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Pungaršek Š, Frajman B. Influence of polyploidy on morphology and distribution of the Cypress Spurge (Euphorbia cyparissias, Euphorbiaceae). PLANT BIOLOGY (STUTTGART, GERMANY) 2024. [PMID: 38979801 DOI: 10.1111/plb.13685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 05/26/2024] [Indexed: 07/10/2024]
Abstract
Polyploidy can cause differences in phenotypic and physiological traits among different cytotypes of the same species. Polyploids may have larger organs or occupy different ecological niches than their diploid counterparts, therefore they are hypothesized to have larger distributions or prosper in stressful environments, such as higher elevations. The Cypress spurge (Euphorbia cyparissias L.; Euphorbiaceae) is a widespread European heteroploid species including di- (2x), tetra- (4x) and hexaploid (6x) cytotypes. We tested the hypotheses that polyploids are more widespread and more abundant at higher elevations and have larger organs than their diploid ancestors in the case of E. cyparissias. We also analysed whether genome downsizing had occurred after polyploidisation. We conducted a comprehensive geographic sampling of 617 populations of E. cyparissias throughout Europe. We estimated their relative genome size using flow cytometry and inferred ploidy level of each population. We scored 13 morphological traits of vegetative and seed characters and performed statistical analyses. The study indicates that polyploidisation facilitated colonisation of new areas in E. cyparissias, where the tetraploids are most widespread, whereas the diploids are limited to putative Pleistocene refugia, mostly in southern Europe. On the other hand, the three ploidies do not differ in their elevational distribution. Although some quantitative morphological traits exhibited an increasing trend with increasing ploidy, most traits did not differ significantly among the three ploidies, and there was no overall phenotypic differentiation among them. Given that individuals of different ploidies thrive in similar habitats across the same elevations, we suggest that ecological segregation following polyploidisation is a more important trigger for morphological differentiation than polyploidisation itself in autopolyploid plants. The study demonstrates that polyploidisation can be crucial for the colonisation of new areas and for range expansion, but it does not necessarily influence elevational distribution nor confer a different phenotype.
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Affiliation(s)
- Š Pungaršek
- Department of Botany, University of Innsbruck, Innsbruck, Austria
- Slovenian Museum of Natural History, Ljubljana, Slovenia
| | - B Frajman
- Department of Botany, University of Innsbruck, Innsbruck, Austria
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2
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Hämälä T, Moore C, Cowan L, Carlile M, Gopaulchan D, Brandrud MK, Birkeland S, Loose M, Kolář F, Koch MA, Yant L. Impact of whole-genome duplications on structural variant evolution in Cochlearia. Nat Commun 2024; 15:5377. [PMID: 38918389 PMCID: PMC11199601 DOI: 10.1038/s41467-024-49679-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. Yet WGDs are hugely disruptive mutations, and we still lack a clear understanding of their fitness consequences. Here, we study whether WGDs result in greater diversity of genomic structural variants (SVs) and how they influence evolutionary dynamics in a plant genus, Cochlearia (Brassicaceae). By using long-read sequencing and a graph-based pangenome, we find both negative and positive interactions between WGDs and SVs. Masking of recessive mutations due to WGDs leads to a progressive accumulation of deleterious SVs across four ploidal levels (from diploids to octoploids), likely reducing the adaptive potential of polyploid populations. However, we also discover putative benefits arising from SV accumulation, as more ploidy-specific SVs harbor signals of local adaptation in polyploids than in diploids. Together, our results suggest that SVs play diverse and contrasting roles in the evolutionary trajectories of young polyploids.
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Affiliation(s)
- Tuomas Hämälä
- School of Life Sciences, University of Nottingham, Nottingham, UK.
- Production Systems, Natural Resources Institute Finland, Jokioinen, Finland.
| | | | - Laura Cowan
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Matthew Carlile
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | | | - Siri Birkeland
- Natural History Museum, University of Oslo, Oslo, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Matthew Loose
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czech Republic
| | - Marcus A Koch
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Levi Yant
- School of Life Sciences, University of Nottingham, Nottingham, UK.
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.
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3
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Sun W, Li M, Wang J. Characteristics of duplicated gene expression and DNA methylation regulation in different tissues of allopolyploid Brassica napus. BMC PLANT BIOLOGY 2024; 24:518. [PMID: 38851683 PMCID: PMC11162574 DOI: 10.1186/s12870-024-05245-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/04/2024] [Indexed: 06/10/2024]
Abstract
Plant polyploidization increases the complexity of epigenomes and transcriptional regulation, resulting in genome evolution and enhanced adaptability. However, few studies have been conducted on the relationship between gene expression and epigenetic modification in different plant tissues after allopolyploidization. In this study, we studied gene expression and DNA methylation modification patterns in four tissues (stems, leaves, flowers and siliques) of Brassica napusand its diploid progenitors. On this basis, the alternative splicing patterns and cis-trans regulation patterns of four tissues in B. napus and its diploid progenitors were also analyzed. It can be seen that the number of alternative splicing occurs in the B. napus is higher than that in the diploid progenitors, and the IR type increases the most during allopolyploidy. In addition, we studied the fate changes of duplicated genes after allopolyploidization in B. napus. We found that the fate of most duplicated genes is conserved, but the number of neofunctionalization and specialization is also large. The genetic fate of B. napus was classified according to five replication types (WGD, PD, DSD, TD, TRD). This study also analyzed generational transmission analysis of expression and DNA methylation patterns. Our study provides a reference for the fate differentiation of duplicated genes during allopolyploidization.
