1
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Improving
C
3
photosynthesis by exploiting natural genetic variation:
Hirschfeldia incana
as a model species. Food Energy Secur 2022. [DOI: 10.1002/fes3.420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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2
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Van Drunen WE, Johnson MTJ. Polyploidy in urban environments. Trends Ecol Evol 2022; 37:507-516. [PMID: 35246321 DOI: 10.1016/j.tree.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 10/19/2022]
Abstract
Polyploidy is a major driver of evolutionary change in plants, but many aspects of polyploidy in natural systems remain enigmatic. We argue that urban landscapes present an unprecedented opportunity to observe polyploidy in action. Integrating polyploid biology and urban evolutionary ecology, we discuss multiple factors expected to promote polyploid formation, establishment, and persistence in urban systems. We develop a predictive framework for the contemporary ecology and evolution of polyploid plants in cities, and through this novel perspective propose that studying polyploidy in an urban context could lead to breakthroughs in understanding fundamental processes in polyploid evolution. We conclude by highlighting the potential consequences of polyploidy in urban environments, and outline a roadmap for research into this currently unexplored field.
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Affiliation(s)
- Wendy E Van Drunen
- Department of Biology, Queen's University, Kingston, Ontario K7L 3N6, Canada; Department of Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada; Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.
| | - Marc T J Johnson
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada; Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
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3
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Xu H, Wang C, Shao G, Wu S, Liu P, Cao P, Jiang P, Wang S, Zhu H, Lin X, Tauqeer A, Lin Y, Chen W, Huang W, Wen Q, Chang J, Zhong F, Wu S. The reference genome and full-length transcriptome of pakchoi provide insights into cuticle formation and heat adaption. HORTICULTURE RESEARCH 2022; 9:uhac123. [PMID: 35949690 PMCID: PMC9358696 DOI: 10.1093/hr/uhac123] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 05/17/2022] [Indexed: 05/20/2023]
Abstract
Brassica rapa includes various vegetables with high economic value. Among them, green petiole type pakchoi (B. rapa ssp. chinensis) is one of the major vegetables grown in southern China. Compared with other B. rapa varieties, green petiole type pakchoi shows a higher level of heat resistance, which is partially derived from the rich epicuticular wax. Here we sequence a high-quality genome of green petiole type pakchoi, which has been widely used as the parent in breeding. Our results reveal that long terminal repeat retrotransposon insertion plays critical roles in promoting the genome expansion and transcriptional diversity of pakchoi genes through preferential insertions, particularly in cuticle biosynthetic genes. After whole-genome triplication, over-retained pakchoi genes escape stringent selection pressure, and among them a set of cuticle-related genes are retained. Using bulked-segregant analysis of a heat-resistant pakchoi cultivar, we identify a frame-shift deletion across the third exon and the subsequent intron of BrcCER1 in candidate regions. Using Nanopore long-read sequencing, we analyze the full-length transcriptome of two pakchoi cultivars with opposite sensitivity to high temperature. We find that the heat-resistant pakchoi cultivar can mitigate heat-caused leaf damage by activating an unfolded protein response, as well as by inhibiting chloroplast development and energy metabolism, which are presumably mediated by both transcriptional regulation and splicing factors. Our study provides valuable resources for Brassica functional genomics and breeding research, and deepens our understanding of plant stress resistance.
