previously unknown functions, each assigned a confidence measure called an SM score, providing a global estimate of SM gene content in a plant genome.
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28
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Edger PP, VanBuren R, Colle M, Poorten TJ, Wai CM, Niederhuth CE, Alger EI, Ou S, Acharya CB, Wang J, Callow P, McKain MR, Shi J, Collier C, Xiong Z, Mower JP, Slovin JP, Hytönen T, Jiang N, Childs KL, Knapp SJ. Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity. Gigascience 2018; 7:1-7. [PMID: 29253147 PMCID: PMC5801600 DOI: 10.1093/gigascience/gix124] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/30/2017] [Indexed: 12/18/2022] Open
Abstract
Background Although draft genomes are available for most agronomically important plant species, the majority are incomplete, highly fragmented, and often riddled with assembly and scaffolding errors. These assembly issues hinder advances in tool development for functional genomics and systems biology. Findings Here we utilized a robust, cost-effective approach to produce high-quality reference genomes. We report a near-complete genome of diploid woodland strawberry (Fragaria vesca) using single-molecule real-time sequencing from Pacific Biosciences (PacBio). This assembly has a contig N50 length of ∼7.9 million base pairs (Mb), representing a ∼300-fold improvement of the previous version. The vast majority (>99.8%) of the assembly was anchored to 7 pseudomolecules using 2 sets of optical maps from Bionano Genomics. We obtained ∼24.96 Mb of sequence not present in the previous version of the F. vesca genome and produced an improved annotation that includes 1496 new genes. Comparative syntenic analyses uncovered numerous, large-scale scaffolding errors present in each chromosome in the previously published version of the F. vesca genome. Conclusions Our results highlight the need to improve existing short-read based reference genomes. Furthermore, we demonstrate how genome quality impacts commonly used analyses for addressing both fundamental and applied biological questions.
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Affiliation(s)
- Patrick P Edger
- Department of Horticulture, Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823.,Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823
| | - Robert VanBuren
- Department of Horticulture, Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823
| | - Marivi Colle
- Department of Horticulture, Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823
| | - Thomas J Poorten
- Department of Plant Sciences, University of California - Davis, Davis, California, 95616
| | - Ching Man Wai
- Department of Horticulture, Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823
| | - Chad E Niederhuth
- Department of Genetics, University of Georgia, Athens, Georgia, 30602
| | - Elizabeth I Alger
- Department of Horticulture, Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823
| | - Shujun Ou
- Department of Horticulture, Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823.,Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823
| | - Charlotte B Acharya
- Department of Plant Sciences, University of California - Davis, Davis, California, 95616
| | - Jie Wang
- Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823
| | - Pete Callow
- Department of Horticulture, Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823
| | - Michael R McKain
- Donald Danforth Plant Science Center, St. Louis, Missouri, 63132
| | - Jinghua Shi
- Bionano Genomics, San Diego, California, 92121
| | | | - Zhiyong Xiong
- Potato Engineering and Technology Research Center, Inner Mongolia University, Hohhot, 010021, China
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska, 68588
| | - Janet P Slovin
- USDA/ARS, Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville, Maryland, 20705
| | - Timo Hytönen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
| | - Ning Jiang
- Department of Horticulture, Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823.,Ecology, Evolutionary Biology, and Behavior, Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823
| | - Kevin L Childs
- Department of Plant Biology, and Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823.,Center for Genomics Enabled Plant Science, Michigan State University, East Lansing, Michigan, 48823
| | - Steven J Knapp
- Department of Plant Sciences, University of California - Davis, Davis, California, 95616
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29
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Pelot KA, Chen R, Hagelthorn DM, Young CA, Addison JB, Muchlinski A, Tholl D, Zerbe P. Functional Diversity of Diterpene Synthases in the Biofuel Crop Switchgrass. PLANT PHYSIOLOGY 2018; 178:54-71. [PMID: 30008447 PMCID: PMC6130043 DOI: 10.1104/pp.18.00590] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/05/2018] [Indexed: 05/06/2023]
Abstract
Diterpenoids constitute a diverse class of metabolites with critical functions in plant development, defense, and ecological adaptation. Major monocot crops, such as maize (Zea mays) and rice (Oryza sativa), deploy diverse blends of specialized diterpenoids as core components of biotic and abiotic stress resilience. Here, we describe the genome-wide identification and functional characterization of stress-related diterpene synthases (diTPSs) in the dedicated bioenergy crop switchgrass (Panicum virgatum). Mining of the allotetraploid switchgrass genome identified an expansive diTPS family of 31 members, and biochemical analysis of 11 diTPSs revealed a modular metabolic network producing a diverse array of diterpenoid metabolites. In addition to ent-copalyl diphosphate (CPP) and ent-kaurene synthases predictably involved in gibberellin biosynthesis, we identified syn-CPP and ent-labda-13-en-8-ol diphosphate (LPP) synthases as well as two diTPSs forming (+)-labda-8,13E-dienyl diphosphate (8,13-CPP) and ent-neo-cis-trans-clerodienyl diphosphate (CT-CLPP) scaffolds not observed previously in plants. Structure-guided mutagenesis of the (+)-8,13-CPP and ent-neo-CT-CLPP synthases revealed residue substitutions in the active sites that altered product outcome, representing potential neofunctionalization events that occurred during diversification of the switchgrass diTPS family. The conversion of ent-CPP, ent-LPP, syn-CPP, and ent-neo-CT-CLPP by promiscuous diTPSs further yielded distinct labdane-type diterpene olefins and alcohols. Of these metabolites, the formation of 9β-hydroxy-syn-pimar-15-ene and the expression of the corresponding genes were induced in roots and leaves in response to oxidative stress and ultraviolet irradiation, indicating their possible roles in abiotic stress adaptation. Together, these findings expand the known chemical space of diterpenoid metabolism in monocot crops toward systematically investigating and ultimately improving stress resilience traits in crop species.
