101
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Hater F, Nakel T, Groß-Hardt R. Reproductive Multitasking: The Female Gametophyte. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:517-546. [PMID: 32442389 DOI: 10.1146/annurev-arplant-081519-035943] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Fertilization of flowering plants requires the organization of complex tasks, many of which become integrated by the female gametophyte (FG). The FG is a few-celled haploid structure that orchestrates division of labor to coordinate successful interaction with the sperm cells and their transport vehicle, the pollen tube. As reproductive outcome is directly coupled to evolutionary success, the underlying mechanisms are under robust molecular control, including integrity check and repair mechanisms. Here, we review progress on understanding the development and function of the FG, starting with the functional megaspore, which represents the haploid founder cell of the FG. We highlight recent achievements that have greatly advanced our understanding of pollen tube attraction strategies and the mechanisms that regulate plant hybridization and gamete fusion. In addition, we discuss novel insights into plant polyploidization strategies that expand current concepts on the evolution of flowering plants.
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Affiliation(s)
- Friederike Hater
- Centre for Biomolecular Interactions, University of Bremen, 28359 Bremen, Germany;
| | - Thomas Nakel
- Centre for Biomolecular Interactions, University of Bremen, 28359 Bremen, Germany;
| | - Rita Groß-Hardt
- Centre for Biomolecular Interactions, University of Bremen, 28359 Bremen, Germany;
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102
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Lavania UC. Plant speciation and polyploidy: in habitat divergence and environmental perspective. THE NUCLEUS 2020. [DOI: 10.1007/s13237-020-00311-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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103
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Hardigan MA, Feldmann MJ, Lorant A, Bird KA, Famula R, Acharya C, Cole G, Edger PP, Knapp SJ. Genome Synteny Has Been Conserved Among the Octoploid Progenitors of Cultivated Strawberry Over Millions of Years of Evolution. FRONTIERS IN PLANT SCIENCE 2020; 10:1789. [PMID: 32158449 PMCID: PMC7020885 DOI: 10.3389/fpls.2019.01789] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/20/2019] [Indexed: 05/18/2023]
Abstract
Allo-octoploid cultivated strawberry (Fragaria × ananassa) originated through a combination of polyploid and homoploid hybridization, domestication of an interspecific hybrid lineage, and continued admixture of wild species over the last 300 years. While genes appear to flow freely between the octoploid progenitors, the genome structures and diversity of the octoploid species remain poorly understood. The complexity and absence of an octoploid genome frustrated early efforts to study chromosome evolution, resolve subgenomic structure, and develop a single coherent linkage group nomenclature. Here, we show that octoploid Fragaria species harbor millions of subgenome-specific DNA variants. Their diversity was sufficient to distinguish duplicated (homoeologous and paralogous) DNA sequences and develop 50K and 850K SNP genotyping arrays populated with co-dominant, disomic SNP markers distributed throughout the octoploid genome. Whole-genome shotgun genotyping of an interspecific segregating population yielded 1.9M genetically mapped subgenome variants in 5,521 haploblocks spanning 3,394 cM in F. chiloensis subsp. lucida, and 1.6M genetically mapped subgenome variants in 3,179 haploblocks spanning 2,017 cM in F. × ananassa. These studies provide a dense genomic framework of subgenome-specific DNA markers for seamlessly cross-referencing genetic and physical mapping information and unifying existing chromosome nomenclatures. Using comparative genomics, we show that geographically diverse wild octoploids are effectively diploidized, nearly completely collinear, and retain strong macro-synteny with diploid progenitor species. The preservation of genome structure among allo-octoploid taxa is a critical factor in the unique history of garden strawberry, where unimpeded gene flow supported its origin and domestication through repeated cycles of interspecific hybridization.
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Affiliation(s)
- Michael A. Hardigan
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Mitchell J. Feldmann
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Anne Lorant
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Kevin A. Bird
- Department of Horticulture, Michigan State University, East Lansing, MI, United States
| | - Randi Famula
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Charlotte Acharya
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Glenn Cole
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Patrick P. Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, United States
| | - Steven J. Knapp
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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104
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Huynh S, Broennimann O, Guisan A, Felber F, Parisod C. Eco‐genetic additivity of diploids in allopolyploid wild wheats. Ecol Lett 2020; 23:663-673. [DOI: 10.1111/ele.13466] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/29/2019] [Accepted: 12/29/2019] [Indexed: 11/25/2022]
Affiliation(s)
- Stella Huynh
- Institute of Plant Sciences University of Bern Bern Switzerland
- Institute of Biology University of Neuchâtel Neuchatel Switzerland
| | - Olivier Broennimann
- Department of Ecology & Evolution University of Lausanne Lausanne Switzerland
- Institute of Earth Surface Dynamics University of Lausanne Lausanne Switzerland
| | - Antoine Guisan
- Department of Ecology & Evolution University of Lausanne Lausanne Switzerland
- Institute of Earth Surface Dynamics University of Lausanne Lausanne Switzerland
| | - François Felber
- Institute of Biology University of Neuchâtel Neuchatel Switzerland
- Department of Ecology & Evolution University of Lausanne Lausanne Switzerland
- Musée et Jardins botaniques cantonaux de Lausanne et Pont‐de‐Nant Lausanne Switzerland
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105
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Wei N, Du Z, Liston A, Ashman TL. Genome duplication effects on functional traits and fitness are genetic context and species dependent: studies of synthetic polyploid Fragaria. AMERICAN JOURNAL OF BOTANY 2020; 107:262-272. [PMID: 31732972 DOI: 10.1002/ajb2.1377] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/09/2019] [Indexed: 05/21/2023]
Abstract
PREMISE Divergence in functional traits and adaptive responses to environmental change underlies the ecological advantage of polyploid plants in the wild. While established polyploids may benefit from combined outcomes of genome doubling, hybridization, and polyploidy-enabled adaptive evolution, whether genome doubling alone can drive ecological divergence or whether the outcome is genetically variable remains less clear. METHODS Using synthetic, colchicine-induced, autotetraploid (4x) plants derived from self-pollinated diploid (2x) seeds, and their colchicine-treated but unconverted diploid (2x.nc) full sibs from two diploid wild strawberry taxa (Fragaria vesca subsp. vesca and F. vesca subsp. bracteata), we examined the effects of genome doubling on functional traits, heat stress tolerance, and fitness components across taxa and maternal families (i.e., genetic families) within taxa. RESULTS Comparisons between 2x and 2x.nc plants indicated a negligible effect of colchicine treatment on functional traits. Genome doubling increased stomatal length and decreased stomatal density, specific leaf area, and leaf vein density, recapitulating patterns observed in wild polyploid Fragaria. Trichome density, heat stress tolerance, and relative growth rate were not significantly affected by genome doubling. Although clonal reproduction was reduced in response to genome doubling, this effect was strongly genetic-family dependent. CONCLUSIONS The results suggest that genome doubling during incipient speciation alone can generate ecological divergence and variation among genetic lineages. This response potentially allows for rapid short-term evolutionary adaptation and fuels genomic diversity and independent origins of polyploidy.
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Affiliation(s)
- Na Wei
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Zhaokui Du
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, and Institute of Ecology, Taizhou University, Taizhou, Zhejiang, 318000, PR China
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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106
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Chrtek J, Mráz P, Belyayev A, Paštová L, Mrázová V, Caklová P, Josefiová J, Zagorski D, Hartmann M, Jandová M, Pinc J, Fehrer J. Evolutionary history and genetic diversity of apomictic allopolyploids in Hieracium s.str.: morphological versus genomic features. AMERICAN JOURNAL OF BOTANY 2020; 107:66-90. [PMID: 31903548 DOI: 10.1002/ajb2.1413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 11/13/2019] [Indexed: 05/02/2023]
Abstract
PREMISE The origin of allopolyploids is believed to shape their evolutionary potential, ecology, and geographical ranges. Morphologically distinct apomictic types sharing the same parental species belong to the most challenging groups of polyploids. We evaluated the origins and variation of two triploid taxa (Hieracium pallidiflorum, H. picroides) presumably derived from the same diploid parental pair (H. intybaceum, H. prenanthoides). METHODS We used a suite of approaches ranging from morphological, phylogenetic (three unlinked molecular markers), and cytogenetic analyses (in situ hybridization) to genome size screening and genome skimming. RESULTS Genotyping proved the expected parentage of all analyzed accessions of H. pallidiflorum and H. picroides and revealed that nearly all of them originated independently. Genome sizes and genome dosage largely corresponded to morphology, whereas the maternal origin of the allopolyploids had no discernable effect. Polyploid accessions of both parental species usually contained genetic material from other species. Given the phylogenetic distance of the parents, their chromosomes appeared only weakly differentiated in genomic in situ hybridization (GISH), as well as in overall comparisons of the repetitive fraction of their genomes. Furthermore, the repeatome of a phylogenetically more closely related species (H. umbellatum) differed significantly more. CONCLUSIONS We proved (1) multiple origins of hybridogeneous apomicts from the same diploid parental taxa, and (2) allopolyploid origins of polyploid accessions of the parental species. We also showed that the evolutionary dynamics of very fast evolving markers such as satellite DNA or transposable elements does not necessarily follow patterns of speciation.
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Affiliation(s)
- Jindřich Chrtek
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ, 128 01, Praha 2, Czech Republic
| | - Patrik Mráz
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ, 128 01, Praha 2, Czech Republic
| | - Alexander Belyayev
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
| | - Ladislava Paštová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
| | - Viera Mrázová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ, 128 01, Praha 2, Czech Republic
| | - Petra Caklová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
| | - Jiřina Josefiová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
| | - Danijela Zagorski
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
| | - Matthias Hartmann
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
| | - Michaela Jandová
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
| | - Jan Pinc
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ, 128 01, Praha 2, Czech Republic
| | - Judith Fehrer
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ, 252 43, Průhonice, Czech Republic
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107
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Aköz G, Nordborg M. The Aquilegia genome reveals a hybrid origin of core eudicots. Genome Biol 2019; 20:256. [PMID: 31779695 PMCID: PMC6883705 DOI: 10.1186/s13059-019-1888-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/14/2019] [Indexed: 11/29/2022] Open
Abstract
Background Whole-genome duplications (WGDs) have dominated the evolutionary history of plants. One consequence of WGD is a dramatic restructuring of the genome as it undergoes diploidization, a process under which deletions and rearrangements of various sizes scramble the genetic material, leading to a repacking of the genome and eventual return to diploidy. Here, we investigate the history of WGD in the columbine genus Aquilegia, a basal eudicot, and use it to illuminate the origins of the core eudicots. Results Within-genome synteny confirms that columbines are ancient tetraploids, and comparison with the grape genome reveals that this tetraploidy appears to be shared with the core eudicots. Thus, the ancient gamma hexaploidy found in all core eudicots must have involved a two-step process: first, tetraploidy in the ancestry of all eudicots, then hexaploidy in the ancestry of core eudicots. Furthermore, the precise pattern of synteny sharing suggests that the latter involved allopolyploidization and that core eudicots thus have a hybrid origin. Conclusions Novel analyses of synteny sharing together with the well-preserved structure of the columbine genome reveal that the gamma hexaploidy at the root of core eudicots is likely a result of hybridization between a tetraploid and a diploid species.