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Affiliation(s)
| | | | | | - Shasha Wu
- College of Life Sciences & College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Peng Liu
- College of Life Sciences & College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ping Cao
- Fujian Jinpin Agricultural Technology Co., Ltd, Fuzhou 350000, China
| | - Peng Jiang
- College of Life Sciences & College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shubin Wang
- College of Life Sciences & College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hong Zhu
- Fujian Seed Chief Station, Fuzhou 350003, China
| | - Xiao Lin
- Fujian Jinpin Agricultural Technology Co., Ltd, Fuzhou 350000, China
| | - Arfa Tauqeer
- College of Life Sciences & College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yizhang Lin
- Fujian Jinpin Agricultural Technology Co., Ltd, Fuzhou 350000, China
| | - Wei Chen
- Fujian Seed Chief Station, Fuzhou 350003, China
| | | | - Qingfang Wen
- Crop Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Jiang Chang
- College of Life Sciences & College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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4
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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: 5] [Impact Index Per Article: 1.7] [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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5
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Carey S, Higuera‐Díaz M, Mankowski P, Rocca A, Hall JC. Virus-induced gene silencing as a tool for functional studies in Cleome violacea. APPLICATIONS IN PLANT SCIENCES 2021; 9:APS311435. [PMID: 34141499 PMCID: PMC8202831 DOI: 10.1002/aps3.11435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
PREMISE Cleomaceae is emerging as a promising family to investigate a wide range of phenomena, such as C4 photosynthesis and floral diversity. However, functional techniques are lacking for elucidating this diversity. Herein, we establish virus-induced gene silencing (VIGS) as a method of generating functional data for Cleome violacea, bolstering Cleomaceae as a model system. METHODS We leveraged the sister relationship of Cleomaceae and Brassicaceae by using constructs readily available for Arabidopsis thaliana to provide initial information about the feasibility of VIGS in C. violacea. We then developed endogenous constructs to optimize VIGS efficiency and viability for fruit development. RESULTS PHYTOENE DESATURASE was successfully downregulated in C. violacea using both heterologous and endogenous constructs. The endogenous construct had the highest degree of downregulation, with many plants displaying strong photobleaching. FRUITFULL-treated plants were also successfully downregulated, with a high rate of survival but less effective silencing; only a small percentage of survivors showed a strong phenotype. DISCUSSION Our optimized VIGS protocol in C. violacea enables functional gene analyses at different developmental stages. Additionally, C. violacea is amenable to heterologous knockdown, which suggests that a first pass using non-endogenous constructs is a possible route to test additional species of Cleomaceae.
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Affiliation(s)
- Shane Carey
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | | | - Peter Mankowski
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
- Present address:
Department of SurgeryUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Alexandra Rocca
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
- Present address:
Administration BuildingUniversity of AlbertaEdmontonAlbertaCanada
| | - Jocelyn C. Hall
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
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6
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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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7
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Pereira-Santana A, Gamboa-Tuz SD, Zhao T, Schranz ME, Vinuesa P, Bayona A, Rodríguez-Zapata LC, Castano E. Fibrillarin evolution through the Tree of Life: Comparative genomics and microsynteny network analyses provide new insights into the evolutionary history of Fibrillarin. PLoS Comput Biol 2020; 16:e1008318. [PMID: 33075080 PMCID: PMC7608942 DOI: 10.1371/journal.pcbi.1008318] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 11/03/2020] [Accepted: 09/07/2020] [Indexed: 12/26/2022] Open
Abstract
Fibrillarin (FIB), a methyltransferase essential for life in the vast majority of eukaryotes, is involved in methylation of rRNA required for proper ribosome assembly, as well as methylation of histone H2A of promoter regions of rRNA genes. RNA viral progression that affects both plants and animals requires FIB proteins. Despite the importance and high conservation of fibrillarins, there little is known about the evolutionary dynamics of this small gene family. We applied a phylogenomic microsynteny-network approach to elucidate the evolutionary history of FIB proteins across the Tree of Life. We identified 1063 non-redundant FIB sequences across 1049 completely sequenced genomes from Viruses, Bacteria, Archaea, and Eukarya. FIB is a highly conserved single-copy gene through Archaea and Eukarya lineages, except for plants, which have a gene family expansion due to paleopolyploidy and tandem duplications. We found a high conservation of the FIB genomic context during plant evolution. Surprisingly, FIB in mammals duplicated after the Eutheria split (e.g., ruminants, felines, primates) from therian mammals (e.g., marsupials) to form two main groups of sequences, the FIB and FIB-like groups. The FIB-like group transposed to another genomic context and remained syntenic in all the eutherian mammals. This transposition correlates with differences in the expression patterns of FIB-like proteins and with elevated Ks values potentially due to reduced evolutionary constraints of the duplicated copy. Our results point to a unique evolutionary event in mammals, between FIB and FIB-like genes, that led to non-redundant roles of the vital processes in which this protein is involved.