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Affiliation(s)
- Weiqi Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Mengdi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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4
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Mertten D, McKenzie CM, Souleyre EJF, Amadeu RR, Lenhard M, Baldwin S, Datson PM. Molecular breeding of flower load related traits in dioecious autotetraploid Actinidia arguta. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:36. [PMID: 38745882 PMCID: PMC11091038 DOI: 10.1007/s11032-024-01476-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/04/2024] [Indexed: 05/16/2024]
Abstract
Flowering plants exhibit a wide range of sexual reproduction systems, with the majority being hermaphroditic. However, some plants, such as Actinidia arguta (kiwiberry), have evolved into dioecious species with distinct female and male vines. In this study, we investigated the flower load and growth habits of female kiwiberry genotypes to identify the genetic basis of high yield with low maintenance requirements. Owing to the different selection approaches between female and male genotypes, we further extended our study to male kiwiberry genotypes. By combining both investigations, we present a novel breeding tool for dioecious crops. A population of A. arguta seedlings was phenotyped for flower load traits, in particular the proportion of non-floral shoots, proportion of floral shoots, and average number of flowers per floral shoot. Quantitative trait locus (QTL) mapping was used to analyse the genetic basis of these traits. We identified putative QTLs on chromosome 3 associated with flower-load traits. A pleiotropic effect of the male-specific region of the Y chromosome (MSY) on chromosome 3 affecting flower load-related traits between female and male vines was observed in an A. arguta breeding population. Furthermore, we utilized Genomic Best Linear Unbiased Prediction (GBLUP) to predict breeding values for the quantitative traits by leveraging genomic data. This approach allowed us to identify and select superior genotypes. Our findings contribute to the understanding of flowering and fruiting dynamics in Actinidia species, providing insights for kiwiberry breeding programs aiming to improve yield through the utilization of genomic methods and trait mapping. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01476-7.
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Affiliation(s)
- Daniel Mertten
- The New Zealand Institute for Plant and Food Research Ltd, Auckland, 1142 New Zealand
- University of Potsdam, Institute for Biochemistry and Biology, 14476 Potsdam-Golm, Germany
| | - Catherine M. McKenzie
- The New Zealand Institute for Plant and Food Research Ltd, Te Puke, 3182 New Zealand
| | - Edwige J. F. Souleyre
- The New Zealand Institute for Plant and Food Research Ltd, Auckland, 1142 New Zealand
| | | | - Michael Lenhard
- University of Potsdam, Institute for Biochemistry and Biology, 14476 Potsdam-Golm, Germany
| | - Samantha Baldwin
- The New Zealand Institute for Plant and Food Research Ltd, Lincoln, 7608 New Zealand
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5
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Brown MR, Abbott RJ, Twyford AD. The emerging importance of cross-ploidy hybridisation and introgression. Mol Ecol 2024; 33:e17315. [PMID: 38501394 DOI: 10.1111/mec.17315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/20/2024]
Abstract
Natural hybridisation is now recognised as pervasive in its occurrence across the Tree of Life. Resurgent interest in natural hybridisation fuelled by developments in genomics has led to an improved understanding of the genetic factors that promote or prevent species cross-mating. Despite this body of work overturning many widely held assumptions about the genetic barriers to hybridisation, it is still widely thought that ploidy differences between species will be an absolute barrier to hybridisation and introgression. Here, we revisit this assumption, reviewing findings from surveys of polyploidy and hybridisation in the wild. In a case study in the British flora, 203 hybrids representing 35% of hybrids with suitable data have formed via cross-ploidy matings, while a wider literature search revealed 59 studies (56 in plants and 3 in animals) in which cross-ploidy hybridisation has been confirmed with genetic data. These results show cross-ploidy hybridisation is readily overlooked, and potentially common in some groups. General findings from these studies include strong directionality of hybridisation, with introgression usually towards the higher ploidy parent, and cross-ploidy hybridisation being more likely to involve allopolyploids than autopolyploids. Evidence for adaptive introgression across a ploidy barrier and cases of cross-ploidy hybrid speciation shows the potential for important evolutionary outcomes.