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Affiliation(s)
- Kyle A Pelot
- Department of Plant Biology, University of California, Davis, California 95616
| | - Ruibing Chen
- Department of Plant Biology, University of California, Davis, California 95616
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, 200433 Shanghai, China
| | - David M Hagelthorn
- Department of Plant Biology, University of California, Davis, California 95616
| | - Cari A Young
- Department of Plant Biology, University of California, Davis, California 95616
| | - J Bennett Addison
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, California 92182
| | - Andrew Muchlinski
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061
| | - Dorothea Tholl
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061
| | - Philipp Zerbe
- Department of Plant Biology, University of California, Davis, California 95616
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30
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Annotation of the Corymbia terpene synthase gene family shows broad conservation but dynamic evolution of physical clusters relative to Eucalyptus. Heredity (Edinb) 2018. [PMID: 29523839 DOI: 10.1038/s41437-018-0058-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Terpenes are economically and ecologically important phytochemicals. Their synthesis is controlled by the terpene synthase (TPS) gene family, which is highly diversified throughout the plant kingdom. The plant family Myrtaceae are characterised by especially high terpene concentrations, and considerable variation in terpene profiles. Many Myrtaceae are grown commercially for terpene products including the eucalypts Corymbia and Eucalyptus. Eucalyptus grandis has the largest TPS gene family of plants currently sequenced, which is largely conserved in the closely related E. globulus. However, the TPS gene family has been well studied only in these two eucalypt species. The recent assembly of two Corymbia citriodora subsp. variegata genomes presents an opportunity to examine the conservation of this important gene family across more divergent eucalypt lineages. Manual annotation of the TPS gene family in C. citriodora subsp. variegata revealed a similar overall number, and relative subfamily representation, to that previously reported in E. grandis and E. globulus. Many of the TPS genes were in physical clusters that varied considerably between Eucalyptus and Corymbia, with several instances of translocation, expansion/contraction and loss. Notably, there was greater conservation in the subfamilies involved in primary metabolism than those involved in secondary metabolism, likely reflecting different selective constraints. The variation in cluster size within subfamilies and the broad conservation between the eucalypts in the face of this variation are discussed, highlighting the potential contribution of selection, concerted evolution and stochastic processes. These findings provide the foundation to better understand terpene evolution within the ecologically and economically important Myrtaceae.
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31
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Edger PP, Hall JC, Harkess A, Tang M, Coombs J, Mohammadin S, Schranz ME, Xiong Z, Leebens-Mack J, Meyers BC, Sytsma KJ, Koch MA, Al-Shehbaz IA, Pires JC. Brassicales phylogeny inferred from 72 plastid genes: A reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses. AMERICAN JOURNAL OF BOTANY 2018; 105:463-469. [PMID: 29574686 DOI: 10.1002/ajb2.1040] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/06/2017] [Indexed: 05/10/2023]
Abstract
PREMISE OF THE STUDY Previous phylogenetic studies employing molecular markers have yielded various insights into the evolutionary history across Brassicales, but many relationships between families remain poorly supported or unresolved. A recent phylotranscriptomic approach utilizing 1155 nuclear markers obtained robust estimates for relationships among 14 of 17 families. Here we report a complete family-level phylogeny estimated using the plastid genome. METHODS We conducted phylogenetic analyses on a concatenated data set comprising 44,926 bp from 72 plastid genes for species distributed across all 17 families. Our analysis includes three additional families, Tovariaceae, Salvadoraceae, and Setchellanthaceae, that were omitted in the previous phylotranscriptomic study. KEY RESULTS Our phylogenetic analyses obtained fully resolved and strongly supported estimates for all nodes across Brassicales. Importantly, these findings are congruent with the topology reported in the phylotranscriptomic study. This consistency suggests that future studies could utilize plastid genomes as markers for resolving relationships within some notoriously difficult clades across Brassicales. We used this new phylogenetic framework to verify the placement of the At-α event near the origin of Brassicaceae, with median date estimates of 31.8 to 42.8 million years ago and restrict the At-β event to one of two nodes with median date estimates between 85 to 92.2 million years ago. These events ultimately gave rise to novel chemical defenses and are associated with subsequent shifts in net diversification rates. CONCLUSIONS We anticipate that these findings will aid future comparative evolutionary studies across Brassicales, including selecting candidates for whole-genome sequencing projects.
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Affiliation(s)
- Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, Michigan, 48864, USA
- Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, 48864, USA
| | - Jocelyn C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Alex Harkess
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
| | - Michelle Tang
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Jill Coombs
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Setareh Mohammadin
- Biosystematics, Plant Science Group, Wageningen University and Research, Wageningen, Netherlands
| | - M Eric Schranz
- Biosystematics, Plant Science Group, Wageningen University and Research, Wageningen, Netherlands
| | - Zhiyong Xiong
- Potato Engineering & Technology Research Center, Inner Mongolia University, Hohhot, China
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
| | - Kenneth J Sytsma
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
| | - Marcus A Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | | | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
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32
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Rehman HM, Nawaz MA, Shah ZH, Ludwig-Müller J, Chung G, Ahmad MQ, Yang SH, Lee SI. Comparative genomic and transcriptomic analyses of Family-1 UDP glycosyltransferase in three Brassica species and Arabidopsis indicates stress-responsive regulation. Sci Rep 2018; 8:1875. [PMID: 29382843 PMCID: PMC5789830 DOI: 10.1038/s41598-018-19535-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 01/03/2018] [Indexed: 12/25/2022] Open
Abstract
In plants, UGTs (UDP-glycosyltransferases) glycosylate various phytohormones and metabolites in response to biotic and abiotic stresses. Little is known about stress-responsive glycosyltransferases in plants. Therefore, it is important to understand the genomic and transcriptomic portfolio of plants with regard to biotic and abiotic stresses. Here, we identified 140, 154, and 251 putative UGTs in Brassica rapa, Brassica oleracea, and Brassica napus, respectively, and clustered them into 14 major phylogenetic groups (A–N). Fourteen major KEGG pathways and 24 biological processes were associated with the UGTs, highlighting them as unique modulators against environmental stimuli. Putative UGTs from B. rapa and B. oleracea showed a negative selection pressure and biased gene fractionation pattern during their evolution. Polyploidization increased the intron proportion and number of UGT-containing introns among Brassica. The putative UGTs were preferentially expressed in developing tissues and at the senescence stage. Differential expression of up- and down-regulated UGTs in response to phytohormone treatments, pathogen responsiveness and abiotic stresses, inferred from microarray and RNA-Seq data in Arabidopsis and Brassica broaden the glycosylation impact at the molecular level. This study identifies unique candidate UGTs for the manipulation of biotic and abiotic stress pathways in Brassica and Arabidopsis.