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Affiliation(s)
- Alejandro Pereira-Santana
- Unidad de Bioquímica y Biología molecular de plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
- Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Zapopan, Jalisco, México
- Dirección de Cátedras, Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | - Samuel David Gamboa-Tuz
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Tao Zhao
- Bioinformatics and Evolutionary Genomics, VIB-UGent Center for Plant Systems Biology, Gent, Belgium
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - M. Eric Schranz
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Andrea Bayona
- Unidad de Bioquímica y Biología molecular de plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | | | - Enrique Castano
- Unidad de Bioquímica y Biología molecular de plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
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8
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Essoh AP, Monteiro F, Pena AR, Pais MS, Moura M, Romeiras MM. Exploring glucosinolates diversity in Brassicaceae: a genomic and chemical assessment for deciphering abiotic stress tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 150:151-161. [PMID: 32142988 DOI: 10.1016/j.plaphy.2020.02.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/29/2020] [Accepted: 02/20/2020] [Indexed: 05/20/2023]
Abstract
Brassica is one of the most economically important genus of the Brassicaceae family, encompassing several key crops like Brassica napus (cabbage) and broccoli (Brassica oleraceae var. italica). This family is well known for their high content of characteristic secondary metabolites such as glucosinolates (GLS) compounds, recognize for their beneficial health properties and role in plants defense. In this work, we have looked through gene clusters involved in the biosynthesis of GLS, by combining genomic analysis with biochemical pathways and chemical diversity assessment. A total of 101 Brassicaceae genes involved in GLS biosynthesis were identified, using a multi-database approach. Through a UPGMA and PCA analysis on the 101 GLS genes recorded, revealed a separation between the genes mainly involved in GLS core structure synthesis and genes belonging to the CYP450s and MYBs gene families. After, a detailed phylogenetic analysis was conducted to better understand the disjunction of the aliphatic and indolic genes, by focusing on CYP79F1-F2 and CYP81F1-F4, respectively. Our results point to a recent diversification of the aliphatic CYP79F1 and F2 genes in Brassica crops, while for indolic genes an earliest diversification is observed for CYP81F1-F4 genes. Chemical diversity revealed that Brassica crops have distinct GLS chemo-profiles from other Brassicaceae genera; being highlighted the high contents of GLS found among the Diplotaxis species. Also, we have explored GLS-rich species as a new source of taxa with great agronomic potential, particularly in abiotic stress tolerance, namely Diplotaxis, the closest wild relatives of Brassica crops.
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Affiliation(s)
- Anyse Pereira Essoh
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal; Research Centre in Biodiversity and Genetic Resources (CIBIO), InBIO Associate Laboratory, Faculdade de Ciências e Tecnologia, Universidade dos Açores, Ponta Delgada, Portugal; Nova School of Business and Economics, 2775-405, Campus de Carcavelos, Portugal
| | - Filipa Monteiro
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal; Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.
| | - Ana Rita Pena
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - M Salomé Pais
- Academia das Ciências de Lisboa, Rua Academia das Ciências 19, 1200-168, Lisboa, Portugal
| | - Mónica Moura
- Research Centre in Biodiversity and Genetic Resources (CIBIO), InBIO Associate Laboratory, Faculdade de Ciências e Tecnologia, Universidade dos Açores, Ponta Delgada, Portugal
| | - Maria Manuel Romeiras
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal; Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Academia das Ciências de Lisboa, Rua Academia das Ciências 19, 1200-168, Lisboa, Portugal.