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Affiliation(s)
- Max R Brown
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
- School of Life Sciences, Anglia Ruskin University, Cambridge, UK
| | - Richard J Abbott
- School of Biology, University of St Andrews, St Andrews, Fife, UK
| | - Alex D Twyford
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
- Royal Botanical Garden Edinburgh, Edinburgh, UK
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6
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Gerstner BP, Laport RG, Rudgers JA, Whitney KD. Plant-soil microbe feedbacks depend on distance and ploidy in a mixed cytotype population of Larrea tridentata. AMERICAN JOURNAL OF BOTANY 2024:e16298. [PMID: 38433501 DOI: 10.1002/ajb2.16298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 03/05/2024]
Abstract
PREMISE Theory predicts that mixed ploidy populations should be short-lived due to strong fitness disadvantages for the rare ploidy. However, mixed ploidy populations are common, suggesting that the fitness costs for rare ploidies are counterbalanced by ecological benefits that emerge when rare. We investigated whether differences in ecological interactions with soil microbes help to maintain a tetraploid-hexaploid population of Larrea tridentata (creosote bush) in the Sonoran Desert, California, United States, where prior work documented ploidy-specific root-associated microbes. METHODS We used a plant-soil feedback (PSF) experiment to test whether host-specific soil microbes can alter the outcomes of intraploidy vs. interploidy competition. Host-specific soil microbes can build up over time; thus, distance from a host plant can affect the fitness of nearby plants. RESULTS Seedlings grown in soils from near plants of a different ploidy produced greater biomass relative to seedlings grown in soils from near plants of the same ploidy. Moreover, seedlings grown in soils from near plants of a different ploidy produced more biomass than those grown in soils that were farther from plants of a different ploidy. These results suggest that the ecological consequences of PSF may facilitate the persistence of mixed ploidy populations. CONCLUSIONS This is the first evidence, to our knowledge, that is consistent with plant-soil microbe feedback as a viable mechanism to maintain the coexistence of multiple ploidy levels in a single population.
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Affiliation(s)
- Benjamin P Gerstner
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Robert G Laport
- Department of Biology, The College of Idaho, Caldwell, ID, 83605, USA
| | - Jennifer A Rudgers
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Kenneth D Whitney
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
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7
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Lopes JML, Nascimento LSDQ, Souza VC, de Matos EM, Fortini EA, Grazul RM, Santos MO, Soltis DE, Soltis PS, Otoni WC, Viccini LF. Water stress modulates terpene biosynthesis and morphophysiology at different ploidal levels in Lippia alba (Mill.) N. E. Brown (Verbenaceae). PROTOPLASMA 2024; 261:227-243. [PMID: 37665420 DOI: 10.1007/s00709-023-01890-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023]
Abstract
Monoterpenes are the main component in essential oils of Lippia alba. In this species, the chemical composition of essential oils varies with genome size: citral (geraniol and neral) is dominant in diploids and tetraploids, and linalool in triploids. Because environmental stress impacts various metabolic pathways, we hypothesized that stress responses in L. alba could alter the relationship between genome size and essential oil composition. Water stress affects the flowering, production, and reproduction of plants. Here, we evaluated the effect of water stress on morphophysiology, essential oil production, and the expression of genes related to monoterpene synthesis in diploid, triploid, and tetraploid accessions of L. alba cultivated in vitro for 40 days. First, using transcriptome data, we performed de novo gene assembly and identified orthologous genes using phylogenetic and clustering-based approaches. The expression of candidate genes related to terpene biosynthesis was estimated by real-time quantitative PCR. Next, we assessed the expression of these genes under water stress conditions, whereby 1% PEG-4000 was added to MS medium. Water stress modulated L. alba morphophysiology at all ploidal levels. Gene expression and essential oil production were affected in triploid accessions. Polyploid accessions showed greater growth and metabolic tolerance under stress compared to diploids. These results confirm the complex regulation of metabolic pathways such as the production of essential oils in polyploid genomes. In addition, they highlight aspects of genotype and environment interactions, which may be important for the conservation of tropical biodiversity.
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Affiliation(s)
- Juliana Mainenti Leal Lopes
- Department of Biology, Insitute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
- School of Life Science and Environment, Department of Genetic and Biotechnology, University of Trás-Os-Montes and Alto Douro, 5001-801, Vila Real, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1649-004, Lisbon, Portugal
| | | | - Vinicius Carius Souza
- Department of Biology, Insitute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Elyabe Monteiro de Matos
- Department of Biology, Insitute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Evandro Alexandre Fortini
- Laboratory of Plant Tissue Culture (LCTII), Department of Plant Biology/BIOAGRO, Universidade Federal de Viçosa, Av. P.H. Rolfs S/N, Campus Universitário, Viçosa, MG, 36570-000, Brazil
| | | | - Marcelo Oliveira Santos
- Department of Biology, Insitute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Wagner Campos Otoni
- Laboratory of Plant Tissue Culture (LCTII), Department of Plant Biology/BIOAGRO, Universidade Federal de Viçosa, Av. P.H. Rolfs S/N, Campus Universitário, Viçosa, MG, 36570-000, Brazil
| | - Lyderson Facio Viccini
- Department of Biology, Insitute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil.
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8
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Feng X, Chen Q, Wu W, Wang J, Li G, Xu S, Shao S, Liu M, Zhong C, Wu CI, Shi S, He Z. Genomic evidence for rediploidization and adaptive evolution following the whole-genome triplication. Nat Commun 2024; 15:1635. [PMID: 38388712 PMCID: PMC10884412 DOI: 10.1038/s41467-024-46080-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 02/13/2024] [Indexed: 02/24/2024] Open
Abstract
Whole-genome duplication (WGD), or polyploidy, events are widespread and significant in the evolutionary history of angiosperms. However, empirical evidence for rediploidization, the major process where polyploids give rise to diploid descendants, is still lacking at the genomic level. Here we present chromosome-scale genomes of the mangrove tree Sonneratia alba and the related inland plant Lagerstroemia speciosa. Their common ancestor has experienced a whole-genome triplication (WGT) approximately 64 million years ago coinciding with a period of dramatic global climate change. Sonneratia, adapting mangrove habitats, experienced extensive chromosome rearrangements post-WGT. We observe the WGT retentions display sequence and expression divergence, suggesting potential neo- and sub-functionalization. Strong selection acting on three-copy retentions indicates adaptive value in response to new environments. To elucidate the role of ploidy changes in genome evolution, we improve a model of the polyploidization-rediploidization process based on genomic evidence, contributing to the understanding of adaptive evolution during climate change.