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Affiliation(s)
- Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Korea
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Korea
| | - Zahid Hussain Shah
- Department of Arid Land Agriculture, King Abdul-Aziz University, Jeddah, Saudi Arabia
| | - Jutta Ludwig-Müller
- Institut für Botanik, Technische Universität Dresden, 01062, Dresden, Germany
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Korea
| | - Muhammad Qadir Ahmad
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, 6000, Pakistan
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Korea.
| | - Soo In Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Jeonju, 54874, Republic of Korea.
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33
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De Smet R, Sabaghian E, Li Z, Saeys Y, Van de Peer Y. Coordinated Functional Divergence of Genes after Genome Duplication in Arabidopsis thaliana. THE PLANT CELL 2017; 29:2786-2800. [PMID: 29070508 PMCID: PMC5728133 DOI: 10.1105/tpc.17.00531] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/10/2017] [Accepted: 10/25/2017] [Indexed: 05/21/2023]
Abstract
Gene and genome duplications have been rampant during the evolution of flowering plants. Unlike small-scale gene duplications, whole-genome duplications (WGDs) copy entire pathways or networks, and as such create the unique situation in which such duplicated pathways or networks could evolve novel functionality through the coordinated sub- or neofunctionalization of its constituent genes. Here, we describe a remarkable case of coordinated gene expression divergence following WGDs in Arabidopsis thaliana We identified a set of 92 homoeologous gene pairs that all show a similar pattern of tissue-specific gene expression divergence following WGD, with one homoeolog showing predominant expression in aerial tissues and the other homoeolog showing biased expression in tip-growth tissues. We provide evidence that this pattern of gene expression divergence seems to involve genes with a role in cell polarity and that likely function in the maintenance of cell wall integrity. Following WGD, many of these duplicated genes evolved separate functions through subfunctionalization in growth/development and stress response. Uncoupling these processes through genome duplications likely provided important adaptations with respect to growth and morphogenesis and defense against biotic and abiotic stress.
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Affiliation(s)
- Riet De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Ehsan Sabaghian
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Yvan Saeys
- Center for Inflammation Research, VIB, B-9052 Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, B-9052 Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, B-9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium
- Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
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34
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Moghe GD, Leong BJ, Hurney SM, Daniel Jones A, Last RL. Evolutionary routes to biochemical innovation revealed by integrative analysis of a plant-defense related specialized metabolic pathway. eLife 2017; 6:28468. [PMID: 28853706 PMCID: PMC5595436 DOI: 10.7554/elife.28468] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/25/2017] [Indexed: 12/22/2022] Open
Abstract
The diversity of life on Earth is a result of continual innovations in molecular networks influencing morphology and physiology. Plant specialized metabolism produces hundreds of thousands of compounds, offering striking examples of these innovations. To understand how this novelty is generated, we investigated the evolution of the Solanaceae family-specific, trichome-localized acylsugar biosynthetic pathway using a combination of mass spectrometry, RNA-seq, enzyme assays, RNAi and phylogenomics in different non-model species. Our results reveal hundreds of acylsugars produced across the Solanaceae family and even within a single plant, built on simple sugar cores. The relatively short biosynthetic pathway experienced repeated cycles of innovation over the last 100 million years that include gene duplication and divergence, gene loss, evolution of substrate preference and promiscuity. This study provides mechanistic insights into the emergence of plant chemical novelty, and offers a template for investigating the ~300,000 non-model plant species that remain underexplored. There are about 300,000 species of plant on Earth, which together produce over a million different small molecules called metabolites. Plants use many of these molecules to grow, to communicate with each other or to defend themselves against pests and disease. Humans have co-opted many of the same molecules as well; for example, some are important nutrients while others are active ingredients in medicines. Many plant metabolites are found in almost all plants, but hundreds of thousands of them are more specialized and only found in small groups of related plant species. These specialized metabolites have a wide variety of structures, and are made by different enzymes working together to carry out a series of biochemical reactions. Acylsugars are an example of a group of specialized metabolites with particularly diverse structures. These small molecules are restricted to plants in the Solanaceae family, which includes tomato and tobacco plants. Moghe et al. have now focused on acylsugars to better understand how plants produce the large diversity of chemical structures found in specialized metabolites, and how these processes have evolved over time. An analysis of over 35 plant species from across the Solanaceae family revealed hundreds of acylsugars, with some plants accumulating 300 or more different types of these specialized metabolites. Moghe et al. then looked at the enzymes that make acylsugars from a poorly studied flowering plant called Salpiglossis sinuata, partly because it produces a large diversity of these small molecules and partly because it sits in a unique position in the Solanaceae family tree. The activities of the enzymes were confirmed both in test tubes and in plants. This suggested that many of the enzymes were “promiscuous”, meaning that they could likely use a variety of molecules as starting points for their chemical reactions. This finding could help to explain how this plant species can make such a wide variety of acylsugars. Moghe et al. also discovered that many of the enzymes that make acylsugars are encoded by genes that were originally copies of other genes and that have subsequently evolved new activities. Plant scientists and plant breeders value tomato plants that produce acylsugars because these natural chemicals protect against pests like whiteflies and spider mites. A clearer understanding of the diversity of acylsugars in the Solanaceae family, as well as the enzymes that make these specialized metabolites, could help efforts to breed crops that are more resistant to pests. Some of the enzymes related to those involved in acylsugar production could also help to make chemicals with pharmaceutical value. These new findings might also eventually lead to innovative ways to produce these chemicals on a large scale.