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9
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Blažević I, Montaut S, Burčul F, Olsen CE, Burow M, Rollin P, Agerbirk N. Glucosinolate structural diversity, identification, chemical synthesis and metabolism in plants. PHYTOCHEMISTRY 2020; 169:112100. [PMID: 31771793 DOI: 10.1016/j.phytochem.2019.112100] [Citation(s) in RCA: 235] [Impact Index Per Article: 58.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 07/04/2019] [Accepted: 08/18/2019] [Indexed: 05/05/2023]
Abstract
The glucosinolates (GSLs) is a well-defined group of plant metabolites characterized by having an S-β-d-glucopyrano unit anomerically connected to an O-sulfated (Z)-thiohydroximate function. After enzymatic hydrolysis, the sulfated aglucone can undergo rearrangement to an isothiocyanate, or form a nitrile or other products. The number of GSLs known from plants, satisfactorily characterized by modern spectroscopic methods (NMR and MS) by mid-2018, is 88. In addition, a group of partially characterized structures with highly variable evidence counts for approximately a further 49. This means that the total number of characterized GSLs from plants is somewhere between 88 and 137. The diversity of GSLs in plants is critically reviewed here, resulting in significant discrepancies with previous reviews. In general, the well-characterized GSLs show resemblance to C-skeletons of the amino acids Ala, Val, Leu, Trp, Ile, Phe/Tyr and Met, or to homologs of Ile, Phe/Tyr or Met. Insufficiently characterized, still hypothetic GSLs include straight-chain alkyl GSLs and chain-elongated GSLs derived from Leu. Additional reports (since 2011) of insufficiently characterized GSLs are reviewed. Usually the crucial missing information is correctly interpreted NMR, which is the most effective tool for GSL identification. Hence, modern use of NMR for GSL identification is also reviewed and exemplified. Apart from isolation, GSLs may be obtained by organic synthesis, allowing isotopically labeled GSLs and any kind of side chain. Enzymatic turnover of GSLs in plants depends on a considerable number of enzymes and other protein factors and furthermore depends on GSL structure. Identification of GSLs must be presented transparently and live up to standard requirements in natural product chemistry. Unfortunately, many recent reports fail in these respects, including reports based on chromatography hyphenated to MS. In particular, the possibility of isomers and isobaric structures is frequently ignored. Recent reports are re-evaluated and interpreted as evidence of the existence of "isoGSLs", i.e. non-GSL isomers of GSLs in plants. For GSL analysis, also with MS-detection, we stress the importance of using authentic standards.
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Affiliation(s)
- Ivica Blažević
- Department of Organic Chemistry, Faculty of Chemistry and Technology, University of Split, Ruđera Boškovića 35, 21000, Split, Croatia.
| | - Sabine Montaut
- Department of Chemistry and Biochemistry, Biomolecular Sciences Programme, Laurentian University, 935 Ramsey Lake Road, Sudbury, ON P3E 2C6, Canada
| | - Franko Burčul
- Department of Analytical Chemistry, Faculty of Chemistry and Technology, University of Split, Ruđera Boškovića 35, 21000, Split, Croatia
| | - Carl Erik Olsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Meike Burow
- DynaMo Center and Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Patrick Rollin
- Institut de Chimie Organique et Analytique (ICOA), Université d'Orléans et CNRS, UMR 7311, BP 6759, F-45067, Orléans Cedex 2, France
| | - Niels Agerbirk
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.