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Affiliation(s)
- Xiao Feng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Qipian Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Weihong Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Jiexin Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Guohong Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Shao Shao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Min Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Cairong Zhong
- Hainan Academy of Forestry (Hainan Academy of Mangrove), 571100, Haikou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China.
| | - Ziwen He
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, 510275, Guangzhou, China.
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9
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Stoeckel S, Becheler R, Bocharova E, Barloy D. GenAPoPop 1.0: A user-friendly software to analyse genetic diversity and structure from partially clonal and selfed autopolyploid organisms. Mol Ecol Resour 2024; 24:e13886. [PMID: 37902131 DOI: 10.1111/1755-0998.13886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 10/05/2023] [Accepted: 10/16/2023] [Indexed: 10/31/2023]
Abstract
Autopolyploidy is quite common in most clades of eukaryotes. The emergence of sequence-based genotyping methods with individual and marker tags now enables confident allele dosage, overcoming the main obstacle to the democratization of the population genetic approaches when studying ecology and evolution of autopolyploid populations and species. Reproductive modes, including clonality, selfing and allogamy, have deep consequences on the ecology and evolution of population and species. Analysing genetic diversity and its dynamics over generations is one efficient way to infer the relative importance of clonality, selfing and allogamy in populations. GenAPoPop is a user-friendly solution to compute the specific corpus of population genetic indices, including indices about genotypic diversity, needed to analyse partially clonal, selfed and allogamous polysomic populations genotyped with confident allele dosage. It also easily provides the posterior probabilities of quantitative reproductive modes in autopolyploid populations genotyped at two-time steps and a graphical representation of the minimum spanning trees of the genetic distances between polyploid individuals, facilitating the interpretation of the genetic coancestry between individuals in hierarchically structured populations. GenAPoPop complements the previously existing solutions, including SPAGEDI and POLYGENE, to use genotypings to study the ecology and evolution of autopolyploid populations. It was specially developed with a simple graphical interface and workflow, and comes with a simulator to facilitate practical courses and teaching of population genetics for autopolyploid populations.
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Affiliation(s)
- Solenn Stoeckel
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, France
- DECOD (Ecosystem Dynamics and Sustainability), Institut Agro, IFREMER, INRAE, Rennes, France
| | - Ronan Becheler
- IGEPP, INRAE, Institut Agro, Université de Rennes, Le Rheu, France
- DECOD (Ecosystem Dynamics and Sustainability), Institut Agro, IFREMER, INRAE, Rennes, France
| | - Ekaterina Bocharova
- Evolutionary Developmental Biology laboratory, Koltzov Institute of Developmental Biology of Russian Academy of Sciences (IDB RAS), Moscow, Russia
| | - Dominique Barloy
- DECOD (Ecosystem Dynamics and Sustainability), Institut Agro, IFREMER, INRAE, Rennes, France
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10
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Mu W, Li K, Yang Y, Breiman A, Yang J, Wu Y, Zhu M, Wang S, Catalan P, Nevo E, Liu J. Subgenomic Stability of Progenitor Genomes During Repeated Allotetraploid Origins of the Same Grass Brachypodium hybridum. Mol Biol Evol 2023; 40:msad259. [PMID: 38000891 PMCID: PMC10708906 DOI: 10.1093/molbev/msad259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/17/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Both homeologous exchanges and homeologous expression bias are generally found in most allopolyploid species. Whether homeologous exchanges and homeologous expression bias differ between repeated allopolyploid speciation events from the same progenitor species remains unknown. Here, we detected a third independent and recent allotetraploid origin for the model grass Brachypodium hybridum. Our homeologous exchange with replacement analyses indicated the absence of significant homeologous exchanges in any of the three types of wild allotetraploids, supporting the integrity of their progenitor subgenomes and the immediate creation of the amphidiploids. Further homeologous expression bias tests did not uncover significant subgenomic dominance in different tissues and conditions of the allotetraploids. This suggests a balanced expression of homeologs under similar or dissimilar ecological conditions in their natural habitats. We observed that the density of transposons around genes was not associated with the initial establishment of subgenome dominance; rather, this feature is inherited from the progenitor genome. We found that drought response genes were highly induced in the two subgenomes, likely contributing to the local adaptation of this species to arid habitats in the third allotetraploid event. These findings provide evidence for the consistency of subgenomic stability of parental genomes across multiple allopolyploidization events that led to the same species at different periods. Our study emphasizes the importance of selecting closely related progenitor species genomes to accurately assess homeologous exchange with replacement in allopolyploids, thereby avoiding the detection of false homeologous exchanges when using less related progenitor species genomes.