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Affiliation(s)
- Gaurav D Moghe
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States
| | - Bryan J Leong
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Department of Plant Biology, Michigan State University, East Lansing, United States
| | - Steven M Hurney
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Department of Chemistry, Michigan State University, East Lansing, United States
| | - A Daniel Jones
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Department of Chemistry, Michigan State University, East Lansing, United States
| | - Robert L Last
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Department of Plant Biology, Michigan State University, East Lansing, United States
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35
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Gianoglio S, Moglia A, Acquadro A, Comino C, Portis E. The genome-wide identification and transcriptional levels of DNA methyltransferases and demethylases in globe artichoke. PLoS One 2017; 12:e0181669. [PMID: 28746368 PMCID: PMC5529103 DOI: 10.1371/journal.pone.0181669] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/05/2017] [Indexed: 11/19/2022] Open
Abstract
Changes to the cytosine methylation status of DNA, driven by the activity of C5 methyltransferases (C5-MTases) and demethylases, exert an important influence over development, transposon movement, gene expression and imprinting. Three groups of C5-MTase enzymes have been identified in plants, namely MET (methyltransferase 1), CMT (chromomethyltransferases) and DRM (domains rearranged methyltransferases). Here the repertoire of genes encoding C5-MTase and demethylase by the globe artichoke (Cynara cardunculus var. scolymus) is described, based on sequence homology, a phylogenetic analysis and a characterization of their functional domains. A total of ten genes encoding C5-MTase (one MET, five CMTs and four DRMs) and five demethylases was identified. An analysis of their predicted product's protein structure suggested an extensive level of conservation has been retained by the C5-MTases. Transcriptional profiling based on quantitative real time PCR revealed a number of differences between the genes encoding maintenance and de novo methyltransferases, sometimes in a tissue- or development-dependent manner, which implied a degree of functional specialization.
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Affiliation(s)
- Silvia Gianoglio
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
| | - Andrea Moglia
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
| | - Cinzia Comino
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
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36
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Mohammadin S, Nguyen TP, van Weij MS, Reichelt M, Schranz ME. Flowering Locus C (FLC) Is a Potential Major Regulator of Glucosinolate Content across Developmental Stages of Aethionema arabicum (Brassicaceae). FRONTIERS IN PLANT SCIENCE 2017; 8:876. [PMID: 28603537 PMCID: PMC5445170 DOI: 10.3389/fpls.2017.00876] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/10/2017] [Indexed: 05/08/2023]
Abstract
The biochemical defense of plants can change during their life-cycle and impact herbivore feeding and plant fitness. The annual species Aethionema arabicum is part of the sister clade to all other Brassicaceae. Hence, it holds a phylogenetically important position for studying crucifer trait evolution. Glucosinolates (GS) are essentially Brassicales-specific metabolites involved in plant defense. Using two Ae. arabicum accessions (TUR and CYP) we identify substantial differences in glucosinolate profiles and quantities between lines, tissues and developmental stages. We find tissue specific side-chain modifications in aliphatic GS: methylthioalkyl in leaves, methylsulfinylalkyl in fruits, and methylsulfonylalkyl in seeds. We also find large differences in absolute glucosinolate content between the two accessions (up to 10-fold in fruits) that suggest a regulatory factor is involved that is not part of the quintessential glucosinolate biosynthetic pathway. Consistent with this hypothesis, we identified a single major multi-trait quantitative trait locus controlling total GS concentration across tissues in a recombinant inbred line population derived from TUR and CYP. With fine-mapping, we narrowed the interval to a 58 kb region containing 15 genes, but lacking any known GS biosynthetic genes. The interval contains homologs of both the sulfate transporter SULTR2;1 and FLOWERING LOCUS C. Both loci have diverse functions controlling plant physiological and developmental processes and thus are potential candidates regulating glucosinolate variation across the life-cycle of Aethionema. Future work will investigate changes in gene expression of the candidates genes, the effects of GS variation on insect herbivores and the trade-offs between defense and reproduction.
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Affiliation(s)
- Setareh Mohammadin
- Biosystematics, Plant Sciences Group, Wageningen University and ResearchWageningen, Netherlands
| | - Thu-Phuong Nguyen
- Biosystematics, Plant Sciences Group, Wageningen University and ResearchWageningen, Netherlands
| | - Marco S. van Weij
- Biosystematics, Plant Sciences Group, Wageningen University and ResearchWageningen, Netherlands
| | - Michael Reichelt
- Department of Biochemistry, Max Planck Institute for Chemical EcologyJena, Germany
| | - Michael E. Schranz
- Biosystematics, Plant Sciences Group, Wageningen University and ResearchWageningen, Netherlands
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37
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Nikolov LA, Tsiantis M. Using mustard genomes to explore the genetic basis of evolutionary change. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:119-128. [PMID: 28285128 DOI: 10.1016/j.pbi.2017.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 02/16/2017] [Accepted: 02/21/2017] [Indexed: 06/06/2023]
Abstract
Recent advances in sequencing technologies and gene manipulation tools have driven mustard species into the spotlight of comparative research and have offered powerful insight how phenotypic space is explored during evolution. Evidence emerged for genome-wide signal of transcription factors and gene duplication contributing to trait divergence, e.g., PLETHORA5/7 in leaf complexity. Trait divergence is often manifested in differential expression due to cis-regulatory divergence, as in KNOX genes and REDUCED COMPLEXITY, and can be coupled with protein divergence. Fruit shape in Capsella rubella results from anisotropic growth during three distinct phases. Brassicaceae exhibit novel fruit dispersal strategy, explosive pod shatter, where the rapid movement depends on slow build-up of tension and its rapid release facilitated by asymmetric cell wall thickenings.
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Affiliation(s)
- Lachezar A Nikolov
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Miltos Tsiantis
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany.