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Affiliation(s)
- Gökçe Aköz
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria.
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108
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Levin DA. Plant speciation in the age of climate change. ANNALS OF BOTANY 2019; 124:769-775. [PMID: 31250895 PMCID: PMC6868396 DOI: 10.1093/aob/mcz108] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/25/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Species diversity is likely to undergo a sharp decline in the next century. Perhaps as many as 33 % of all plant species may expire as a result of climate change. All parts of the globe will be impacted, and all groups of organisms will be affected. Hundreds of species throughout the world have already experienced local extinction. PERSPECTIVES While thousands of species may become extinct in the next century and beyond, species formation will still occur. I consider which modes of plant species formation are likely to prevail in the next 500 years. I argue that speciation primarily will involve mechanisms that produce reproductively isolated lineages within less (often much less) than 100 generations. I will not especially consider the human element in promoting species formation, because it will continue and because the conclusions presented here are unaffected by it. The impact of climate change may be much more severe and widespread. CONCLUSIONS The most common modes of speciation likely to be operative in the next 500 years ostensibly will be auto- and allopolyploidy. Polyploid species or the antecedents thereof can arise within two generations. Moreover, polyploids often have broader ecological tolerances, and are likely to be more invasive than are their diploid relatives. Polyploid species may themselves spawn additional higher level polyploids either through crosses with diploid species or between pre-existing polyploids. The percentage of polyploid species is likely to exceed 50 % within the next 500 years vs. 35 % today. The stabilized hybrid derivatives (homoploid hybrid speciation) could emerge within a hundred generations after species contact, as could speciation involving chromosomal rearrangements (and perhaps number), but the number of such events is likely to be low. Speciation involving lineage splitting will be infrequent because the formation of substantive pre- and post-zygotic barriers typically takes many thousands of years.
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Affiliation(s)
- Donald A Levin
- Department of Integrative Biology, University of Texas, Austin, USA
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109
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Zhao Q, Wang Y, Bi Y, Zhai Y, Yu X, Cheng C, Wang P, Li J, Lou Q, Chen J. Oligo-painting and GISH reveal meiotic chromosome biases and increased meiotic stability in synthetic allotetraploid Cucumis ×hytivus with dysploid parental karyotypes. BMC PLANT BIOLOGY 2019; 19:471. [PMID: 31694540 PMCID: PMC6833230 DOI: 10.1186/s12870-019-2060-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/27/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND Meiosis of newly formed allopolyploids frequently encounter perturbations induced by the merging of divergent and hybridizable genomes. However, to date, the meiotic properties of allopolyploids with dysploid parental karyotypes have not been studied in detail. The allotetraploid Cucumis ×hytivus (HHCC, 2n = 38) was obtained from interspecific hybridization between C. sativus (CC, 2n = 14) and C. hystrix (HH, 2n = 24) followed by chromosome doubling. The results of this study thus offer an excellent opportunity to explore the meiotic properties of allopolyploids with dysploid parental karyotypes. RESULTS In this report, we describe the meiotic properties of five chromosomes (C5, C7, H1, H9 and H10) and two genomes in interspecific hybrids and C. ×hytivus (the 4th and 14th inbred family) through oligo-painting and genomic in situ hybridization (GISH). We show that 1) only two translocations carrying C5-oligo signals were detected on the chromosomes C2 and C4 of one 14th individual by the karyotyping of eight 4th and 36 14th plants based on C5- and C7-oligo painting, and possible cytological evidence was observed in meiosis of the 4th generation; 2) individual chromosome have biases for homoeologous pairing and univalent formation in F1 hybrids and allotetraploids; 3) extensive H-chromosome autosyndetic pairings (e.g., H-H, 25.5% PMCs) were observed in interspecific F1 hybrid, whereas no C-chromosome autosyndetic pairings were observed (e.g. C-C); 4) the meiotic properties of two subgenomes have significant biases in allotetraploids: H-subgenome exhibits higher univalent and chromosome lagging frequencies than C-subgenome; and 5) increased meiotic stability in the S14 generation compared with the S4 generation, including synchronous meiosis behavior, reduced incidents of univalent and chromosome lagging. CONCLUSIONS These results suggest that the meiotic behavior of two subgenomes has dramatic biases in response to interspecific hybridization and allopolyploidization, and the meiotic behavior harmony of subgenomes is a key subject of meiosis evolution in C. ×hytivus. This study helps to elucidate the meiotic properties and evolution of nascent allopolyploids with the dysploid parental karyotypes.
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Affiliation(s)
- Qinzheng Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095, China
| | - Yunzhu Wang
- Institue of Horticulture, Zhejiang Academy of Agriculture Sciences, Hangzhou, 310021, China
| | - Yunfei Bi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095, China
| | - Yufei Zhai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095, China
| | - Xiaqing Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095, China
| | - Chunyan Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095, China
| | - Panqiao Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095, China
| | - Ji Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095, China
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095, China.
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Weigang Street No.1, Nanjing, 210095, China.
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110
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Hornych O, Ekrt L, Riedel F, Koutecký P, Košnar J. Asymmetric hybridization in Central European populations of the Dryopteris carthusiana group. AMERICAN JOURNAL OF BOTANY 2019; 106:1477-1486. [PMID: 31634425 DOI: 10.1002/ajb2.1369] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 08/30/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Hybridization is a key process in plant speciation. Despite its importance, there is no detailed study of hybridization rates in fern populations. A proper estimate of hybridization rates is needed to understand factors regulating hybridization. METHODS We studied hybridization in the European Dryopteris carthusiana group, represented by one diploid and two tetraploid species and their hybrids. We sampled ~100 individuals per population in 40 mixed populations of the D. carthusiana group across Europe. All plants were identified by measuring genome size (DAPI staining) using flow cytometry. To determine the maternal parentage of hybrids, we sequenced the chloroplast region trnL-trnF of all taxa involved. RESULTS We found hybrids in 85% of populations. Triploid D. ×ambroseae occurred in every population that included both parent species and is most abundant when the parent species are equally abundant. By contrast, tetraploid D. ×deweveri was rare (15 individuals total) and triploid D. ×sarvelae was absent. The parentage of hybrid taxa is asymmetric. Despite expectations from previous studies, tetraploid D. dilatata is the predominant male parent of its triploid hybrid. CONCLUSIONS This is a thorough investigation of hybridization rates in natural populations of ferns. Hybridization rates differ greatly even among closely related fern taxa. In contrast to angiosperms, our data suggest that hybridization rates are highest in balanced parent populations and support the notion that some ferns possess very weak barriers to hybridization. Our results from sequencing cpDNA challenge established notions about the correlation of ploidy level and mating tendencies.
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Affiliation(s)
- Ondřej Hornych
- Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
| | - Libor Ekrt
- Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
| | - Felix Riedel
- Botanischer Garten der Universität Potsdam, Maulbeerallee 3, Potsdam, D-14469, Germany
- Arboretum der Humboldt-Universität zu Berlin, Späthstrasse 80/81, Berlin, D-12437, Germany
| | - Petr Koutecký
- Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
| | - Jiří Košnar
- Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
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111
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Van Drunen WE, Husband BC. Evolutionary associations between polyploidy, clonal reproduction, and perenniality in the angiosperms. THE NEW PHYTOLOGIST 2019; 224:1266-1277. [PMID: 31215649 DOI: 10.1111/nph.15999] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/10/2019] [Indexed: 05/10/2023]
Abstract
Clonal reproduction is thought to facilitate polyploid establishment in the angiosperms, but the evolutionary relationship between polyploidy and clonality has not been thoroughly tested. A perennial life history may confer many of the same advantages, and the relative importance of clonality versus perenniality is unknown. We used phylogenetic comparative analyses of 1751 species to examine associations between polyploidy, clonality, and life history. We test hypotheses of co-evolution by determining the sequence of trait development. Polyploidy is associated with both clonality and perenniality across species, and analyses show that clonality can be an important predictor of polyploidy beyond perenniality. Tests of directionality on our full dataset suggest that polyploidy is more likely to promote clonality or perenniality than vice versa, although there are significant differences in patterns of co-evolution among major angiosperm groups. Our results suggest that polyploidy and clonal reproduction are evolutionarily associated across the angiosperms, even when perenniality is considered, but we find little evidence at the whole-angiosperm level for the hypothesis that clonality promotes polyploidy. However, variation among different clades indicates that polyploidy and clonality are interacting in diverse ways, likely to be due to the variable roles of clonality in their evolutionary histories.
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Affiliation(s)
- Wendy E Van Drunen
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Brian C Husband
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
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112
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Wang J, Qin J, Sun P, Ma X, Yu J, Li Y, Sun S, Lei T, Meng F, Wei C, Li X, Guo H, Liu X, Xia R, Wang L, Ge W, Song X, Zhang L, Guo D, Wang J, Bao S, Jiang S, Feng Y, Li X, Paterson AH, Wang X. Polyploidy Index and Its Implications for the Evolution of Polyploids. Front Genet 2019; 10:807. [PMID: 31552101 PMCID: PMC6746930 DOI: 10.3389/fgene.2019.00807] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/02/2019] [Indexed: 11/13/2022] Open
Abstract
Polyploidy has contributed to the divergence and domestication of plants; however, estimation of the relative roles that different types of polyploidy have played during evolution has been difficult. Unbalanced and balanced gene removal was previously related to allopolyploidies and autopolyploidies, respectively. Here, to infer the types of polyploidies and evaluate their evolutionary effects, we devised a statistic, the Polyploidy-index or P-index, to characterize the degree of divergence between subgenomes of a polyploidy, to find whether there has been a balanced or unbalanced gene removal from the homoeologous regions. Based on a P-index threshold of 0.3 that distinguishes between known or previously inferred allo- or autopolyploidies, we found that 87.5% of 24 angiosperm paleo-polyploidies were likely produced by allopolyploidizations, responsible for establishment of major tribes such as Poaceae and Fabaceae, and large groups such as monocots and eudicots. These findings suggest that >99.7% of plant genomes likely derived directly from allopolyploidies, with autopolyploidies responsible for the establishment of only a few small genera, including Glycine, Malus, and Populus, each containing tens of species. Overall, these findings show that polyploids with high divergence between subgenomes (presumably allopolyploids) established the major plant groups, possibly through secondary contact between previously isolated populations and hybrid vigor associated with their re-joining.