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Affiliation(s)
- Wenjie Mu
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Kexin Li
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Yongzhi Yang
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Adina Breiman
- Department of Evolutionary and Environmental Biology, University of Tel-Aviv, Tel-Aviv 6997801, Israel
| | - Jiao Yang
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Ying Wu
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Mingjia Zhu
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Shuai Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Pilar Catalan
- Escuela Politecnica Superior de Huesca, Universidad de Zaragoza, Huesca 22071, Spain
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel
| | - Jianquan Liu
- State Key Laboratory of Herbage Innovation and Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou 730000, China
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11
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Busoms S, Fischer S, Yant L. Chasing the mechanisms of ecologically adaptive salinity tolerance. PLANT COMMUNICATIONS 2023; 4:100571. [PMID: 36883005 PMCID: PMC10721451 DOI: 10.1016/j.xplc.2023.100571] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/12/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Plants adapted to challenging environments offer fascinating models of evolutionary change. Importantly, they also give information to meet our pressing need to develop resilient, low-input crops. With mounting environmental fluctuation-including temperature, rainfall, and soil salinity and degradation-this is more urgent than ever. Happily, solutions are hiding in plain sight: the adaptive mechanisms from natural adapted populations, once understood, can then be leveraged. Much recent insight has come from the study of salinity, a widespread factor limiting productivity, with estimates of 20% of all cultivated lands affected. This is an expanding problem, given increasing climate volatility, rising sea levels, and poor irrigation practices. We therefore highlight recent benchmark studies of ecologically adaptive salt tolerance in plants, assessing macro- and microevolutionary mechanisms, and the recently recognized role of ploidy and the microbiome on salinity adaptation. We synthesize insight specifically on naturally evolved adaptive salt-tolerance mechanisms, as these works move substantially beyond traditional mutant or knockout studies, to show how evolution can nimbly "tweak" plant physiology to optimize function. We then point to future directions to advance this field that intersect evolutionary biology, abiotic-stress tolerance, breeding, and molecular plant physiology.
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Affiliation(s)
- Silvia Busoms
- Plant Physiology Laboratory, Bioscience Faculty, Universitat Autònoma de Barcelona, Bellaterra, Barcelona E-08193, Spain
| | - Sina Fischer
- Future Food Beacon of Excellence, University of Nottingham, Nottingham NG7 2RD, UK; School of Biosciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Levi Yant
- Future Food Beacon of Excellence, University of Nottingham, Nottingham NG7 2RD, UK; School of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UK.
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12
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Leung K, van de Zande L, Beukeboom LW. Effects of polyploidization and their evolutionary implications are revealed by heritable polyploidy in the haplodiploid wasp Nasonia vitripennis. PLoS One 2023; 18:e0288278. [PMID: 37917617 PMCID: PMC10621845 DOI: 10.1371/journal.pone.0288278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 06/23/2023] [Indexed: 11/04/2023] Open
Abstract
Recurrent polyploidization occurred in the evolutionary history of most Eukaryota. However, how neopolyploid detriment (sterility, gigantism, gene dosage imbalances) has been overcome and even been bridged to evolutionary advantage (gene network diversification, mass radiation, range expansion) is largely unknown, particularly for animals. We used the parasitoid wasp Nasonia vitripennis, a rare insect system with heritable polyploidy, to begin addressing this knowledge gap. In Hymenoptera the sexes have different ploidies (haploid males, diploid females) and neopolyploids (diploid males, triploid females) occur for various species. Although such polyploids are usually sterile, those of N. vitripennis are reproductively capable and can even establish stable polyploid lines. To assess the effects of polyploidization, we compared a long-established polyploid line, the Whiting polyploid line (WPL) and a newly generated transformer knockdown line (tKDL) for fitness traits, absolute gene expression, and cell size and number. WPL polyploids have high male fitness and low female fecundity, while tKDL polyploids have poor male mate competition ability and high fertility. WPL has larger cells and cell number reduction, but the tKDL does not differ in this respect. Expression analyses of two housekeeping genes indicated that gene dosage is linked to sex irrespective of ploidy. Our study suggests that polyploid phenotypic variation may explain why some polyploid lineages thrive and others die out; a commonly proposed but difficult-to-test hypothesis. This documentation of diploid males (tKDL) with impaired competitive mating ability; triploid females with high fitness variation; and hymenopteran sexual dosage compensation (despite the lack of sex chromosomes) all challenges general assumptions on hymenopteran biology. We conclude that polyploidization is dependent on the duplicated genome characteristics and that genomes of different lines are unequally suited to survive diploidization. These results demonstrate the utility of N. vitripennis for delineating mechanisms of animal polyploid evolution, analogous to more advanced polyploid plant models.