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38
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Olsen CE, Huang XC, Hansen CIC, Cipollini D, Ørgaard M, Matthes A, Geu-Flores F, Koch MA, Agerbirk N. Glucosinolate diversity within a phylogenetic framework of the tribe Cardamineae (Brassicaceae) unraveled with HPLC-MS/MS and NMR-based analytical distinction of 70 desulfoglucosinolates. PHYTOCHEMISTRY 2016; 132:33-56. [PMID: 27743600 DOI: 10.1016/j.phytochem.2016.09.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 08/29/2016] [Accepted: 09/29/2016] [Indexed: 05/22/2023]
Abstract
As a basis for future investigations of evolutionary trajectories and biosynthetic mechanisms underlying variations in glucosinolate structures, we screened members of the crucifer tribe Cardamineae by HPLC-MS/MS, isolated and identified glucosinolates by NMR, searched the literature for previous data for the tribe, and collected HPLC-MS/MS data for nearly all glucosinolates known from the tribe as well as some related structures (70 in total). This is a considerable proportion of the approximately 142 currently documented natural glucosinolates. Calibration with authentic references allowed distinction (or elucidation) of isomers in many cases, such as distinction of β-hydroxyls, methylthios, methylsulfinyls and methylsulfonyls. A mechanism for fragmentation of secondary β-hydroxyls in MS was elucidated, and two novel glucosinolates were discovered: 2-hydroxy-3-methylpentylglucosinolate in roots of Cardamine pratensis and 2-hydroxy-8-(methylsulfinyl)octylglucosinolate in seeds of Rorippa amphibia. A large number of glucosinolates (ca. 54 with high structural certainty and a further 28 or more suggested from tandem MS), representing a wide structural variation, is documented from the tribe. This included glucosinolates apparently derived from Met, Phe, Trp, Val/Leu, Ile and higher homologues. Normal side chain elongation and side chain decoration by oxidation or methylation was observed, as well as rare abnormal side chain decoration (hydroxylation of aliphatics at the δ rather than β-position). Some species had diverse profiles, e.g. R. amphibia and C. pratensis (19 and 16 individual glucosinolates, respectively), comparable to total diversity in literature reports of Armoracia rusticana (17?), Barbarea vulgaris (20-24), and Rorippa indica (>20?). The ancestor or the tribe would appear to have used Trp, Met, and homoPhe as glucosinolate precursor amino acids, and to exhibit oxidation of thio to sulfinyl, formation of alkenyls, β-hydroxylation of aliphatic chains and hydroxylation and methylation of indole glucosinolates. Two hotspots of apparent biochemical innovation and loss were identified: C. pratensis and the genus Barbarea. Diversity in other species mainly included structures also known from other crucifers. In addition to a role of gene duplication, two contrasting genetic/biochemical mechanisms for evolution of such combined diversity and redundancy are discussed: (i) involvement of widespread genes with expression varying during evolution, and (ii) mutational changes in substrate specificities of CYP79F and GS-OH enzymes.
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Affiliation(s)
- Carl Erik Olsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Xiao-Chen Huang
- Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Cecilie I C Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Don Cipollini
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Highway, Dayton, OH 45435, USA
| | - Marian Ørgaard
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Annemarie Matthes
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Fernando Geu-Flores
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Marcus A Koch
- Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Niels Agerbirk
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark; Copenhagen Plant Science Center, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark.
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39
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The pangenome of an agronomically important crop plant Brassica oleracea. Nat Commun 2016; 7:13390. [PMID: 27834372 PMCID: PMC5114598 DOI: 10.1038/ncomms13390] [Citation(s) in RCA: 251] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 09/28/2016] [Indexed: 02/07/2023] Open
Abstract
There is an increasing awareness that as a result of structural variation, a reference sequence representing a genome of a single individual is unable to capture all of the gene repertoire found in the species. A large number of genes affected by presence/absence and copy number variation suggest that it may contribute to phenotypic and agronomic trait diversity. Here we show by analysis of the Brassica oleracea pangenome that nearly 20% of genes are affected by presence/absence variation. Several genes displaying presence/absence variation are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis. Brassica oleracea is a single species that includes diverse crops such as cabbage, broccoli and Brussels sprouts. Here, the authors identify genes not captured in existing B. oleracea reference genomes by the assembly of a pangenome and show variations in gene content that may be related to important agronomic traits
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40
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Zhou W, Brockmöller T, Ling Z, Omdahl A, Baldwin IT, Xu S. Evolution of herbivore-induced early defense signaling was shaped by genome-wide duplications in Nicotiana. eLife 2016; 5:e19531. [PMID: 27813478 PMCID: PMC5115867 DOI: 10.7554/elife.19531] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 11/01/2016] [Indexed: 01/01/2023] Open
Abstract
Herbivore-induced defenses are widespread, rapidly evolving and relevant for plant fitness. Such induced defenses are often mediated by early defense signaling (EDS) rapidly activated by the perception of herbivore associated elicitors (HAE) that includes transient accumulations of jasmonic acid (JA). Analyzing 60 HAE-induced leaf transcriptomes from closely-related Nicotiana species revealed a key gene co-expression network (M4 module) which is co-activated with the HAE-induced JA accumulations but is elicited independently of JA, as revealed in plants silenced in JA signaling. Functional annotations of the M4 module were consistent with roles in EDS and a newly identified hub gene of the M4 module (NaLRRK1) mediates a negative feedback loop with JA signaling. Phylogenomic analysis revealed preferential gene retention after genome-wide duplications shaped the evolution of HAE-induced EDS in Nicotiana. These results highlight the importance of genome-wide duplications in the evolution of adaptive traits in plants.
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Affiliation(s)
- Wenwu Zhou
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Thomas Brockmöller
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Zhihao Ling
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Ashton Omdahl
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
- Brigham Young University, Provo, United States
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Shuqing Xu
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
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41
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Gupta M, Atri C, Agarwal N, Banga SS. Development and molecular-genetic characterization of a stable Brassica allohexaploid. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:2085-2100. [PMID: 27480156 DOI: 10.1007/s00122-016-2759-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 07/22/2016] [Indexed: 05/18/2023]
Abstract
We report first-time synthesis of a stable Brassica allohexaploid. It may evolve into a new species and also advance our understanding of pairing regulation and genome evolution in complex allopolyploids. Crop Brassicas include both monogenomic and digenomic species. A trigenomic Brassica (AABBCC) is not known to exist in nature. Past attempts to synthesize a stable allohexaploid were not successful due to aberrant meiosis and very high proportion of aneuploid plants in the selfed progenies. We report the development of a stable allohexaploid Brassica (2n = 54; AABBCC). Genomic in situ hybridization confirmed the complete assemblage of three genomes. Only allohexaploids involving B. rapa cv. R01 (2n = 20; AA) as pollinator with a set of B. carinata (2n = 34; BBCC) were stable. These exhibited a high proportion (0.78-0.94) of pollen mother cells with normal meiosis and an excellent hexaploid ratio (0.80-0.94) in the selfed progenies. Stability of two allohexaploid combinations was demonstrated from H1 to H4 generations at two very diverse locations in India. Graphical genotyping of allohexaploids allowed detection of chromosome fragment exchanges among three genomes. These were much smaller for meiotically stable allohexaploids as compared to unstable ones. The putative hexaploids were morphologically closer to the female donor, B. carinata, for leaf morphology, inflorescence structure and flower shape. The newly formed allohexaploid may also provide unique opportunities to investigate the immediate genetic and genomic consequences of a Brassica allohexaploid with three resident genomes.