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Affiliation(s)
- Jinpeng Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China.,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jun Qin
- Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Pengchuan Sun
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xuelian Ma
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Jigao Yu
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Yuxian Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Sangrong Sun
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Tianyu Lei
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Fanbo Meng
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Chendan Wei
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xinyu Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - He Guo
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xiaojian Liu
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Ruiyan Xia
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Li Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Weina Ge
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xiaoming Song
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Lan Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Di Guo
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Jinyu Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Shoutong Bao
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Shan Jiang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Yishan Feng
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Xueping Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
| | - Xiyin Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
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113
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Comparative linkage mapping of diploid, tetraploid, and hexaploid Avena species suggests extensive chromosome rearrangement in ancestral diploids. Sci Rep 2019; 9:12298. [PMID: 31444367 DOI: 10.1038/s41598-019-48639-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 07/10/2019] [Indexed: 12/30/2022] Open
Abstract
The genus Avena (oats) contains diploid, tetraploid and hexaploid species that evolved through hybridization and polyploidization. Four genome types (named A through D) are generally recognized. We used GBS markers to construct linkage maps of A genome diploid (Avena strigosa x A. wiestii, 2n = 14), and AB genome tetraploid (A. barbata 2n = 28) oats. These maps greatly improve coverage from older marker systems. Seven linkage groups in the tetraploid showed much stronger homology and synteny with the A genome diploids than did the other seven, implying an allopolyploid hybrid origin of A. barbata from distinct A and B genome diploid ancestors. Inferred homeologies within A. barbata revealed that the A and B genomes are differentiated by several translocations between chromosomes within each subgenome. However, no translocation exchanges were observed between A and B genomes. Comparison to a consensus map of ACD hexaploid A. sativa (2n = 42) revealed that the A and D genomes of A. sativa show parallel rearrangements when compared to the A genomes of the diploids and tetraploids. While intergenomic translocations are well known in polyploid Avena, our results are most parsimoniously explained if translocations also occurred in the A, B and D genome diploid ancestors of polyploid Avena.
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114
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Wang R, Liu H, Liu Z, Zou J, Meng J, Wang J. Genome-wide analysis of alternative splicing divergences between Brassica hexaploid and its parents. PLANTA 2019; 250:603-628. [PMID: 31139927 DOI: 10.1007/s00425-019-03198-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 05/24/2019] [Indexed: 05/23/2023]
Abstract
Compared with its parents, Brassica hexaploid underwent significant AS changes, which may provide diversified gene expression regulation patterns and could enhance its adaptability during evolution Polyploidization is considered a significant evolution force that promotes species formation. Alternative splicing (AS) plays a crucial role in multiple biological processes during plant growth and development. To explore the effects of allopolyploidization on the AS patterns of genes, a genome-wide AS analysis was performed by RNA-seq in Brassica hexaploid and its parents. In total, we found 7913 (27540 AS events), 14447 (70179 AS events), and 13205 (60804 AS events) AS genes in Brassica rapa, Brassica carinata, and Brassica hexaploid, respectively. A total of 920 new AS genes were discovered in Brassica hexaploid. There were 56 differently spliced genes between Brassica hexaploid and its parents. In addition, most of the alternative 5' splice sites were located 4 bp upstream of the dominant 5' splice sites, and most of the alternative 3' splice sites were located 3 bp downstream of the dominant 3' splice sites in Brassica hexapliod, which was similar to B. carinata. Furthermore, we cloned and sequenced all amplicons from the RT-PCR products of GRP7/8, namely, Bol045859, Bol016025 and Bol02880. The three genes were found to produce AS transcripts in a new way. The AS patterns of genes were diverse between Brassica hexaploid and its parents, including the loss and gain of AS events. Allopolyploidization changed alternative splicing sites of pre-mRNAs in Brassica hexaploid, which brought about alterations in the sequences of transcripts. Our study provided novel insights into the AS patterns of genes in allopolyploid plants, which may provide a reference for the study of polyploidy adaptability.
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Affiliation(s)
- Ruihua Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Helian Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhengyi Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.
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115
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Hadle JJ, Russell FL, Beck JB. Are buffalograss (Buchloë dactyloides) cytotypes spatially and ecologically differentiated? AMERICAN JOURNAL OF BOTANY 2019; 106:1116-1125. [PMID: 31334845 DOI: 10.1002/ajb2.1327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 05/13/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Although autopolyploidy is common among dominant Great Plains grasses, the distribution of cytotypes within a given species is typically poorly understood. This study aims to establish the geographic distribution of cytotypes within buffalograss (Buchloë dactyloides) and to assess whether individual cytotypes have differing ecological tolerances. METHODS A range-wide set of 578 B. dactyloides individuals was obtained through field collecting and sampling from herbarium specimens. The cytotype of each sample was estimated by determining allele numbers at 13 simple sequence repeat loci, a strategy that was assessed by comparing estimated to known cytotype in 79 chromosome-counted samples. Ecological differentiation between the dominant tetraploid and hexaploid cytotypes was assessed with analyses of macroclimatic variables. RESULTS Simple sequence repeat variation accurately estimated cytotype in 89% of samples from which a chromosome count had been obtained. Applying this approach to samples of unknown ploidy established that diploids and pentaploids are rare, with the common tetraploid and hexaploid cytotypes generally occurring in sites to the north/west (tetraploid) or south/east (hexaploid) portions of the species range. Both MANOVA and niche modeling approaches identified significant but subtle differences in macroclimatic conditions at the set of locations occupied by these two dominant cytotypes. CONCLUSIONS Incorporating chromosome count vouchers and cytotype-estimated herbarium records allowed us to perform the largest study of cytotype niche differentiation to date. Buffalograss cytotypes differ greatly in frequency, the common tetraploid and hexaploid cytotypes are non-randomly distributed, and these two cytotypes are subtly ecologically differentiated.
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Affiliation(s)
- Jacob J Hadle
- Department of Biological Sciences, Wichita State University, Wichita, KS, 67260, USA
| | - F Leland Russell
- Department of Biological Sciences, Wichita State University, Wichita, KS, 67260, USA
| | - James B Beck
- Department of Biological Sciences, Wichita State University, Wichita, KS, 67260, USA
- Botanical Research Institute of Texas, Fort Worth, TX, 76107, USA
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116
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Zhang Z, Fu T, Liu Z, Wang X, Xun H, Li G, Ding B, Dong Y, Lin X, Sanguinet KA, Liu B, Wu Y, Gong L. Extensive changes in gene expression and alternative splicing due to homoeologous exchange in rice segmental allopolyploids. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2295-2308. [PMID: 31098756 DOI: 10.1007/s00122-019-03355-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 04/26/2019] [Indexed: 06/09/2023]
Abstract
We report rampant homoeologous exchanges in progenies of a newly synthesized rice segmental allotetraploid and demonstrate their consequences to changes of gene expression and alternative splicing. Allopolyploidization is recurrent across the tree of angiosperms and known as a driving evolutionary force in both plants and animals. A salient feature of allopolyploidization is the induction of homoeologous exchange (HE) events between the constituent subgenomes, which may in turn cause changes in gene expression, transcript alternative splicing, and phenotypic novelty. However, this issue has been poorly studied, largely because lack of a system in which the exact parentage donating the subgenomes is known and the HE events are occurring in real time. Here, we employed whole-genome re-sequencing and RNA-seq-based transcriptome profiling in four randomly chosen progeny individuals (at the 10th-selfed generation) of segmental allotetraploids that were constructed by colchicine-mediated whole-genome doubling of F1 hybrids between the two subspecies (japonica and indica) of Asian cultivated Oryza sativa. We show that rampant HE events occurred in these tetraploid individuals, which converted most of the otherwise heterozygous genomic regions into a homogenized state of one parental subgenome. We demonstrate that genes within these homogenized genomic regions in the tetraploids showed high frequencies of altered expression and enhanced alternative splicing relative to their counterparts in the corresponding diploid parents in the embryo tissue. Intriguingly, limited overlaps between the differentially expressed genes and the differential alternative spliced genes were identified, which were partitioned to distinctly enriched gene ontology terms. Together, our results indicate that HE is a major mechanism to rapidly generate novelty in gene expression and transcriptome diversity, which may facilitate phenotypic innovation in nascent allopolyploids and relevant to allopolyploid crop breeding.
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Affiliation(s)
- Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Tiansi Fu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zhijian Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xutong Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Hongwei Xun
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Guo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Baoxu Ding
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yuzhu Dong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Xiuyun Lin
- Jilin Academy of Agricultural Sciences (JAAS), Changchun, 136100, China
| | - Karen A Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ying Wu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China.
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117
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Vogt G, Dorn NJ, Pfeiffer M, Lukhaup C, Williams BW, Schulz R, Schrimpf A. The dimension of biological change caused by autotriploidy: A meta-analysis with triploid crayfish Procambarus virginalis and its diploid parent Procambarus fallax. ZOOL ANZ 2019. [DOI: 10.1016/j.jcz.2019.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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118
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Hanušová K, Čertner M, Urfus T, Koutecký P, Košnar J, Rothfels CJ, Jarolímová V, Ptáček J, Ekrt L. Widespread co-occurrence of multiple ploidy levels in fragile ferns (Cystopteris fragilis complex; Cystopteridaceae) probably stems from similar ecology of cytotypes, their efficient dispersal and inter-ploidy hybridization. ANNALS OF BOTANY 2019; 123:845-855. [PMID: 30541055 PMCID: PMC6526313 DOI: 10.1093/aob/mcy219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 11/09/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Polyploidy has played an important role in the evolution of ferns. However, the dearth of data on cytotype diversity, cytotype distribution patterns and ecology in ferns is striking in comparison with angiosperms and prevents an assessment of whether cytotype coexistence and its mechanisms show similar patterns in both plant groups. Here, an attempt to fill this gap was made using the ploidy-variable and widely distributed Cystopteris fragilis complex. METHODS Flow cytometry was used to assess DNA ploidy level and monoploid genome size (Cx value) of 5518 C. fragilis individuals from 449 populations collected over most of the species' global distributional range, supplemented with data from 405 individuals representing other related species from the complex. Ecological preferences of C. fragilis tetraploids and hexaploids were compared using field-recorded parameters and database-extracted climate data. KEY RESULTS Altogether, five different ploidy levels (2x, 4x, 5x, 6x, 8x) were detected and three species exhibited intraspecific ploidy-level variation: C. fragilis, C. alpina and C. diaphana. Two predominant C. fragilis cytotypes, tetraploids and hexaploids, co-occur over most of Europe in a diffuse, mosaic-like pattern. Within this contact zone, 40 % of populations were mixed-ploidy and most also contained pentaploid hybrids. Environmental conditions had only a limited effect on the distribution of cytotypes. Differences were found in the Cx value of tetraploids and hexaploids: between-cytotype divergence was higher in uniform-ploidy than in mixed-ploidy populations. CONCLUSIONS High ploidy-level diversity and widespread cytotype coexistence in the C. fragilis complex match the well-documented patterns in some angiosperms. While ploidy coexistence in C. fragilis is not driven by environmental factors, it could be facilitated by the perennial life-form of the species, its reproductive modes and efficient wind dispersal of spores. Independent origins of hexaploids and/or inter-ploidy gene flow may be expected in mixed-ploidy populations according to Cx value comparisons.