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Affiliation(s)
- Kelley Leung
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Louis van de Zande
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Leo W. Beukeboom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
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Ebadi M, Bafort Q, Mizrachi E, Audenaert P, Simoens P, Van Montagu M, Bonte D, Van de Peer Y. The duplication of genomes and genetic networks and its potential for evolutionary adaptation and survival during environmental turmoil. Proc Natl Acad Sci U S A 2023; 120:e2307289120. [PMID: 37788315 PMCID: PMC10576144 DOI: 10.1073/pnas.2307289120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/07/2023] [Indexed: 10/05/2023] Open
Abstract
The importance of whole-genome duplication (WGD) for evolution is controversial. Whereas some view WGD mainly as detrimental and an evolutionary dead end, there is growing evidence that polyploidization can help overcome environmental change, stressful conditions, or periods of extinction. However, despite much research, the mechanistic underpinnings of why and how polyploids might be able to outcompete or outlive nonpolyploids at times of environmental upheaval remain elusive, especially for autopolyploids, in which heterosis effects are limited. On the longer term, WGD might increase both mutational and environmental robustness due to redundancy and increased genetic variation, but on the short-or even immediate-term, selective advantages of WGDs are harder to explain. Here, by duplicating artificially generated Gene Regulatory Networks (GRNs), we show that duplicated GRNs-and thus duplicated genomes-show higher signal output variation than nonduplicated GRNs. This increased variation leads to niche expansion and can provide polyploid populations with substantial advantages to survive environmental turmoil. In contrast, under stable environments, GRNs might be maladaptive to changes, a phenomenon that is exacerbated in duplicated GRNs. We believe that these results provide insights into how genome duplication and (auto)polyploidy might help organisms to adapt quickly to novel conditions and to survive ecological uproar or even cataclysmic events.
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Affiliation(s)
- Mehrshad Ebadi
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent9052, Belgium
- Center for Plant Systems Biology, VIB, Gent9052, Belgium
| | - Quinten Bafort
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent9052, Belgium
- Center for Plant Systems Biology, VIB, Gent9052, Belgium
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria0028, South Africa
| | - Pieter Audenaert
- Department of Information Technology–IDLab, Ghent University-IMEC, Gent9052, Belgium
| | - Pieter Simoens
- Department of Information Technology–IDLab, Ghent University-IMEC, Gent9052, Belgium
| | - Marc Van Montagu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent9052, Belgium
- Center for Plant Systems Biology, VIB, Gent9052, Belgium
| | - Dries Bonte
- Department of Biology, Terrestrial Ecology Unit, Ghent University, Ghent9000, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent9052, Belgium
- Center for Plant Systems Biology, VIB, Gent9052, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing210095, China
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14
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Mertten D, Baldwin S, Cheng CH, McCallum J, Thomson S, Ashton DT, McKenzie CM, Lenhard M, Datson PM. Implementation of different relationship estimate methodologies in breeding value prediction in kiwiberry ( Actinidia arguta). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:75. [PMID: 37868140 PMCID: PMC10584781 DOI: 10.1007/s11032-023-01419-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/02/2023] [Indexed: 10/24/2023]
Abstract
In dioecious crops such as Actinidia arguta (kiwiberries), some of the main challenges when breeding for fruit characteristics are the selection of potential male parents and the long juvenile period. Currently, breeding values of male parents are estimated through progeny tests, which makes the breeding of new kiwiberry cultivars time-consuming and costly. The application of best linear unbiased prediction (BLUP) would allow direct estimation of sex-related traits and speed up kiwiberry breeding. In this study, we used a linear mixed model approach to estimate narrow sense heritability for one vine-related trait and five fruit-related traits for two incomplete factorial crossing designs. We obtained BLUPs for all genotypes, taking into consideration whether the relationship was pedigree-based or marker-based. Owing to the high cost of genome sequencing, it is important to understand the effects of different sources of relationship matrices on estimating breeding values across a breeding population. Because of the increasing implementation of genomic selection in crop breeding, we compared the effects of incorporating different sources of information in building relationship matrices and ploidy levels on the accuracy of BLUPs' heritability and predictive ability. As kiwiberries are autotetraploids, multivalent chromosome formation and occasionally double reduction can occur during meiosis, and this can affect the accuracy of prediction. This study innovates the breeding programme of autotetraploid kiwiberries. We demonstrate that the accuracy of BLUPs of male siblings, without phenotypic observations, strongly improved when a tetraploid marker-based relationship matrix was used rather than parental BLUPs and female siblings with phenotypic observations. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01419-8.
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Affiliation(s)
- Daniel Mertten
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Auckland, 1142 New Zealand
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam-Golm, Germany
| | | | | | | | | | | | | | - Michael Lenhard
- Institute for Biochemistry and Biology, University of Potsdam, 14476 Potsdam-Golm, Germany
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15
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Abstract
AbstractEvolutionary biologists have thought about the role of genetic variation during adaptation for a very long time-before we understood the organization of the genetic code, the provenance of genetic variation, and how such variation influenced the phenotypes on which natural selection acts. Half a century after the discovery of the structure of DNA and the unraveling of the genetic code, we have a rich understanding of these problems and the means to both delve deeper and widen our perspective across organisms and natural populations. The 2022 Vice Presidential Symposium of the American Society of Naturalists highlighted examples of recent insights into the role of genetic variation in adaptive processes, which are compiled in this special section. The work was conducted in different parts of the world, included theoretical and empirical studies with diverse organisms, and addressed distinct aspects of how genetic variation influences adaptation. In our introductory article to the special section, we discuss some important recent insights about the generation and maintenance of genetic variation, its impacts on phenotype and fitness, its fate in natural populations, and its role in driving adaptation. By placing the special section articles in the broader context of recent developments, we hope that this overview will also serve as a useful introduction to the field.