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10
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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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11
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Charlesworth D. Young sex chromosomes in plants and animals. THE NEW PHYTOLOGIST 2019; 224:1095-1107. [PMID: 31222890 DOI: 10.1111/nph.16002] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/10/2019] [Indexed: 05/28/2023]
Abstract
A major reason for studying plant sex chromosomes is that they may often be 'young' systems. There is considerable evidence for the independent evolution of separate sexes within plant families or genera, in some cases showing that the maximum possible time during which their sex-determining genes have existed must be much shorter than those of several animal taxa. Consequently, their sex-linked regions could either have evolved soon after genetic sex determination arose or considerably later. Plants, therefore, include species with both young and old systems. I review several questions about the evolution of sex-determining systems and sex chromosomes that require studies of young systems, including: the kinds of mutations involved in the transition to unisexual reproduction from hermaphroditism or monoecy (a form of functional hermaphroditism); the times when they arose; and the extent to which the properties of sex-linked regions of genomes reflect responses to new selective situations created by the presence of a sex-determining locus. I also evaluate which questions are best studied in plants, vs other suitable candidate organisms. Studies of young plant systems can help understand general evolutionary processes that are shared with the sex chromosomes of other organisms.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh, EH9 3LF, UK
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12
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Bayat S, Schranz ME, Roalson EH, Hall JC. Lessons from Cleomaceae, the Sister of Crucifers. TRENDS IN PLANT SCIENCE 2018; 23:808-821. [PMID: 30006074 DOI: 10.1016/j.tplants.2018.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 06/06/2018] [Accepted: 06/17/2018] [Indexed: 05/21/2023]
Abstract
Cleomaceae is a diverse group well-suited to addressing fundamental genomic and evolutionary questions as the sister group to Brassicaceae, facilitating transfer of knowledge from the model Arabidopsis thaliana. Phylogenetic and taxonomic revisions provide a framework for examining the evolution of substantive morphological and physiology diversity in Cleomaceae, but not necessarily in Brassicaceae. The investigation of both nested and contrasting whole-genome duplications (WGDs) between Cleomaceae and Brassicaceae allows comparisons of independently duplicated genes and investigation of whether they may be drivers of the observed innovations. Further, a wealth of outstanding genetic research has provided insight into how the important alternative carbon fixation pathway, C4 photosynthesis, has evolved via differential expression of a suite of genes, of which the underlying mechanisms are being elucidated.
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Affiliation(s)
- Soheila Bayat
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada; RG Plant Cytogenomics, Central European Institute of Technology, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Eric H Roalson
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Jocelyn C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada.
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Cheng F, Wu J, Cai X, Liang J, Freeling M, Wang X. Gene retention, fractionation and subgenome differences in polyploid plants. NATURE PLANTS 2018; 4:258-268. [PMID: 29725103 DOI: 10.1038/s41477-018-0136-7] [Citation(s) in RCA: 170] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 03/20/2018] [Indexed: 05/22/2023]
Abstract
All natural plant species are evolved from ancient polyploids. Polyloidization plays an important role in plant genome evolution, species divergence and crop domestication. We review how the pattern of polyploidy within the plant phylogenetic tree has engendered hypotheses involving mass extinctions, lag-times following polyploidy, and epochs of asexuality. Polyploidization has happened repeatedly in plant evolution and, we conclude, is important for crop domestication. Once duplicated, the effect of purifying selection on any one duplicated gene is relaxed, permitting duplicate gene and regulatory element loss (fractionation). We review the general topic of fractionation, and how some gene categories are retained more than others. Several explanations, including neofunctionalization, subfunctionalization and gene product dosage balance, have been shown to influence gene content over time. For allopolyploids, genetic differences between parental lines immediately manifest as subgenome dominance in the wide-hybrid, and persist and propagate for tens of millions of years. While epigenetic modifications are certainly involved in genome dominance, it has been difficult to determine which came first, the chromatin marks being measured or gene expression. Data support the conclusion that genome dominance and heterosis are antagonistic and mechanically entangled; both happen immediately in the synthetic wide-cross hybrid. Also operating in this hybrid are mechanisms of 'paralogue interference'. We present a foundation model to explain gene expression and vigour in a wide hybrid/new allotetraploid. This Review concludes that some mechanisms operate immediately at the wide-hybrid, and other mechanisms begin their operations later. Direct interaction of new paralogous genes, as measured using high-resolution chromatin conformation capture, should inform future research and single cell transcriptome sequencing should help achieve specificity while studying gene sub- and neo-functionalization.
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Affiliation(s)
- Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Jian Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Xu Cai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Jianli Liang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Michael Freeling
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
| | - Xiaowu Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
- Shandong Provincial Key Laboratory of Protected Vegetable Molecular Breeding, Shandong Shouguang Vegetable Seed Industry Group Co. Ltd., Shandong Province, China.