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Affiliation(s)
- Kristýna Hanušová
- Department of Botany, Faculty of Science, Charles University, Benátská, Praha, Czech Republic
| | - Martin Čertner
- Department of Botany, Faculty of Science, Charles University, Benátská, Praha, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Zámek, Průhonice, Czech Republic
| | - Tomáš Urfus
- Department of Botany, Faculty of Science, Charles University, Benátská, Praha, Czech Republic
| | - Petr Koutecký
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská, České Budějovice, Czech Republic
| | - Jiří Košnar
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská, České Budějovice, Czech Republic
| | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Vlasta Jarolímová
- Institute of Botany, The Czech Academy of Sciences, Zámek, Průhonice, Czech Republic
| | - Jan Ptáček
- Department of Botany, Faculty of Science, Charles University, Benátská, Praha, Czech Republic
| | - Libor Ekrt
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská, České Budějovice, Czech Republic
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119
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Rodionov AV, Amosova AV, Belyakov EA, Zhurbenko PM, Mikhailova YV, Punina EO, Shneyer VS, Loskutov IG, Muravenko OV. Genetic Consequences of Interspecific Hybridization, Its Role in Speciation and Phenotypic Diversity of Plants. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419030141] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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120
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Genomic Prediction of Autotetraploids; Influence of Relationship Matrices, Allele Dosage, and Continuous Genotyping Calls in Phenotype Prediction. G3-GENES GENOMES GENETICS 2019; 9:1189-1198. [PMID: 30782769 PMCID: PMC6469427 DOI: 10.1534/g3.119.400059] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Estimation of allele dosage, using genomic data, in autopolyploids is challenging and current methods often result in the misclassification of genotypes. Some progress has been made when using SNP arrays, but the major challenge is when using next generation sequencing data. Here we compare the use of read depth as continuous parameterization with ploidy parameterizations in the context of genomic selection (GS). Additionally, different sources of information to build relationship matrices were compared. A real breeding population of the autotetraploid species blueberry (Vaccinium corybosum), composed of 1,847 individuals was phenotyped for eight yield and fruit quality traits over two years. Continuous genotypic based models performed as well as the best models. This approach also reduces the computational time and avoids problems associated with misclassification of genotypic classes when assigning dosage in polyploid species. This approach could be very valuable for species with higher ploidy levels or for emerging crops where ploidy is not well understood. To our knowledge, this work constitutes the first study of genomic selection in blueberry. Accuracies are encouraging for application of GS for blueberry breeding. GS could reduce the time for cultivar release by three years, increasing the genetic gain per cycle by 86% on average when compared to phenotypic selection, and 32% when compared with pedigree-based selection. Finally, the genotypic and phenotypic data used in this study are made available for comparative analysis of dosage calling and genomic selection prediction models in the context of autopolyploids.
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121
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Li M, Wang R, Liang Z, Wu X, Wang J. Genome-wide identification and analysis of the EIN3/EIL gene family in allotetraploid Brassica napus reveal its potential advantages during polyploidization. BMC PLANT BIOLOGY 2019; 19:110. [PMID: 30898097 PMCID: PMC6429743 DOI: 10.1186/s12870-019-1716-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 03/12/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND Polyploidization is a common event in the evolutionary history of angiosperms, and there will be some changes in the genomes of plants other than a simple genomic doubling after polyploidization. Allotetraploid Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are a good group for studying the problems associated with polyploidization. On the other hand, the EIN3/EIL gene family is an important gene family in plants, all members of which are key genes in the ethylene signaling pathway. Until now, the EIN3/EIL gene family in B. napus and its diploid progenitors have been largely unknown, so it is necessary to comprehensively identify and analyze this gene family. RESULTS In this study, 13, 7 and 7 EIN3/EIL genes were identified in B. napus (2n = 4x = 38, AnCn), B. rapa (2n = 2x = 20, Ar) and B. oleracea (2n = 2x = 18, Co). All of the identified EIN3/EIL proteins were divided into 3 clades and further divided into 8 sub-clades. Ka/Ks analysis showed that all identified EIN3/EIL genes underwent purifying selection after the duplication events. Moreover, gene structure analysis showed that some EIN3/EIL genes in B. napus acquired introns during polyploidization, and homolog expression bias analysis showed that B. napus was biased towards its diploid progenitor B. rapa. The promoters of the EIN3/EIL genes in B. napus contained more cis-acting elements, which were mainly involved in endosperm gene expression and light responsiveness, than its diploid progenitors. Thus, B. napus might have potential advantages in some biological aspects. CONCLUSIONS The results indicated allotetraploid B. napus might have potential advantages in some biological aspects. Moreover, our results can increase the understanding of the evolution of the EIN3/EIL gene family in B. napus, and provided more reference for future research about polyploidization.
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Affiliation(s)
- Mengdi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Ruihua Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Ziwei Liang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan, 430062 China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 China
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122
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Morales-Briones DF, Tank DC. Extensive allopolyploidy in the neotropical genus Lachemilla (Rosaceae) revealed by PCR-based target enrichment of the nuclear ribosomal DNA cistron and plastid phylogenomics. AMERICAN JOURNAL OF BOTANY 2019; 106:415-437. [PMID: 30882906 DOI: 10.1002/ajb2.1253] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 01/10/2019] [Indexed: 06/09/2023]
Abstract
PREMISE OF THE STUDY Polyploidy has been long recognized as an important force in plant evolution. Previous studies had suggested widespread occurrence of polyploidy and the allopolyploid origin of several species in the diverse neotropical genus Lachemilla (Rosaceae). Nonetheless, this evidence has relied mostly on patterns of cytonuclear discordance, and direct evidence from nuclear allelic markers is still needed. METHODS Here we used PCR target enrichment in combination with high throughput sequencing to obtain multiple copies of the nuclear ribosomal (nr) DNA cistron and 45 regions of the plastid genome (cpDNA) from 219 accessions representing 48 species of Lachemilla and to explore the allopolyploid origin of species in this group. KEY RESULTS We were able to identify multiple nrDNA ribotypes and establish clear evidence of allopolyploidy in 33 species of Lachemilla, showing that this condition is common and widespread in the genus. Additionally, we found evidence for three autopolyploid species. We also established multiple, independent origins of several allopolyploid species. Finally, based solely on the cpDNA phylogeny, we identified that the monotypic genus Farinopsis is the sister group of Lachemilla and allied genera within subtribe Fragariinae. CONCLUSIONS Our study demonstrates the utility of the nuclear ribosomal DNA cistron to detect allopolyploidy when concerted evolution of this region is not complete. Additionally, with a robust chloroplast phylogeny in place, the direction of hybridization events can be established, and multiple, independent origins of allopolyploid species can be identified.
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Affiliation(s)
- Diego F Morales-Briones
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, ID, 83844-3051, USA
- Stillinger Herbarium, University of Idaho, 875 Perimeter Drive, MS 1133, Moscow, ID, 83844-1133, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, ID, 83844-3051, USA
| | - David C Tank
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, ID, 83844-3051, USA
- Stillinger Herbarium, University of Idaho, 875 Perimeter Drive, MS 1133, Moscow, ID, 83844-1133, USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, ID, 83844-3051, USA
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123
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Porturas LD, Anneberg TJ, Curé AE, Wang S, Althoff DM, Segraves KA. A meta-analysis of whole genome duplication and the effects on flowering traits in plants. AMERICAN JOURNAL OF BOTANY 2019; 106:469-476. [PMID: 30901499 DOI: 10.1002/ajb2.1258] [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] [Received: 11/03/2018] [Accepted: 01/14/2019] [Indexed: 06/09/2023]
Abstract
PREMISE OF THE STUDY Polyploidy, or whole genome duplication (WGD), is common in plants despite theory suggesting that polyploid establishment is challenging and polyploids should be evolutionarily transitory. There is renewed interest in understanding the mechanisms that could facilitate polyploid establishment and explain their pervasiveness in nature. In particular, premating isolation from their diploid progenitors is suggested to be a crucial factor. To evaluate how changes in assortative mating occur, we need to understand the phenotypic effects of WGD on reproductive traits. METHODS We used literature surveys and a meta-analysis to assess how WGD affects floral morphology, flowering phenology, and reproductive output in plants. We focused specifically on comparisons of newly generated polyploids (neopolyploids) and their parents to mitigate potential confounding effects of adaptation and drift that may be present in ancient polyploids. KEY RESULTS The results indicated that across a broad representation of angiosperms, floral morphology traits increased in size, reproductive output decreased, and flowering phenology was unaffected by WGD. Additionally, we found that increased trait variation after WGD was uncommon for the phenotypic traits examined. CONCLUSIONS Our results suggest that the phenotypic effects on traits important to premating isolation of neopolyploids are small, in general. Changes in flowering phenology, reproductive output, and phenotypic variation resulting from WGD may be less critical in facilitating premating isolation and neopolyploid establishment. However, floral traits for which size is an important component of function (e.g., pollen transfer) could be strongly influenced by WGD.
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Affiliation(s)
- Laura D Porturas
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Thomas J Anneberg
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Anne E Curé
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Shengpei Wang
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - David M Althoff
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Kari A Segraves
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
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Wei N, Cronn R, Liston A, Ashman T. Functional trait divergence and trait plasticity confer polyploid advantage in heterogeneous environments. THE NEW PHYTOLOGIST 2019; 221:2286-2297. [PMID: 30281801 PMCID: PMC6587808 DOI: 10.1111/nph.15508] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/24/2018] [Indexed: 05/09/2023]
Abstract
Polyploidy, or whole-genome duplication often with hybridization, is common in eukaryotes and is thought to drive ecological and evolutionary success, especially in plants. The mechanisms of polyploid success in ecologically relevant contexts, however, remain largely unknown. We conducted an extensive test of functional trait divergence and plasticity in conferring polyploid fitness advantage in heterogeneous environments, by growing clonal replicates of a worldwide genotype collection of six allopolyploid and five diploid wild strawberry (Fragaria) taxa in three climatically different common gardens. Among leaf functional traits, we detected divergence in trait means but not plasticities between polyploids and diploids, suggesting that increased genomic redundancy in polyploids does not necessarily translate into greater trait plasticity in response to environmental change. Across the heterogeneous garden environments, however, polyploids exhibited fitness advantage, which was conferred by both trait means and adaptive trait plasticities, supporting a 'jack-and-master' hypothesis for polyploids. Our findings elucidate essential ecological mechanisms underlying polyploid adaptation to heterogeneous environments, and provide an important insight into the prevalence and persistence of polyploid plants.