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16
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Rougemont Q, Leroy T, Rondeau EB, Koop B, Bernatchez L. Allele surfing causes maladaptation in a Pacific salmon of conservation concern. PLoS Genet 2023; 19:e1010918. [PMID: 37683018 PMCID: PMC10545117 DOI: 10.1371/journal.pgen.1010918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 10/02/2023] [Accepted: 08/11/2023] [Indexed: 09/10/2023] Open
Abstract
How various factors, including demography, recombination or genome duplication, may impact the efficacy of natural selection and the burden of deleterious mutations, is a central question in evolutionary biology and genetics. In this study, we show that key evolutionary processes, including variations in i) effective population size (Ne) ii) recombination rates and iii) chromosome inheritance, have influenced the genetic load and efficacy of selection in Coho salmon (Oncorhynchus kisutch), a widely distributed salmonid species on the west coast of North America. Using whole genome resequencing data from 14 populations at different migratory distances from their southern glacial refugium, we found evidence supporting gene surfing, wherein reduced Ne at the postglacial recolonization front, leads to a decrease in the efficacy of selection and a surf of deleterious alleles in the northernmost populations. Furthermore, our results indicate that recombination rates play a prime role in shaping the load along the genome. Additionally, we identified variation in polyploidy as a contributing factor to within-genome variation of the load. Overall, our results align remarkably well with expectations under the nearly neutral theory of molecular evolution. We discuss the fundamental and applied implications of these findings for evolutionary and conservation genomics.
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Affiliation(s)
- Quentin Rougemont
- Centre d’Ecologie Fonctionnelle et Evolutive, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Thibault Leroy
- GenPhySE, INRAE, INP, ENVT, Université de Toulouse, Auzeville- Tolosane, France
| | - Eric B. Rondeau
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, Canada
| | - Ben Koop
- Department of Biology, University of Victoria, Victoria, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
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17
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Blischak PD, Sajan M, Barker MS, Gutenkunst RN. Demographic history inference and the polyploid continuum. Genetics 2023; 224:iyad107. [PMID: 37279657 PMCID: PMC10411560 DOI: 10.1093/genetics/iyad107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 04/17/2023] [Accepted: 05/18/2023] [Indexed: 06/08/2023] Open
Abstract
Polyploidy is an important generator of evolutionary novelty across diverse groups in the Tree of Life, including many crops. However, the impact of whole-genome duplication depends on the mode of formation: doubling within a single lineage (autopolyploidy) versus doubling after hybridization between two different lineages (allopolyploidy). Researchers have historically treated these two scenarios as completely separate cases based on patterns of chromosome pairing, but these cases represent ideals on a continuum of chromosomal interactions among duplicated genomes. Understanding the history of polyploid species thus demands quantitative inferences of demographic history and rates of exchange between subgenomes. To meet this need, we developed diffusion models for genetic variation in polyploids with subgenomes that cannot be bioinformatically separated and with potentially variable inheritance patterns, implementing them in the dadi software. We validated our models using forward SLiM simulations and found that our inference approach is able to accurately infer evolutionary parameters (timing, bottleneck size) involved with the formation of auto- and allotetraploids, as well as exchange rates in segmental allotetraploids. We then applied our models to empirical data for allotetraploid shepherd's purse (Capsella bursa-pastoris), finding evidence for allelic exchange between the subgenomes. Taken together, our model provides a foundation for demographic modeling in polyploids using diffusion equations, which will help increase our understanding of the impact of demography and selection in polyploid lineages.
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Affiliation(s)
- Paul D Blischak
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
- Bayer Crop Science, Chesterfield, MO 63017, USA
| | - Mathews Sajan
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Ryan N Gutenkunst
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
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18
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Liu SH, Hung KH, Hsu TW, Hoch PC, Peng CI, Chiang TY. New insights into polyploid evolution and dynamic nature of Ludwigia section Isnardia (Onagraceae). BOTANICAL STUDIES 2023; 64:14. [PMID: 37269434 DOI: 10.1186/s40529-023-00387-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 05/17/2023] [Indexed: 06/05/2023]
Abstract
BACKGROUND While polyploids are common in plants, the evolutionary history and natural dynamics of most polyploid groups are still unclear. Owing to plentiful earlier systematic studies, Ludwigia sect. Isnardia (comprising 22 wetland taxa) is an ideal allopolyploid complex to investigate polyploid evolution and natural dynamics within and among taxa. With a considerable sampling, we concentrated on revisiting earlier phylogenies of Isnardia, reevaluating the earlier estimated age of the most recent common ancestor (TMRCA), exploring the correlation between infraspecific genetic diversity and ploidy levels, and inspecting interspecific gene flows among taxa. RESULTS Phylogenetic trees and network concurred with earlier phylogenies and hypothesized genomes by incorporating 192 atpB-rbcL and ITS sequences representing 91% of Isnardia taxa. Moreover, we detected three multi-origin taxa. Our findings on L. repens and L. sphaerocarpa were consistent with earlier studies; L. arcuata was reported as a multi-origin taxon here, and an additional evolutionary scenario of L. sphaerocarpa was uncovered, both for the first time. Furthermore, estimated Isnardia TMRCA ages based on our data (5.9 or 8.9 million years ago) are in accordance with earlier estimates, although younger than fossil dates (Middle Miocene). Surprisingly, infraspecific genetic variations of Isnardia taxa did not increase with ploidy levels as anticipated from many other polyploid groups. In addition, the exuberant, low, and asymmetrical gene flows among Isnardia taxa indicated that the reproductive barriers may be weakened owing to allopolyploidization, which has rarely been reported. CONCLUSIONS The present research gives new perceptions of the reticulate evolution and dynamic nature of Isnardia and points to gaps in current knowledge about allopolyploid evolution.