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Affiliation(s)
- Mehak Gupta
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, India
| | - Chhaya Atri
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, India
| | - Neha Agarwal
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, India
| | - Surinder Singh Banga
- DBT Centre of Excellence on Brassicas, Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, India.
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Moglia A, Acquadro A, Eljounaidi K, Milani AM, Cagliero C, Rubiolo P, Genre A, Cankar K, Beekwilder J, Comino C. Genome-Wide Identification of BAHD Acyltransferases and In vivo Characterization of HQT-like Enzymes Involved in Caffeoylquinic Acid Synthesis in Globe Artichoke. FRONTIERS IN PLANT SCIENCE 2016; 7:1424. [PMID: 27721818 PMCID: PMC5033976 DOI: 10.3389/fpls.2016.01424] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 09/07/2016] [Indexed: 05/25/2023]
Abstract
Globe artichoke (Cynara cardunculus L. var. scolymus) is a rich source of compounds promoting human health (phytonutrients), among them caffeoylquinic acids (CQAs), mainly represented by chlorogenic acid (CGA), and dicaffeoylquinic acids (diCQAs). The enzymes involved in their biosynthesis belong to the large family of BAHD acyltransferases. Following a survey of the globe artichoke genome, we identified 69 BAHD proteins carrying the catalytic site (HXXXD). Their phylogenetic analysis together with another 43 proteins, from 21 species, representative of the BAHD family, highlighted their grouping in seven major clades. Nine globe artichoke acyltransferases clustered in a sub-group of Clade V, with 3 belonging to hydroxycinnamoyl-CoA:quinate hydroxycinnamoyl transferase (HQT) and 2 to hydroxycinnamoyl-CoA:shikimate/quinate hydroxycinnamoyl transferase (HCT) like proteins. We focused our attention on the former, HQT1, HQT2, and HQT3, as they are known to play a key role in CGA biosynthesis. The expression of genes coding for the three HQTs and correlation of expression with the CQA content is reported for different globe artichoke tissues. For the first time in the globe artichoke, we developed and applied the virus-induced gene silencing approach with the goal of assessing in vivo the effect of HQT1 silencing, which resulted in a marked reduction of both CGA and diCQAs. On the other hand, when the role of the three HQTs was assessed in leaves of Nicotiana benthamiana through their transient overexpression, significant increases in mono- and diCQAs content were observed. Using transient GFP fusion proteins expressed in N. benthamiana leaves we also established the sub-cellular localization of these three enzymes.
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Affiliation(s)
- Andrea Moglia
- Department of Agricultural, Forest and Food Sciences, University of TorinoGrugliasco, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences, University of TorinoGrugliasco, Italy
| | - Kaouthar Eljounaidi
- Department of Agricultural, Forest and Food Sciences, University of TorinoGrugliasco, Italy
| | - Anna M. Milani
- Department of Agricultural, Forest and Food Sciences, University of TorinoGrugliasco, Italy
| | - Cecilia Cagliero
- Department of Drug Science and Technology, University of TorinoTorino, Italy
| | - Patrizia Rubiolo
- Department of Drug Science and Technology, University of TorinoTorino, Italy
| | - Andrea Genre
- Department of Life Sciences and Systems Biology, University of TorinoTorino, Italy
| | | | | | - Cinzia Comino
- Department of Agricultural, Forest and Food Sciences, University of TorinoGrugliasco, Italy
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Franzke A, Koch MA, Mummenhoff K. Turnip Time Travels: Age Estimates in Brassicaceae. TRENDS IN PLANT SCIENCE 2016; 21:554-561. [PMID: 26917156 DOI: 10.1016/j.tplants.2016.01.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/19/2016] [Accepted: 01/31/2016] [Indexed: 05/07/2023]
Abstract
Results of research in life sciences acquire a deeper meaning if they can also be discussed in temporal contexts of evolution. Despite the importance of the mustard family (Brassicaceae) as a prominent angiosperm model family, a robust, generally accepted hypothesis for a family-wide temporal framework does not yet exist. The main cause for this situation is a poor fossil record of the family. We suggest that the few known fossils require a critical re-evaluation of phylogenetic and temporal assignments as a prerequisite for appropriate molecular dating analyses within the family. In addition, (palaeo)biogeographical calibrations, not explored so far in the family, should be integrated in a synthesis of various dating approaches, with each contributing their specific possibilities and limitations.
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Affiliation(s)
- Andreas Franzke
- Heidelberg Botanic Garden, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany.
| | - Marcus A Koch
- Heidelberg Botanic Garden, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, Germany; Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, D-69120 Heidelberg, German
| | - Klaus Mummenhoff
- Biology Department, Botany, Osnabrück University, D-49069 Osnabrück, Germany
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van den Bergh E, Hofberger JA, Schranz ME. Flower power and the mustard bomb: Comparative analysis of gene and genome duplications in glucosinolate biosynthetic pathway evolution in Cleomaceae and Brassicaceae. AMERICAN JOURNAL OF BOTANY 2016; 103:1212-22. [PMID: 27313198 DOI: 10.3732/ajb.1500445] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 04/04/2016] [Indexed: 05/08/2023]
Abstract
PREMISE OF THE STUDY Glucosinolates (GS) are a class of plant secondary metabolites that provide defense against herbivores and may play an important role in pollinator attraction. Through coevolution with plant-interacting organisms, glucosinolates have diversified into a variety of chemotypes through gene sub- and neofunctionalization. Polyploidy has been of major importance in the evolutionary history of these gene families and the development of chemically separate GS types. Here we study the effects of polyploidy in Tarenaya hassleriana (Cleomaceae) on the genes underlying GS biosynthesis. METHODS We established putative orthologs of all gene families involved in GS biosynthesis through sequence comparison and their duplication method through calculation of synonymous substitution ratios, phylogenetic gene trees, and synteny comparison. We drew expression data from previously published work of the identified genes and compared expression in several tissues. KEY RESULTS We show that the majority of gene family expansion in T. hassleriana has taken place through the retention of polyploid duplicates, together with tandem and transpositional duplicates. We also show that the large majority (>75%) is actively expressed either globally or in specific tissues. We show that MAM and CYP83 gene families, which are crucial to GS diversification in Brassicaceae, are also recruited into specific tissue expression pathways in Cleomaceae. CONCLUSIONS Many GS genes have expanded through polyploidy, gene transposition duplication, and tandem duplication in Cleomaceae. Duplicate retention through these mechanisms is similar to A. thaliana, but based on the expression of GS genes, Cleomaceae-specific diversification of GS genes has taken place.