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14
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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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15
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Landis JB, Soltis DE, Li Z, Marx HE, Barker MS, Tank DC, Soltis PS. Impact of whole-genome duplication events on diversification rates in angiosperms. AMERICAN JOURNAL OF BOTANY 2018; 105:348-363. [PMID: 29719043 DOI: 10.1002/ajb2.1060] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/12/2017] [Indexed: 05/18/2023]
Abstract
PREMISE OF THE STUDY Polyploidy or whole-genome duplication (WGD) pervades the evolutionary history of angiosperms. Despite extensive progress in our understanding of WGD, the role of these events in promoting diversification is still not well understood. We seek to clarify the possible association between WGD and diversification rates in flowering plants. METHODS Using a previously published phylogeny spanning all land plants (31,749 tips) and WGD events inferred from analyses of the 1000 Plants (1KP) transcriptome data, we analyzed the association of WGDs and diversification rates following numerous WGD events across the angiosperms. We used a stepwise AIC approach (MEDUSA), a Bayesian mixture model approach (BAMM), and state-dependent diversification analyses (MuSSE) to investigate patterns of diversification. Sister-clade comparisons were used to investigate species richness after WGDs. KEY RESULTS Based on the density of 1KP taxon sampling, 106 WGDs were unambiguously placed on the angiosperm phylogeny. We identified 334-530 shifts in diversification rates. We found that 61 WGD events were tightly linked to changes in diversification rates, and state-dependent diversification analyses indicated higher speciation rates for subsequent rounds of WGD. Additionally, 70 of 99 WGD events showed an increase in species richness compared to the sister clade. CONCLUSIONS Forty-six of the 106 WGDs analyzed appear to be closely associated with upshifts in the rate of diversification in angiosperms. Shifts in diversification do not appear more likely than random within a four-node lag phase following a WGD; however, younger WGD events are more likely to be followed by an upshift in diversification than older WGD events.
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Affiliation(s)
- Jacob B Landis
- Department of Botany and Plant Sciences, University of California-Riverside, Riverside, California, 92521, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, Florida, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Zheng Li
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721, USA
| | - Hannah E Marx
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721, USA
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona, 85721, USA
| | - David C Tank
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, 83844, USA
- Stillinger Herbarium, University of Idaho, Moscow, Idaho, 83844, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, 32611, USA
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16
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Hohmann N, Koch MA. An Arabidopsis introgression zone studied at high spatio-temporal resolution: interglacial and multiple genetic contact exemplified using whole nuclear and plastid genomes. BMC Genomics 2017; 18:810. [PMID: 29058582 PMCID: PMC5651623 DOI: 10.1186/s12864-017-4220-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/16/2017] [Indexed: 12/30/2022] Open
Abstract
Background Gene flow between species, across ploidal levels, and even between evolutionary lineages is a common phenomenon in the genus Arabidopsis. However, apart from two genetically fully stabilized allotetraploid species that have been investigated in detail, the extent and temporal dynamics of hybridization are not well understood. An introgression zone, with tetraploid A. arenosa introgressing into A. lyrata subsp. petraea in the Eastern Austrian Forealps and subsequent expansion towards pannonical lowlands, was described previously based on morphological observations as well as molecular data using microsatellite and plastid DNA markers. Here we investigate the spatio-temporal context of this suture zone, making use of the potential of next-generation sequencing and whole-genome data. By utilizing a combination of nuclear and plastid genomic data, the extent, direction and temporal dynamics of gene flow are elucidated in detail and Late Pleistocene evolutionary processes are resolved. Results Analysis of nuclear genomic data significantly recognizes the clinal structure of the introgression zone, but also reveals that hybridization and introgression is more common and substantial than previously thought. Also tetraploid A. lyrata and A. arenosa subsp. borbasii from outside the previously defined suture zone show genomic signals of past introgression. A. lyrata is shown to serve usually as the maternal parent in these hybridizations, but one exception is identified from plastome-based phylogenetic reconstruction. Using plastid phylogenomics with secondary time calibration, the origin of A. lyrata and A. arenosa lineages is pre-dating the last three glaciation complexes (approx. 