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Affiliation(s)
- Na Wei
- Department of Biological SciencesUniversity of PittsburghPittsburghPA15260USA
| | - Richard Cronn
- Pacific Northwest Research StationUnited States Department of Agriculture Forest ServiceCorvallisOR97331USA
| | - Aaron Liston
- Department of Botany and Plant PathologyOregon State UniversityCorvallisOR97331USA
| | - Tia‐Lynn Ashman
- Department of Biological SciencesUniversity of PittsburghPittsburghPA15260USA
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125
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Visger CJ, Wong GKS, Zhang Y, Soltis PS, Soltis DE. Divergent gene expression levels between diploid and autotetraploid Tolmiea relative to the total transcriptome, the cell, and biomass. AMERICAN JOURNAL OF BOTANY 2019; 106:280-291. [PMID: 30779448 DOI: 10.1002/ajb2.1239] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/03/2018] [Indexed: 05/28/2023]
Abstract
PREMISE OF THE STUDY Studies of gene expression and polyploidy are typically restricted to characterizing differences in transcript concentration. Using diploid and autotetraploid Tolmiea, we present an integrated approach for cross-ploidy comparisons that account for differences in transcriptome size and cell density and make multiple comparisons of transcript abundance. METHODS We use RNA spike-in standards in concert with cell size and density to identify and correct for differences in transcriptome size and compare levels of gene expression across multiple scales: per transcriptome, per cell, and per biomass. KEY RESULTS In total, ~17% of all loci were identified as differentially expressed (DEGs) between the diploid and autopolyploid species. The per-transcriptome normalization, the method researchers typically use, captured the fewest DEGs (58% of total DEGs) and failed to detect any DEGs not found by the alternative normalizations. When transcript abundance was normalized per biomass and per cell, ~66% and ~82% of the total DEGs were recovered, respectively. The discrepancy between per-transcriptome and per-cell recovery of DEGs occurs because per-transcriptome normalizations are concentration-based and therefore blind to differences in transcriptome size. CONCLUSIONS While each normalization enables valid comparisons at biologically relevant scales, a holistic comparison of multiple normalizations provides additional explanatory power not available from any single approach. Notably, autotetraploid loci tend to conserve diploid-like transcript abundance per biomass through increased gene expression per cell, and these loci are enriched for photosynthesis-related functions.
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Affiliation(s)
- Clayton J Visger
- Department of Biological Sciences, California State University Sacramento, Sacramento, CA, 95819, USA
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- Beijing Genomics Institute-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Yong Zhang
- Beijing Genomics Institute-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
- Shenzhen Hua Han Gene Co. Ltd., 7F Jian An Shan Hai Building, No. 8000, Shennan Road, Futian District, Shenzhen, 518040, China
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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126
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Wang W, Guan R, Liu X, Zhang H, Song B, Xu Q, Fan G, Chen W, Wu X, Liu X, Wang J. Chromosome level comparative analysis of Brassica genomes. PLANT MOLECULAR BIOLOGY 2019; 99:237-249. [PMID: 30632049 DOI: 10.1007/s11103-018-0814-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/14/2018] [Indexed: 06/09/2023]
Abstract
We provided a chromosome-length assembly of B. nigra and show the comprehensive chromosome-scale variations among Brassica genomes. Chromosome-level assembly of the Brassica species, which include many important crops, is essential for the agricultural and evolutionary studies. While the present B. nigra chromosomes was connected with genetic map of B. juncea, hindering the comparative analysis of the B chromosomes. Here we present a chromosome-length B. nigra assembly constructed with Hi-C connections and its variations on chromosome level compared with other Brassica species. We produced an assembly of 484 Mb annotated with 51,829 genes, of which 393 Mb were anchored onto 8 chromosomes, taking 81.26% of the assembly. Comparison of the B chromosomes shows high concordance of the two B. nigra assemblies and reveals comprehensive variations of the B chromosomes after polyploidization and gene loss in syntenic regions. Chromosome blocks with variations have lower gene density and higher TE content. Furthermore, we compared the chromosomes of the three major Brassica diploids, which showed that most of the variations between B and A/C had completed before A/C divergence and there are more variations on C chromosomes after their divergence. In summary, our work presents a chromosome-length assembly of B. nigra and comprehensive comparative analysis of the Brassica chromosomes, which provides a useful reference for other studies and comprehensive information of Brassica chromosome evolution.
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Affiliation(s)
- Wenliang Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083, China
| | - Rui Guan
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083, China
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Xing Liu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083, China
| | - Haorui Zhang
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083, China
| | - Bo Song
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083, China
| | - Qiwu Xu
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083, China
| | - Guangyi Fan
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083, China
| | - Wenbin Chen
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083, China
| | - Xiaoming Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, 518083, China.
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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127
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Li Q, Qiao X, Yin H, Zhou Y, Dong H, Qi K, Li L, Zhang S. Unbiased subgenome evolution following a recent whole-genome duplication in pear ( Pyrus bretschneideri Rehd.). HORTICULTURE RESEARCH 2019; 6:34. [PMID: 30854211 PMCID: PMC6395616 DOI: 10.1038/s41438-018-0110-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 11/09/2018] [Accepted: 11/23/2018] [Indexed: 05/06/2023]
Abstract
Genome fractionation (also known as diploidization) frequently occurs following paleopolyploidization events. Biased fractionation between subgenomes has been found in some paleo-allopolyploids, while this phenomenon is absent in paleo-autopolyploids. Pear (Pyrus bretschneideri Rehd.) experienced a recent whole-genome duplication (WGD, ~30 million years ago); however, the evolutionary fate of the two subgenomes derived from this WGD event is not clear. In this study, we identified the two paleo-subgenomes in pear using peach (Prunus persica) as an outgroup and investigated differences in the gene loss rate, evolutionary rate, gene expression level, and DNA methylation level between these two subgenomes. Fractionation bias was not found between the two pear subgenomes, which evolved at similar evolutionary rates. The DNA methylation level of the two subgenomes showed little bias, and we found no expression dominance between the subgenomes. However, we found that singleton genes and homeologous genes within each subgenome showed divergent evolutionary patterns of selective constraints, expression and epigenetic modification. These results provide insights into subgenome evolution following paleopolyploidization in pear.
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Affiliation(s)
- Qionghou Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, 210095 Nanjing, China
| | - Xin Qiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, 210095 Nanjing, China
| | - Hao Yin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, 210095 Nanjing, China
| | - Yuhang Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, 210095 Nanjing, China
| | - Huizhen Dong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, 210095 Nanjing, China
| | - Kaijie Qi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, 210095 Nanjing, China
| | - Leiting Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, 210095 Nanjing, China
| | - Shaoling Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, 210095 Nanjing, China
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128
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Frajman B, Schönswetter P, Weiss-Schneeweiss H, Oxelman B. Origin and Diversification of South American Polyploid Silene Sect. Physolychnis (Caryophyllaceae) in the Andes and Patagonia. Front Genet 2018; 9:639. [PMID: 30619464 PMCID: PMC6297176 DOI: 10.3389/fgene.2018.00639] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/27/2018] [Indexed: 12/18/2022] Open
Abstract
The Andes are an important biogeographic region in South America extending for about 8000 km from Venezuela to Argentina. They are - along with the Patagonian steppes - the main distribution area of ca. 18 polyploid species of Silene sect. Physolychnis. Using nuclear ITS and plastid psbE-petG and matK sequences, flow cytometric ploidy level estimations and chromosome counts, and including 13 South American species, we explored the origin and diversification of this group. Our data suggest a single, late Pliocene or early Pleistocene migration of the North American S. verecunda lineage to South America, which was followed by dispersal and diversification of this tetraploid lineage in the Andes, other Argentinian mountain ranges and the Patagonian steppes. Later in the Pleistocene South American populations hybridized with the S. uralensis lineage, which led to allopolyploidisation and origin of decaploid S. chilensis and S. echegarayi occurring at high elevations. Additionally, we show that the morphological differentiation in leaf shape correlated with divergent habitats (high elevation Andes vs. lower elevation Patagonian steppes) is also supported phylogenetically, especially in the ITS tree. Lastly, the species boundaries among the narrow-leaved Patagonian steppe species are poorly resolved and need more thorough taxonomic revision.
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Affiliation(s)
- Božo Frajman
- Department of Botany, University of Innsbruck, Innsbruck, Austria
| | | | | | - Bengt Oxelman
- Department of Plant and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
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129
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Mairal M, Šurinová M, Castro S, Münzbergová Z. Unmasking cryptic biodiversity in polyploids: origin and diversification of Aster amellus aggregate. ANNALS OF BOTANY 2018; 122:1047-1059. [PMID: 30107389 PMCID: PMC6266133 DOI: 10.1093/aob/mcy149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/18/2018] [Indexed: 05/14/2023]
Abstract
BACKGROUND AND AIMS The origin of different cytotypes by autopolyploidy may be an important mechanism in plant diversification. Although cryptic autopolyploids probably comprise the largest fraction of overlooked plant diversity, our knowledge of their origin and evolution is still rather limited. Here we study the presumed autopolyploid aggregate of Aster amellus, which encompasses diploid and hexaploid cytotypes. Although the cytotypes of A. amellus are not morphologically distinguishable, previous studies showed spatial segregation and limited gene flow between them, which could result in different evolutionary trajectories for each cytotype. METHODS We combine macroevolutionary, microevolutionary and niche modelling tools to disentangle the origin and the demographic history of the cytotypes, using chloroplast and nuclear markers in a dense population sampling in central Europe. KEY RESULTS Our results revealed a segregation between diploid and hexaploid cytotypes in the nuclear genome, where each cytotype represents a monophyletic lineage probably homogenized by concerted evolution. In contrast, the chloroplast genome showed intermixed connections between the cytotypes, which may correspond to shared ancestral relationships. Phylogeny, demographic analyses and ecological niche modelling supported an ongoing differentiation of the cytotypes, where the hexaploid cytotype is experiencing a demographic expansion and niche differentiation with respect to its diploid relative. CONCLUSIONS The two cytotypes may be considered as two different lineages at the onset of their evolutionary diversification. Polyploidization led to the occurrence of hexaploids, which expanded and changed their ecological niche.