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Affiliation(s)
- Erik van den Bergh
- Biosystematics Group, Wageningen University & Research Center, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Johannes A Hofberger
- Biosystematics Group, Wageningen University & Research Center, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands Big Data Analytics, Detecon Co., Ltd., 100600 Beijing, PR China
| | - M Eric Schranz
- Biosystematics Group, Wageningen University & Research Center, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
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Lachowiec J, Queitsch C, Kliebenstein DJ. Molecular mechanisms governing differential robustness of development and environmental responses in plants. ANNALS OF BOTANY 2016; 117:795-809. [PMID: 26473020 PMCID: PMC4845800 DOI: 10.1093/aob/mcv151] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 07/08/2015] [Accepted: 08/25/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND Robustness to genetic and environmental perturbation is a salient feature of multicellular organisms. Loss of developmental robustness can lead to severe phenotypic defects and fitness loss. However, perfect robustness, i.e. no variation at all, is evolutionarily unfit as organisms must be able to change phenotype to properly respond to changing environments and biotic challenges. Plasticity is the ability to adjust phenotypes predictably in response to specific environmental stimuli, which can be considered a transient shift allowing an organism to move from one robust phenotypic state to another. Plants, as sessile organisms that undergo continuous development, are particularly dependent on an exquisite fine-tuning of the processes that balance robustness and plasticity to maximize fitness. SCOPE AND CONCLUSIONS This paper reviews recently identified mechanisms, both systems-level and molecular, that modulate robustness, and discusses their implications for the optimization of plant fitness. Robustness in living systems arises from the structure of genetic networks, the specific molecular functions of the underlying genes, and their interactions. This very same network responsible for the robustness of specific developmental states also has to be built such that it enables plastic yet robust shifts in response to environmental changes. In plants, the interactions and functions of signal transduction pathways activated by phytohormones and the tendency for plants to tolerate whole-genome duplications, tandem gene duplication and hybridization are emerging as major regulators of robustness in development. Despite their obvious implications for plant evolution and plant breeding, the mechanistic underpinnings by which plants modulate precise levels of robustness, plasticity and evolvability in networks controlling different phenotypes are under-studied.
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Affiliation(s)
- Jennifer Lachowiec
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48197, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, WA 98155, USA
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA and DynaMo Center of Excellence, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
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Biogeography and diversification of Brassicales: A 103million year tale. Mol Phylogenet Evol 2016; 99:204-224. [PMID: 26993763 DOI: 10.1016/j.ympev.2016.02.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 02/24/2016] [Accepted: 02/25/2016] [Indexed: 11/23/2022]
Abstract
Brassicales is a diverse order perhaps most famous because it houses Brassicaceae and, its premier member, Arabidopsis thaliana. This widely distributed and species-rich lineage has been overlooked as a promising system to investigate patterns of disjunct distributions and diversification rates. We analyzed plastid and mitochondrial sequence data from five gene regions (>8000bp) across 151 taxa to: (1) produce a chronogram for major lineages in Brassicales, including Brassicaceae and Arabidopsis, based on greater taxon sampling across the order and previously overlooked fossil evidence, (2) examine biogeographical ancestral range estimations and disjunct distributions in BioGeoBEARS, and (3) determine where shifts in species diversification occur using BAMM. The evolution and radiation of the Brassicales began 103Mya and was linked to a series of inter-continental vicariant, long-distance dispersal, and land bridge migration events. North America appears to be a significant area for early stem lineages in the order. Shifts to Australia then African are evident at nodes near the core Brassicales, which diverged 68.5Mya (HPD=75.6-62.0). This estimated age combined with fossil evidence, indicates that some New World clades embedded amongst Old World relatives (e.g., New World capparoids) are the result of different long distance dispersal events, whereas others may be best explained by land bridge migration (e.g., Forchhammeria). Based on these analyses, the Brassicaceae crown group diverged in Europe/Northern Africa in the Eocene, circa 43.4Mya (HPD=46.6-40.3) and Arabidopsis separated from close congeners circa 10.4Mya. These ages fall between divergent dates that were previously published, suggesting we are slowly converging on a robust age estimate for the family. Three significant shifts in species diversification are observed in the order: (1) 58Mya at the crown of Capparaceae, Cleomaceae and Brassicaceae, (2) 38Mya at the crown of Resedaceae+Stixis clade, and (3) 21Mya at the crown of the tribes Brassiceae and Sisymbrieae within Brassicaceae.
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47
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Scossa F, Brotman Y, de Abreu E Lima F, Willmitzer L, Nikoloski Z, Tohge T, Fernie AR. Genomics-based strategies for the use of natural variation in the improvement of crop metabolism. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:47-64. [PMID: 26566824 DOI: 10.1016/j.plantsci.2015.05.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/29/2015] [Accepted: 05/31/2015] [Indexed: 05/08/2023]
Abstract
Next-generation genomics holds great potential in the study of plant phenotypic variation. With several crop reference genomes now available, the affordable costs of de novo genome assembly or target resequencing offer the opportunity to mine the enormous amount of genetic diversity hidden in crop wild relatives. Wide introgressions from these wild ancestors species or land races represent a possible strategy to improve cultivated varieties. In this review, we discuss the mechanisms underlying metabolic diversity within plant species and the possible strategies (and barriers) to introgress novel metabolic traits into cultivated varieties. We show how deep genomic surveys uncover various types of structural variants from extended gene pools of major crops and highlight how this variation may be used for the improvement of crop metabolism.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany; Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per la Frutticoltura, Via di Fioranello 52, 00134 Rome, Italy.
| | - Yariv Brotman
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | | | - Lothar Willmitzer
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Zoran Nikoloski
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam, Germany.