550,000 years ago). Hybridization and introgression followed during the last two glacial-interglacial periods (since approx. 300,000 years ago) with later secondary contact at the northern and southern border of the introgression zone during the Holocene. Conclusions Footprints of adaptive introgression in the Northeastern Forealps are older than expected and predate the Last Glaciation Maximum. This correlates well with high genetic diversity found within areas that served as refuge area multiple times. Our data also provide some first hints that early introgressed and presumably preadapted populations account for successful and rapid postglacial re-colonization and range expansion. Electronic supplementary material The online version of this article (doi: 10.1186/s12864-017-4220-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nora Hohmann
- Center for Organismal Studies (COS) Heidelberg/Botanic Garden and Herbarium Heidelberg (HEID), University of Heidelberg, Im Neuenheimer Feld 345, D-69120, Heidelberg, Germany.,Present address: Department of Environmental Sciences, Botany, University of Basel, Hebelstrasse 1, CH-4056, Basel, Switzerland
| | - Marcus A Koch
- Center for Organismal Studies (COS) Heidelberg/Botanic Garden and Herbarium Heidelberg (HEID), University of Heidelberg, Im Neuenheimer Feld 345, D-69120, Heidelberg, Germany.
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17
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Segraves KA. The effects of genome duplications in a community context. THE NEW PHYTOLOGIST 2017; 215:57-69. [PMID: 28418074 DOI: 10.1111/nph.14564] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/16/2017] [Indexed: 06/07/2023]
Abstract
Contents 57 I. 57 II. 59 III. 59 IV. 63 V. 64 VI. 64 VII. 66 66 References 66 SUMMARY: Whole-genome duplication (WGD), or polyploidy, has important effects on the genotype and phenotype of plants, potentially altering ecological interactions with other organisms. Even though the connections between polyploidy and species interactions have been recognized for some time, we are only just beginning to test whether WGD affects community context. Here I review the sparse information on polyploidy and community context and then present a set of hypotheses for future work. Thus far, community-level studies of polyploids suggest an array of outcomes, from no changes in community context to shifts in the abundance and composition of interacting species. I propose a number of mechanisms for how WGD could alter community context and how the emergence of polyploids in populations could also alter the community context of parental diploids and other plant species. Resolving how and when these changes are expected to occur will require a deeper understanding of the connections among WGD, phenotypic changes, and the direct and indirect effects of species interactions.
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Affiliation(s)
- Kari A Segraves
- Department of Biology, Syracuse University, Syracuse, NY, 13244, USA
- Archbold Biological Station, Venus, FL, 33960, USA
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18
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Abstract
Polyploidy, or the duplication of entire genomes, has been observed in prokaryotic and eukaryotic organisms, and in somatic and germ cells. The consequences of polyploidization are complex and variable, and they differ greatly between systems (clonal or non-clonal) and species, but the process has often been considered to be an evolutionary 'dead end'. Here, we review the accumulating evidence that correlates polyploidization with environmental change or stress, and that has led to an increased recognition of its short-term adaptive potential. In addition, we discuss how, once polyploidy has been established, the unique retention profile of duplicated genes following whole-genome duplication might explain key longer-term evolutionary transitions and a general increase in biological complexity.