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Affiliation(s)
- Mario Mairal
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Population Ecology, Czech Academy of Science, Průhonice, Czech Republic
- Department of Botany and Zoology, Stellenbosch University, Matieland, South Africa
- For correspondence. E-mail
| | - Mária Šurinová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Population Ecology, Czech Academy of Science, Průhonice, Czech Republic
| | - Sílvia Castro
- Centre for Functional Ecology, Department of Life Sciences of the University of Coimbra and Botanic Garden of the University of Coimbra, Coimbra, Portugal
| | - Zuzana Münzbergová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Population Ecology, Czech Academy of Science, Průhonice, Czech Republic
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Chase MW, Christenhusz MJM, Conran JG, Dodsworth S, Medeiros de Assis FN, Felix LP, Fay MF. UNEXPECTED DIVERSITY OF AUSTRALIAN TOBACCO SPECIES (NICOTIANASECTIONSUAVEOLENTES,SOLANACEAE). ACTA ACUST UNITED AC 2018. [DOI: 10.1111/curt.12241] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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131
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Blischak PD, Mabry ME, Conant GC, Pires JC. Integrating Networks, Phylogenomics, and Population Genomics for the Study of Polyploidy. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2018. [DOI: 10.1146/annurev-ecolsys-121415-032302] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Duplication events are regarded as sources of evolutionary novelty, but our understanding of general trends for the long-term trajectory of additional genomic material is still lacking. Organisms with a history of whole genome duplication (WGD) offer a unique opportunity to study potential trends in the context of gene retention and/or loss, gene and network dosage, and changes in gene expression. In this review, we discuss the prevalence of polyploidy across the tree of life, followed by an overview of studies investigating genome evolution and gene expression. We then provide an overview of methods in network biology, phylogenomics, and population genomics that are critical for advancing our understanding of evolution post-WGD, highlighting the need for models that can accommodate polyploids. Finally, we close with a brief note on the importance of random processes in the evolution of polyploids with respect to neutral versus selective forces, ancestral polymorphisms, and the formation of autopolyploids versus allopolyploids.
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Affiliation(s)
- Paul D. Blischak
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Makenzie E. Mabry
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Gavin C. Conant
- Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
- Current affiliation: Bioinformatics Research Center, Program in Genetics and Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - J. Chris Pires
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211-7310, USA
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Mandáková T, Guo X, Özüdoğru B, Mummenhoff K, Lysak MA. Hybridization-facilitated genome merger and repeated chromosome fusion after 8 million years. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:748-760. [PMID: 30101476 DOI: 10.1111/tpj.14065] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/01/2018] [Accepted: 08/06/2018] [Indexed: 05/22/2023]
Abstract
The small genus Ricotia (nine species, Brassicaceae) is confined to the eastern Mediterranean. By comparative chromosome painting and a dated multi-gene chloroplast phylogeny, we reconstructed the origin and subsequent evolution of Ricotia. The ancestral Ricotia genome originated through hybridization between two older genomes with n = 7 and n = 8 chromosomes, respectively, on the Turkish mainland during the Early Miocene (c. 17.8 million years ago, Ma). Since then, the allotetraploid (n = 15) genome has been altered by two independent descending dysploidies (DD) to n = 14 in Ricotia aucheri and the Tenuifolia clade (2 spp.). By the Late Miocene (c. 10 Ma), the latter clade started to evolve in the most diverse Ricotia core clade (6 spp.), the process preceded by a DD event to n = 13. It is noteworthy that this dysploidy was mediated by a unique chromosomal rearrangement, merging together the same two chromosomes as were merged during the origin of a fusion chromosome within the paternal n = 7 genome c. 20 Ma. This shows that within a time period of c. 8 Myr genome evolution can repeat itself and that structurally very similar chromosomes may originate repeatedly from the same ancestral chromosomes by different pathways (end-to-end translocation versus nested chromosome insertion).
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Affiliation(s)
- Terezie Mandáková
- CEITEC - Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
| | - Xinyi Guo
- CEITEC - Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
| | - Barış Özüdoğru
- Department of Biology, Faculty of Science, Hacettepe University, 06800, Beytepe, Ankara, Turkey
| | - Klaus Mummenhoff
- Department of Biology/Botany, University of Osnabrück, Barbarastraße 11, 49076, Osnabrück, Germany
| | - Martin A Lysak
- CEITEC - Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
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García MA, Stefanović S, Weiner C, Olszewski M, Costea M. Cladogenesis and reticulation in Cuscuta sect. Denticulatae (Convolvulaceae). ORG DIVERS EVOL 2018; 18:383-398. [PMID: 30930685 PMCID: PMC6405177 DOI: 10.1007/s13127-018-0383-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 10/11/2018] [Indexed: 01/08/2023]
Abstract
As traditionally circumscribed, Cuscuta sect. Denticulatae is a group of three parasitic plant species native to the deserts of Western USA (Cuscuta denticulata, Cuscuta nevadensis) and the central region of Baja California, Mexico (Cuscuta veatchii). Molecular phylogenetic studies confirmed the monophyly of this group and suggested that the disjunct C. veatchii is a hybrid between the other two species. However, the limited sampling left the possibility of alternative biological and methodological explanations. We expanded our sampling to multiple individuals of all the species collected from across their entire geographical ranges. Sequence data from the nuclear and plastid regions were used to reconstruct the phylogeny and find out if the topological conflict was maintained. We obtained karyotype information from multiple individuals, investigated the morphological variation of the group thorough morphometric analyses, and compiled data on ecology, host range, and geographical distribution. Our results confirmed that C. veatchii is an allotetraploid. Furthermore, we found previously unknown autotetraploid population of C. denticulata, and we describe a new hybrid species, Cuscuta psorothamnensis. We suggest that this newly discovered natural hybrid is resulting from an independent (and probably more recent) hybridization event between the same diploid parental species as those of C. veatchii. All the polyploids showed host shift associated with hybridization and/or polyploidy and are found growing on hosts that are rarely or never frequented by their diploid progenitors. The great potential of this group as a model to study host shift in parasitic plants associated with recurrent allopolyploidy is discussed.
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Affiliation(s)
- Miguel A García
- 1Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6 Canada.,2Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AE UK
| | - Saša Stefanović
- 1Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6 Canada
| | - Catherine Weiner
- 3Department of Biology, Wilfrid Laurier University, Waterloo, ON N2L3C5 Canada
| | - Magdalena Olszewski
- 3Department of Biology, Wilfrid Laurier University, Waterloo, ON N2L3C5 Canada
| | - Mihai Costea
- 3Department of Biology, Wilfrid Laurier University, Waterloo, ON N2L3C5 Canada
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Jørgensen KM, Wennevik V, Eide Sørvik AG, Unneland L, Prusov S, Ayllon F, Glover KA. Investigating the frequency of triploid Atlantic salmon in wild Norwegian and Russian populations. BMC Genet 2018; 19:90. [PMID: 30285613 PMCID: PMC6171226 DOI: 10.1186/s12863-018-0676-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/19/2018] [Indexed: 12/18/2022] Open
Abstract
Background Fish may display variations in ploidy, including three sets of chromosomes, known as triploidy. A recent study revealed a frequency of ~ 2% spontaneous (i.e., non-intentional) triploidy in domesticated Atlantic salmon produced in Norwegian aquaculture in the period 2007–2014. In contrast, the frequency of triploidy in wild salmon populations has not been studied thus far, and in wild populations of other organisms, it has been very rarely studied. In population genetic data sets, individuals that potentially display chromosome abnormalities, such as triploids with three alleles, are typically excluded on the premise that they may reflect polluted or otherwise compromised samples. Here, we critically re-investigated the microsatellite genetic profile of ~ 6000 wild Atlantic salmon sampled from 80 rivers in Norway and Russia, to investigate the frequency of triploid individuals in wild salmon populations for the first time. Results We detected a single triploid salmon, and five individuals displaying three alleles at one of the loci, thus regarded as putatively trisomic. This gave an overall frequency of triploid and putatively trisomic individuals in the data set of 0.017 and 0.083% respectively. The triploid salmon was an adult female, and had spent 2 years in freshwater and 2 years in the sea. Conclusions We conclude that the frequency of naturally-occurring triploid Atlantic salmon in wild Norwegian and Russian populations is very low, and many-fold lower than the frequency of spontaneous triploids observed in aquaculture. Our results suggest that aquaculture rearing conditions substantially increase the probability of triploidy to develop, and/or permits greater survival of triploid individuals, in comparison to the wild. Electronic supplementary material The online version of this article (10.1186/s12863-018-0676-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Vidar Wennevik
- Institute of Marine Research, Postboks 1870 Nordnes, N-5817, Bergen, Norway
| | | | - Laila Unneland
- Institute of Marine Research, Postboks 1870 Nordnes, N-5817, Bergen, Norway
| | - Sergey Prusov
- The Knipovich Polar Research Institute of Marine Fisheries and Oceanography (PINRO), Murmansk, 183038, Russia
| | - Fernando Ayllon
- Institute of Marine Research, Postboks 1870 Nordnes, N-5817, Bergen, Norway
| | - Kevin A Glover
- Institute of Marine Research, Postboks 1870 Nordnes, N-5817, Bergen, Norway.,Sea lice Research Centre, Department of Biology, University of Bergen, N-5020, Bergen, Norway
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135
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Van Drunen WE, Husband BC. Whole-genome duplication decreases clonal stolon production and genet size in the wild strawberry Fragaria vesca. AMERICAN JOURNAL OF BOTANY 2018; 105:1712-1724. [PMID: 30248174 DOI: 10.1002/ajb2.1159] [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: 02/23/2018] [Accepted: 06/28/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Clonal reproduction is often associated with polyploidy and is expected to influence polyploid establishment success, but the immediate effects of whole-genome duplication (WGD) on clonal reproduction in autopolyploids are unknown. METHODS We used synthesized neopolyploids to assess the direct effects of WGD on stolon and plantlet production in the wild strawberry Fragaria vesca by (1) comparing absolute clonal investment between diploids and neotetraploids under high and low resource conditions in the greenhouse and (2) determining realized clonal plantlet establishment and genet spatial structure using artificial field populations comprising both cytotypes. KEY RESULTS Neotetraploids produced fewer stolons and plantlets than diploids at slower weekly rates in the greenhouse when resources were high, resulting in lower total investment in clonal reproduction. Low resources led to smaller reductions in clonal biomass for neotetraploids and less pronounced differences between cytotypes. Comparisons between neotetraploids representing 13 independent WGD events and close diploid relatives revealed considerable variation in the response to polyploidization for some clonal traits. Field populations corroborated greenhouse results; neotetraploid genets were smaller than diploid genets, containing 28% fewer stolons and 46% fewer rooted plantlets. CONCLUSIONS WGD significantly decreases the clonal output of neotetraploid F. vesca, which is likely attributable to slower whole-plant growth of the neotetraploids than the diploids. In natural populations, smaller neotetraploid genets could decrease the probability of polyploid establishment in this species. However, variation between separate neopolyploid lines emphasizes that the response of clonal investment to WGD may not be uniform across polyploid origins.