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Fuchs R, Kopischke M, Klapprodt C, Hause G, Meyer AJ, Schwarzländer M, Fricker MD, Lipka V. Immobilized Subpopulations of Leaf Epidermal Mitochondria Mediate PENETRATION2-Dependent Pathogen Entry Control in Arabidopsis. THE PLANT CELL 2016; 28:130-45. [PMID: 26721862 PMCID: PMC4746686 DOI: 10.1105/tpc.15.00887] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/30/2015] [Indexed: 05/05/2023]
Abstract
The atypical myrosinase PENETRATION2 (PEN2) is required for broad-spectrum invasion resistance to filamentous plant pathogens. Previous localization studies suggested PEN2-GFP association with peroxisomes. Here, we show that PEN2 is a tail-anchored protein with dual-membrane targeting to peroxisomes and mitochondria and that PEN2 has the capacity to form homo-oligomer complexes. We demonstrate pathogen-induced recruitment and immobilization of mitochondrial subpopulations at sites of attempted fungal invasion and show that mitochondrial arrest is accompanied by peripheral accumulation of GFP-tagged PEN2. PEN2 substrate production by the cytochrome P450 monooxygenase CYP81F2 is localized to the surface of the endoplasmic reticulum, which focally reorganizes close to the immobilized mitochondria. Exclusive targeting of PEN2 to the outer membrane of mitochondria complements the pen2 mutant phenotype, corroborating the functional importance of the mitochondrial PEN2 protein subpool for controlled local production of PEN2 hydrolysis products at subcellular plant-microbe interaction domains. Moreover, live-cell imaging shows that mitochondria arrested at these domains exhibit a pathogen-induced redox imbalance, which may lead to the production of intracellular signals.
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Affiliation(s)
- Rene Fuchs
- Department of Plant Cell Biology, Albrecht-von-Haller-Institute, Georg-August-University Göttingen, 37077 Göttingen, Germany The Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom
| | - Michaela Kopischke
- Department of Plant Cell Biology, Albrecht-von-Haller-Institute, Georg-August-University Göttingen, 37077 Göttingen, Germany The Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom
| | - Christine Klapprodt
- Department of Plant Cell Biology, Albrecht-von-Haller-Institute, Georg-August-University Göttingen, 37077 Göttingen, Germany The Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom
| | - Gerd Hause
- Martin-Luther-Universität Halle-Wittenberg, Universitätsbiozentrum, 06120 Halle, Germany
| | - Andreas J Meyer
- University of Bonn, INRES-Chemical Signalling, 53113 Bonn, Germany
| | | | - Mark D Fricker
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Volker Lipka
- Department of Plant Cell Biology, Albrecht-von-Haller-Institute, Georg-August-University Göttingen, 37077 Göttingen, Germany The Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom
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Tang H, Bomhoff MD, Briones E, Zhang L, Schnable JC, Lyons E. SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand. Genome Biol Evol 2015; 7:3286-98. [PMID: 26560340 PMCID: PMC4700967 DOI: 10.1093/gbe/evv219] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The identification of conserved syntenic regions enables discovery of predicted
locations for orthologous and homeologous genes, even when no such gene is present.
This capability means that synteny-based methods are far more effective than sequence
similarity-based methods in identifying true-negatives, a necessity for studying gene
loss and gene transposition. However, the identification of syntenic regions requires
complex analyses which must be repeated for pairwise comparisons between any two
species. Therefore, as the number of published genomes increases, there is a growing
demand for scalable, simple-to-use applications to perform comparative genomic
analyses that cater to both gene family studies and genome-scale studies. We
implemented SynFind, a web-based tool that addresses this need. Given one query
genome, SynFind is capable of identifying conserved syntenic regions in any set of
target genomes. SynFind is capable of reporting per-gene information, useful for
researchers studying specific gene families, as well as genome-wide data sets of
syntenic gene and predicted gene locations, critical for researchers focused on
large-scale genomic analyses. Inference of syntenic homologs provides the basis for
correlation of functional changes around genes of interests between related
organisms. Deployed on the CoGe online platform, SynFind is connected to the genomic
data from over 15,000 organisms from all domains of life as well as supporting
multiple releases of the same organism. SynFind makes use of a powerful job execution
framework that promises scalability and reproducibility. SynFind can be accessed at
http://genomevolution.org/CoGe/SynFind.pl. A video tutorial of SynFind
using Phytophthrora as an example is available at http://www.youtube.com/watch?v=2Agczny9Nyc.
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Affiliation(s)
- Haibao Tang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China School of Plant Sciences, iPlant Collaborative, University of Arizona
| | - Matthew D Bomhoff
- School of Plant Sciences, iPlant Collaborative, University of Arizona
| | - Evan Briones
- School of Plant Sciences, iPlant Collaborative, University of Arizona
| | - Liangsheng Zhang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln
| | - Eric Lyons
- School of Plant Sciences, iPlant Collaborative, University of Arizona
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50
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Tohge T, Scossa F, Fernie AR. Integrative Approaches to Enhance Understanding of Plant Metabolic Pathway Structure and Regulation. PLANT PHYSIOLOGY 2015; 169:1499-511. [PMID: 26371234 PMCID: PMC4634077 DOI: 10.1104/pp.15.01006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/10/2015] [Indexed: 05/05/2023]
Abstract
Huge insight into molecular mechanisms and biological network coordination have been achieved following the application of various profiling technologies. Our knowledge of how the different molecular entities of the cell interact with one another suggests that, nevertheless, integration of data from different techniques could drive a more comprehensive understanding of the data emanating from different techniques. Here, we provide an overview of how such data integration is being used to aid the understanding of metabolic pathway structure and regulation. We choose to focus on the pairwise integration of large-scale metabolite data with that of the transcriptomic, proteomics, whole-genome sequence, growth- and yield-associated phenotypes, and archival functional genomic data sets. In doing so, we attempt to provide an update on approaches that integrate data obtained at different levels to reach a better understanding of either single gene function or metabolic pathway structure and regulation within the context of a broader biological process.
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Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T., A.R.F.); andConsiglio per la Ricerca e Analisi dell'Economia Agraria, Centro di Ricerca per la Frutticoltura, 00134 Rome, Italy (F.S.)
| | - Federico Scossa
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T., A.R.F.); andConsiglio per la Ricerca e Analisi dell'Economia Agraria, Centro di Ricerca per la Frutticoltura, 00134 Rome, Italy (F.S.)
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (T.T., A.R.F.); andConsiglio per la Ricerca e Analisi dell'Economia Agraria, Centro di Ricerca per la Frutticoltura, 00134 Rome, Italy (F.S.)
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