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19
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Baker RL, Yarkhunova Y, Vidal K, Ewers BE, Weinig C. Polyploidy and the relationship between leaf structure and function: implications for correlated evolution of anatomy, morphology, and physiology in Brassica. BMC PLANT BIOLOGY 2017; 17:3. [PMID: 28056801 PMCID: PMC5217196 DOI: 10.1186/s12870-016-0957-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 12/19/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND Polyploidy is well studied from a genetic and genomic perspective, but the morphological, anatomical, and physiological consequences of polyploidy remain relatively uncharacterized. Whether these potential changes bear on functional integration or are idiosyncratic remains an open question. Repeated allotetraploid events and multiple genomic combinations as well as overlapping targets of artificial selection make the Brassica triangle an excellent system for exploring variation in the connection between plant structure (anatomy and morphology) and function (physiology). We examine phenotypic integration among structural aspects of leaves including external morphology and internal anatomy with leaf-level physiology among several species of Brassica. We compare diploid and allotetraploid species to ascertain patterns of phenotypic correlations among structural and functional traits and test the hypothesis that allotetraploidy results in trait disintegration allowing for transgressive phenotypes and additional evolutionary and crop improvement potential. RESULTS Among six Brassica species, we found significant effects of species and ploidy level for morphological, anatomical and physiological traits. We identified three suites of intercorrelated traits in both diploid parents and allotetraploids: Morphological traits (such as leaf area and perimeter) anatomic traits (including ab- and ad- axial epidermis) and aspects of physiology. In general, there were more correlations between structural and functional traits for allotetraploid hybrids than diploid parents. Parents and hybrids did not have any significant structure-function correlations in common. Of particular note, there were no significant correlations between morphological structure and physiological function in the diploid parents. Increased phenotypic integration in the allotetraploid hybrids may be due, in part, to increased trait ranges or simply different structure-function relationships. CONCLUSIONS Genomic and chromosomal instability in early generation allotetraploids may allow Brassica species to explore new trait space and potentially reach higher adaptive peaks than their progenitor species could, despite temporary fitness costs associated with unstable genomes. The trait correlations that disappear after hybridization as well as the novel trait correlations observed in allotetraploid hybrids may represent relatively evolutionarily labile associations and therefore could be ideal targets for artificial selection and crop improvement.
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Affiliation(s)
- Robert L Baker
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA.
| | - Yulia Yarkhunova
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
- Program in Ecology, University of Wyoming, Laramie, WY, 82071, USA
| | - Katherine Vidal
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | - Brent E Ewers
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
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20
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Rodriguez-Corona U, Pereira-Santana A, Sobol M, Rodriguez-Zapata LC, Hozak P, Castano E. Novel Ribonuclease Activity Differs between Fibrillarins from Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2017; 8:1878. [PMID: 29163603 PMCID: PMC5674935 DOI: 10.3389/fpls.2017.01878] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 10/16/2017] [Indexed: 05/09/2023]
Abstract
Fibrillarin is one of the most important nucleolar proteins that have been shown as essential for life. Fibrillarin localizes primarily at the periphery between fibrillar center and dense fibrillar component as well as in Cajal bodies. In most plants there are at least two different genes for fibrillarin. In Arabidopsis thaliana both genes show high level of expression in transcriptionally active cells. Here, we focus on two important differences between A. thaliana fibrillarins. First and most relevant is the enzymatic activity by AtFib2. The AtFib2 shows a novel ribonuclease activity that is not seen with AtFib1. Second is a difference in the ability to interact with phosphoinositides and phosphatidic acid between both proteins. We also show that the novel ribonuclease activity as well as the phospholipid binding region of fibrillarin is confine to the GAR domain. The ribonuclease activity of fibrillarin reveals in this study represents a new role for this protein in rRNA processing.
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Affiliation(s)
- Ulises Rodriguez-Corona
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Alejandro Pereira-Santana
- Biosystematics Group, Department of Plant Sciences, Wageningen University and Research, Wageningen, Netherlands
| | - Margarita Sobol
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, Prague, Czechia
| | | | - Pavel Hozak
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, Prague, Czechia
| | - Enrique Castano
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
- *Correspondence: Enrique Castano,
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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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22
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Barker MS, Husband BC, Pires JC. Spreading Winge and flying high: The evolutionary importance of polyploidy after a century of study. AMERICAN JOURNAL OF BOTANY 2016; 103:1139-45. [PMID: 27480249 DOI: 10.3732/ajb.1600272] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 07/20/2016] [Indexed: 05/10/2023]
Affiliation(s)
- Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 USA
| | - Brian C Husband
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1 Canada
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 USA
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