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Affiliation(s)
- Wendy E Van Drunen
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Brian C Husband
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
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136
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A Robust Methodology for Assessing Differential Homeolog Contributions to the Transcriptomes of Allopolyploids. Genetics 2018; 210:883-894. [PMID: 30213855 DOI: 10.1534/genetics.118.301564] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/07/2018] [Indexed: 12/18/2022] Open
Abstract
Polyploidy has played a pivotal and recurring role in angiosperm evolution. Allotetraploids arise from hybridization between species and possess duplicated gene copies (homeologs) that serve redundant roles immediately after polyploidization. Although polyploidization is a major contributor to plant evolution, it remains poorly understood. We describe an analytical approach for assessing homeolog-specific expression that begins with de novo assembly of parental transcriptomes and effectively (i) reduces redundancy in de novo assemblies, (ii) identifies putative orthologs, (iii) isolates common regions between orthologs, and (iv) assesses homeolog-specific expression using a robust Bayesian Poisson-Gamma model to account for sequence bias when mapping polyploid reads back to parental references. Using this novel methodology, we examine differential homeolog contributions to the transcriptome in the recently formed allopolyploids Tragopogon mirus and T. miscellus (Compositae). Notably, we assess a larger Tragopogon gene set than previous studies of this system. Using carefully identified orthologous regions and filtering biased orthologs, we find in both allopolyploids largely balanced expression with no strong parental bias. These new methods can be used to examine homeolog expression in any tetrapolyploid system without requiring a reference genome.
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137
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Saenjundaeng P, de Bello Cioffi M, de Oliveira EA, Tanomtong A, Supiwong W, Phimphan S, Collares-Pereira MJ, Sember A, Bertollo LAC, Liehr T, Yano CF, Hatanaka T, Ráb P. Chromosomes of Asian cyprinid fishes: cytogenetic analysis of two representatives of small paleotetraploid tribe Probarbini. Mol Cytogenet 2018; 11:51. [PMID: 30202442 PMCID: PMC6123905 DOI: 10.1186/s13039-018-0399-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 08/23/2018] [Indexed: 12/01/2022] Open
Abstract
Background Polyploidy, although still poorly explored, represents an important evolutionary event in several cyprinid clades. Herein, Catlocarpio siamensis and Probarbus jullieni - representatives of the paleotetraploid tribe Probarbini, were characterized both by conventional and molecular cytogenetic methods. Results Alike most other paleotetraploid cyprinids (with 2n = 100), both species studied here shared 2n = 98 but differed in karyotypes: C. siamensis displayed 18m + 34sm + 46st/a; NF = 150, while P. jullieni exhibited 26m + 14sm + 58st/a; NF = 138. Fluorescence in situ hybridization (FISH) with rDNA probes revealed two (5S) and eight (18S) signals in C. siamensis, respectively, and six signals for both probes in P. jullieni. FISH with microsatellite motifs evidenced substantial genomic divergence between both species. The almost doubled size of the chromosome pairs #1 in C. siamensis and #14 in P. jullieni compared to the rest of corresponding karyotypes indicated chromosomal fusions. Conclusion Based on our findings, together with likely the same reduced 2n = 98 karyotypes in the remainder Probarbini species, we hypothesize that the karyotype 2n = 98 might represent a derived character, shared by all members of the Probarbini clade. Besides, we also witnessed considerable changes in the amount and distribution of certain repetitive DNA classes, suggesting complex post-polyploidization processes in this small paleotetraploid tribe.
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Affiliation(s)
- Pasakorn Saenjundaeng
- 1Toxic Substances in Livestock and Aquatic Animals Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Muang District, Khon Kaen, Thailand
| | - Marcelo de Bello Cioffi
- 2Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Ezequiel Aguiar de Oliveira
- 2Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP Brazil.,Secretaria de Estado de Educação de Mato Grosso - SEDUC-MT, Cuiabá, MT Brazil
| | - Alongklod Tanomtong
- 1Toxic Substances in Livestock and Aquatic Animals Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Muang District, Khon Kaen, Thailand
| | - Weerayuth Supiwong
- 4Faculty of Applied Science and Engineering, Khon Kaen University, Nong Kai Campus, Muang, Nong Kai Thailand
| | - Sumalee Phimphan
- 1Toxic Substances in Livestock and Aquatic Animals Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Muang District, Khon Kaen, Thailand
| | - Maria João Collares-Pereira
- 5Faculdade de Ciencias, Centre for Ecology, Evolution and Environmental Changes, Universidade de Lisboa, Campo Grande, PT-1749-016 Lisbon, Portugal
| | - Alexandr Sember
- 6Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | | | - Thomas Liehr
- 7Institute of Human Genetics, Jena University Hospital, Am Klinikum 1, D-07747 Jena, Germany
| | - Cassia Fernanda Yano
- 2Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Terumi Hatanaka
- 2Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Petr Ráb
- 6Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
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138
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Baduel P, Bray S, Vallejo-Marin M, Kolář F, Yant L. The “Polyploid Hop”: Shifting Challenges and Opportunities Over the Evolutionary Lifespan of Genome Duplications. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00117] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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139
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Divide and conquer! Data-mining tools and sequential multivariate analysis to search for diagnostic morphological characters within a plant polyploid complex (Veronica subsect. Pentasepalae, Plantaginaceae). PLoS One 2018; 13:e0199818. [PMID: 29958275 PMCID: PMC6025878 DOI: 10.1371/journal.pone.0199818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 06/14/2018] [Indexed: 11/19/2022] Open
Abstract
This study exhaustively explores leaf features seeking diagnostic characters to aid the classification (assigning cases to groups, i.e. populations to taxa) in a polyploid plant-species complex. A challenging case study was selected: Veronica subsection Pentasepalae, a taxonomically intricate group. The “divide and conquer” approach was implemented—that is, a difficult primary dataset was split into more manageable subsets. Three techniques were explored: two data-mining tools (artificial neural networks and decision trees) and one unsupervised discriminant analysis. However, only the decision trees and discriminant analysis were finally used to select diagnostic traits. A previously established classification hypothesis based on other data sources was used as a starting point. A guided discriminant analysis (i.e. involving manual character selection) was used to produce a grouping scheme fitting this hypothesis so that it could be taken as a reference. Sequential unsupervised multivariate analysis enabled the recognition of all species and infraspecific taxa; however, a suboptimal classification rate was achieved. Decision trees resulted in better classification rates than unsupervised multivariate analysis, but three complete taxa were misidentified (not present in terminal nodes). The variable selection led to a different grouping scheme in the case of decision trees. The resulting groups displayed low misclassification rates when analyzed using artificial neural networks. The decision trees as well as the discriminant analysis are recommended in the search of diagnostic characters. Due to the high sensitivity that artificial neural networks have to the combination of input/output layers, they are proposed as evaluation tools for morphometric studies. The “divide and conquer” principle is a promising strategy, providing success in the present case study.
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140
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Martínez LM, Fernández-Ocaña A, Rey PJ, Salido T, Amil-Ruiz F, Manzaneda AJ. Variation in functional responses to water stress and differentiation between natural allopolyploid populations in the Brachypodium distachyon species complex. ANNALS OF BOTANY 2018; 121:1369-1382. [PMID: 29893879 PMCID: PMC6007385 DOI: 10.1093/aob/mcy037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 02/26/2018] [Indexed: 05/21/2023]
Abstract
Background and Aims Some polyploid species show enhanced physiological tolerance to drought compared with their progenitors. However, very few studies have examined the consistency of physiological drought response between genetically differentiated natural polyploid populations, which is key to evaluation of the importance of adaptive evolution after polyploidization in those systems where drought exerts a selective pressure. Methods A comparative functional approach was used to investigate differentiation of drought-tolerance-related traits in the Brachypodium species complex, a model system for grass polyploid adaptive speciation and functional genomics that comprises three closely related annual species: the two diploid parents, B. distachyon and B. stacei, and the allotetraploid derived from them, B. hybridum. Differentiation of drought-tolerance-related traits between ten genetically distinct B. hybridum populations and its ecological correlates was further analysed. Key Results The functional drought response is overall well differentiated between Brachypodium species. Brachypodium hybridum allotetraploids showed a transgressive expression pattern in leaf phytohormone content in response to drought. In contrast, other B. hybridum physiological traits correlated to B. stacei ones. Particularly, proline and water content were the traits that best discriminated these species from B. distachyon under drought. Conclusions After polyploid formation and/or colonization, B. hybridum populations have adaptively diverged physiologically and genetically in response to variations in aridity.
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Affiliation(s)
- Luisa M Martínez
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
| | - Ana Fernández-Ocaña
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
| | - Pedro J Rey
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
| | - Teresa Salido
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
| | - Francisco Amil-Ruiz
- Bioinformatics Unit, Central Service for Research Support (SCAI), University of Córdoba, Córdoba, Spain
| | - Antonio J Manzaneda
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaén, Spain
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141
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Gomes SSL, Vidal JD, Neves CS, Zorzatto C, Campacci TVS, Lima AK, Koehler S, Viccini LF. Genome size and climate segregation suggest distinct colonization histories of an orchid species from Neotropical high-elevation rocky complexes. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Shaiany Sabrina Lopes Gomes
- Laboratório de Genética, Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, MG, Brazil
| | - João D Vidal
- Programa de Pós-Graduação em Botânica, Instituto de Biociências de Botucatu, Universidade Estadual Paulista ‘Júlio de Mesquita Filho’, Botucatu, SP, Brazil
| | - Camila Siqueira Neves
- Laboratório de Genética, Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, MG, Brazil
| | - Cristiane Zorzatto
- Laboratório de Genética, Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, MG, Brazil
| | | | - Amanda Kassia Lima
- Laboratório de Genética, Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, MG, Brazil
| | - Samantha Koehler
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Lyderson Facio Viccini
- Laboratório de Genética, Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Juiz de Fora, MG, Brazil
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142
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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: 181] [Impact Index Per Article: 30.2] [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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143
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Gaynor ML, Ng J, Laport RG. Phylogenetic Structure of Plant Communities: Are Polyploids Distantly Related to Co-occurring Diploids? Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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144
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Bourke PM, Voorrips RE, Visser RGF, Maliepaard C. Tools for Genetic Studies in Experimental Populations of Polyploids. FRONTIERS IN PLANT SCIENCE 2018; 9:513. [PMID: 29720992 PMCID: PMC5915555 DOI: 10.3389/fpls.2018.00513] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/04/2018] [Indexed: 05/19/2023]
Abstract
Polyploid organisms carry more than two copies of each chromosome, a condition rarely tolerated in animals but which occurs relatively frequently in the plant kingdom. One of the principal challenges faced by polyploid organisms is to evolve stable meiotic mechanisms to faithfully transmit genetic information to the next generation upon which the study of inheritance is based. In this review we look at the tools available to the research community to better understand polyploid inheritance, many of which have only recently been developed. Most of these tools are intended for experimental populations (rather than natural populations), facilitating genomics-assisted crop improvement and plant breeding. This is hardly surprising given that a large proportion of domesticated plant species are polyploid. We focus on three main areas: (1) polyploid genotyping; (2) genetic and physical mapping; and (3) quantitative trait analysis and genomic selection. We also briefly review some miscellaneous topics such as the mode of inheritance and the availability of polyploid simulation software. The current polyploid analytic toolbox includes software for assigning marker genotypes (and in particular, estimating the dosage of marker alleles in the heterozygous condition), establishing chromosome-scale linkage phase among marker alleles, constructing (short-range) haplotypes, generating linkage maps, performing genome-wide association studies (GWAS) and quantitative trait locus (QTL) analyses, and simulating polyploid populations. These tools can also help elucidate the mode of inheritance (disomic, polysomic or a mixture of both as in segmental allopolyploids) or reveal whether double reduction and multivalent chromosomal pairing occur. An increasing number of polyploids (or associated diploids) are being sequenced, leading to publicly available reference genome assemblies. Much work remains in order to keep pace with developments in genomic technologies. However, such technologies also offer the promise of understanding polyploid genomes at a level which hitherto has remained elusive.
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Affiliation(s)
| | | | | | - Chris Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
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145
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Jang TS, Parker JS, Emadzade K, Temsch EM, Leitch AR, Weiss-Schneeweiss H. Multiple Origins and Nested Cycles of Hybridization Result in High Tetraploid Diversity in the Monocot Prospero. FRONTIERS IN PLANT SCIENCE 2018; 9:433. [PMID: 29755483 PMCID: PMC5932365 DOI: 10.3389/fpls.2018.00433] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/21/2018] [Indexed: 06/08/2023]
Abstract
Polyploidy is a major driving force in angiosperm evolution, but our understanding of establishment and early diversification processes following allo- vs. auto-polyploidy is limited. An excellent system to address such questions is the monocot plant Prospero autumnale, as it comprises several genomically and chromosomally distinct diploid cytotypes and their auto- and allotetraploid derivatives. To infer origins and evolutionary trajectories of the tetraploids, we use genome size data, in situ hybridization with parental genomic DNAs and specific probes (satDNA, rDNAs), as well as molecular-phylogenetic analyses. Thus, we demonstrate that an astounding range of allotetraploid lineages has been formed recurrently by chromosomal re-patterning, interactions of chromosomally variable parental genomes and nested cycles of extensive hybridization, whereas autotetraploids have originated at least twice and are cytologically stable. During the recurrent formation and establishment across wide geographic areas hybridization in some populations could have inhibited lineage diversification and nascent speciation of such a hybrid swarm. However, cytotypes that became fixed in populations enhanced the potential for species diversification, possibly exploiting the extended allelic base, and fixed heterozygosity that polyploidy confers. The time required for polyploid cytotype fixation may in part reflect the lag phase reported for polyploids between their formation and species diversification.
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Affiliation(s)
- Tae-Soo Jang
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - John S. Parker
- Cambridge University Botanic Garden, Cambridge, United Kingdom
| | - Khatere Emadzade
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Eva M. Temsch
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Andrew R. Leitch
- Queen Mary College, University of London, London, United Kingdom
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146
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Voyaging through chromosomal studies in hairy root cultures towards unravelling their relevance to medicinal plant research: An updated review. THE NUCLEUS 2018. [DOI: 10.1007/s13237-018-0227-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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147
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Sember A, Bohlen J, Šlechtová V, Altmanová M, Pelikánová Š, Ráb P. Dynamics of tandemly repeated DNA sequences during evolution of diploid and tetraploid botiid loaches (Teleostei: Cobitoidea: Botiidae). PLoS One 2018; 13:e0195054. [PMID: 29590207 PMCID: PMC5874072 DOI: 10.1371/journal.pone.0195054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/15/2018] [Indexed: 12/16/2022] Open
Abstract
Polyploidization has played an important role in the evolution of vertebrates, particularly at the base of Teleostei-an enormously successful ray-finned fish group with additional genome doublings on lower taxonomic levels. The investigation of post-polyploid genome dynamics might provide important clues about the evolution and ecology of respective species and can help to decipher the role of polyploidy per se on speciation. Few studies have attempted to investigate the dynamics of repetitive DNA sequences in the post-polyploid genome using molecular cytogenetic tools in fishes, though recent efforts demonstrated their usefulness. The demonstrably monophyletic freshwater loach family Botiidae, branching to evolutionary diploid and tetraploid lineages separated >25 Mya, offers a suited model group for comparing the long-term repetitive DNA evolution. For this, we integrated phylogenetic analyses with cytogenetical survey involving Giemsa- and Chromomycin A3 (CMA3)/DAPI stainings and fluorescence in situ hybridization with 5S/45S rDNA, U2 snDNA and telomeric probes in representative sample of 12 botiid species. The karyotypes of all diploids were composed of 2n = 50 chromosomes, while majority of tetraploids had 2n = 4x = 100, with only subtle interspecific karyotype differences. The exceptional karyotype of Botia dario (2n = 4x = 96) suggested centric fusions behind the 2n reduction. Variable patterns of FISH signals revealed cases of intraspecific polymorphisms, rDNA amplification, variable degree of correspondence with CMA3+ sites and almost no phylogenetic signal. In tetraploids, either additivity or loci gain/loss was recorded. Despite absence of classical interstitial telomeric sites, large blocks of interspersed rDNA/telomeric regions were found in diploids only. We uncovered different molecular drives of studied repetitive DNA classes within botiid genomes as well as the advanced stage of the re-diploidization process in tetraploids. Our results may contribute to link genomic approach with molecular cytogenetic analyses in addressing the origin and mechanism of this polyploidization event.
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Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Jörg Bohlen
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Vendula Šlechtová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Marie Altmanová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, Czech Republic
| | - Šárka Pelikánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
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148
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Wendel JF, Lisch D, Hu G, Mason AS. The long and short of doubling down: polyploidy, epigenetics, and the temporal dynamics of genome fractionation. Curr Opin Genet Dev 2018; 49:1-7. [PMID: 29438956 DOI: 10.1016/j.gde.2018.01.004] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/07/2017] [Accepted: 01/23/2018] [Indexed: 01/09/2023]
Abstract
We consider the rapidly advancing discipline of plant evolutionary genomics, with a focus on the evolution of polyploid genomes. In many lineages, polyploidy is followed by 'biased fractionation', the unequal loss of genes from ancestral progenitor genomes. Mechanistically, it has been proposed that biased fractionation results from changes in the epigenetic landscape near genes, likely mediated by transposable elements. These epigenetic changes result in unequal gene expression between duplicates, establishing differential fitness that leads to biased gene loss with respect to ancestral genomes. We propose a unifying conceptual framework and a set of testable hypotheses based on this model, relating genome size, the proximity of transposable elements to genes, epigenetic reprogramming, chromatin accessibility, and gene expression.
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Affiliation(s)
- Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, United States.
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, United States
| | - Guanjing Hu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, United States
| | - Annaliese S Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
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149
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Zou J, Hu D, Mason AS, Shen X, Wang X, Wang N, Grandke F, Wang M, Chang S, Snowdon RJ, Meng J. Genetic changes in a novel breeding population of Brassica napus synthesized from hundreds of crosses between B. rapa and B. carinata. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:507-519. [PMID: 28703467 PMCID: PMC5811809 DOI: 10.1111/pbi.12791] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 06/29/2017] [Accepted: 07/07/2017] [Indexed: 05/20/2023]
Abstract
Introgression of genomic variation between and within related crop species is a significant evolutionary approach for population differentiation, genome reorganization and trait improvement. Using the Illumina Infinium Brassica 60K SNP array, we investigated genomic changes in a panel of advanced generation new-type Brassica napus breeding lines developed from hundreds of interspecific crosses between 122 Brassica rapa and 74 Brassica carinata accessions, and compared them with representative accessions of their three parental species. The new-type B. napus population presented rich genetic diversity and abundant novel genomic alterations, consisting of introgressions from B. rapa and B. carinata, novel allelic combinations, reconstructed linkage disequilibrium patterns and haplotype blocks, and frequent deletions and duplications (nonrandomly distributed), particularly in the C subgenome. After a much shorter, but very intensive, selection history compared to traditional B. napus, a total of 15 genomic regions with strong selective sweeps and 112 genomic regions with putative signals of selective sweeps were identified. Some of these regions were associated with important agronomic traits that were selected for during the breeding process, while others were potentially associated with restoration of genome stability and fertility after interspecific hybridization. Our results demonstrate how a novel method for population-based crop genetic improvement can lead to rapid adaptation, restoration of genome stability and positive responses to artificial selection.
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Affiliation(s)
- Jun Zou
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Dandan Hu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Annaliese S. Mason
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Xueqi Shen
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Xiaohua Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Nian Wang
- College of Horticulture & Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Fabian Grandke
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Meng Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Shihao Chang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Rod J. Snowdon
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Jinling Meng
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
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150
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Marques I, Loureiro J, Draper D, Castro M, Castro S. How much do we know about the frequency of hybridisation and polyploidy in the Mediterranean region? PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20 Suppl 1:21-37. [PMID: 28963818 DOI: 10.1111/plb.12639] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 09/25/2017] [Indexed: 06/07/2023]
Abstract
Natural hybridisation and polyploidy are currently recognised as drivers of biodiversity, despite early scepticism about their importance. The Mediterranean region is a biodiversity hotspot where geological and climatic events have created numerous opportunities for speciation through hybridisation and polyploidy. Still, our knowledge on the frequency of these mechanisms in the region is largely limited, despite both phenomena are frequently cited in studies of Mediterranean plants. We reviewed information available from biodiversity and cytogenetic databases to provide the first estimates of hybridisation and polyploidy frequency in the Mediterranean region. We also inspected the most comprehensive modern Mediterranean Flora (Flora iberica) to survey the frequency and taxonomic distribution of hybrids and polyploids in Iberian Peninsula. We found that <6% of Mediterranean plants were hybrids, although a higher frequency was estimated for the Iberian Peninsula (13%). Hybrids were concentrated in few families and in even fewer genera. The overall frequency of polyploidy (36.5%) was comparable with previous estimates in other regions; however our estimates increased when analysing the Iberian Peninsula (48.8%). A surprisingly high incidence of species harbouring two or more ploidy levels was also observed (21.7%). A review of the available literature also showed that the ecological factors driving emergence and establishment of new entities are still poorly studied in the Mediterranean flora, although geographic barriers seem to play a major role in polyploid complexes. Finally, this study reveals several gaps and limitations in our current knowledge about the frequency of hybridisation and polyploidy in the Mediterranean region. The obtained estimates might change in the future with the increasing number of studies; still, rather than setting the complete reality, we hope that this work triggers future studies on hybridisation and polyploidy in the Mediterranean region.
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Affiliation(s)
- I Marques
- Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, Huesca, Spain
| | - J Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - D Draper
- Centro de Ecologia, Evolução e Alterações Ambientais (cE3c), Universidade de Lisboa, Lisbon, Portugal
- UBC Botanical Garden & Centre for Plant Research, and Department of Botany, University of British Columbia, Vancouver, Canada
| | - M Castro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - S Castro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- Botanic Garden of the University of Coimbra, Coimbra, Portugal
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