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Affiliation(s)
- Shih-Hui Liu
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, 804, Taiwan
| | - Kuo-Hsiang Hung
- Graduate Institute of Bioresources, National Pingtung University of Science and Technology, Pingtung, 912, Taiwan
| | - Tsai-Wen Hsu
- Endemic Species Research Institute, Nantou, 552, Taiwan
| | - Peter C Hoch
- Missouri Botanical Garden, St. Louis, MO, 63166, USA
| | - Ching-I Peng
- Biodiversity Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Tzen-Yuh Chiang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
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19
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Mezzasalma M, Brunelli E, Odierna G, Guarino FM. Evolutionary and Genomic Diversity of True Polyploidy in Tetrapods. Animals (Basel) 2023; 13:ani13061033. [PMID: 36978574 PMCID: PMC10044425 DOI: 10.3390/ani13061033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/02/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
True polyploid organisms have more than two chromosome sets in their somatic and germline cells. Polyploidy is a major evolutionary force and has played a significant role in the early genomic evolution of plants, different invertebrate taxa, chordates, and teleosts. However, the contribution of polyploidy to the generation of new genomic, ecological, and species diversity in tetrapods has traditionally been underestimated. Indeed, polyploidy represents an important pathway of genomic evolution, occurring in most higher-taxa tetrapods and displaying a variety of different forms, genomic configurations, and biological implications. Herein, we report and discuss the available information on the different origins and evolutionary and ecological significance of true polyploidy in tetrapods. Among the main tetrapod lineages, modern amphibians have an unparalleled diversity of polyploids and, until recently, they were considered to be the only vertebrates with closely related diploid and polyploid bisexual species or populations. In reptiles, polyploidy was thought to be restricted to squamates and associated with parthenogenesis. In birds and mammals, true polyploidy has generally been considered absent (non-tolerated). These views are being changed due to an accumulation of new data, and the impact as well as the different evolutionary and ecological implications of polyploidy in tetrapods, deserve a broader evaluation.
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Affiliation(s)
- Marcello Mezzasalma
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy
- Correspondence: (M.M.); (E.B.)
| | - Elvira Brunelli
- Department of Biology, Ecology and Earth Science, University of Calabria, Via P. Bucci 4/B, 87036 Rende, Italy
- Correspondence: (M.M.); (E.B.)
| | - Gaetano Odierna
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, Italy (F.M.G.)
| | - Fabio Maria Guarino
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126 Naples, Italy (F.M.G.)
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20
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Phylogeography and population structure of the global, wide host-range hybrid pathogen Phytophthora × cambivora. IMA Fungus 2023; 14:4. [PMID: 36823663 PMCID: PMC9951538 DOI: 10.1186/s43008-023-00109-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/08/2023] [Indexed: 02/25/2023] Open
Abstract
Invasive, exotic plant pathogens pose a major threat to native and agricultural ecosystems. Phytophthora × cambivora is an invasive, destructive pathogen of forest and fruit trees causing severe damage worldwide to chestnuts (Castanea), apricots, peaches, plums, almonds and cherries (Prunus), apples (Malus), oaks (Quercus), and beech (Fagus). It was one of the first damaging invasive Phytophthora species to be introduced to Europe and North America, although its origin is unknown. We determined its population genetic history in Europe, North and South America, Australia and East Asia (mainly Japan) using genotyping-by-sequencing. Populations in Europe and Australia appear clonal, those in North America are highly clonal yet show some degree of sexual reproduction, and those in East Asia are partially sexual. Two clonal lineages, each of opposite mating type, and a hybrid lineage derived from these two lineages, dominated the populations in Europe and were predominantly found on fagaceous forest hosts (Castanea, Quercus, Fagus). Isolates from fruit trees (Prunus and Malus) belonged to a separate lineage found in Australia, North America, Europe and East Asia, indicating the disease on fruit trees could be caused by a distinct lineage of P. × cambivora, which may potentially be a separate sister species and has likely been moved with live plants. The highest genetic diversity was found in Japan, suggesting that East Asia is the centre of origin of the pathogen. Further surveys in unsampled, temperate regions of East Asia are needed to more precisely identify the location and range of the centre of diversity.
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21
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Oruganti V, Toegelová H, Pečinka A, Madlung A, Schneeberger K. Rapid large-scale genomic introgression in Arabidopsis suecica via an autoallohexaploid bridge. Genetics 2023; 223:iyac132. [PMID: 36124968 PMCID: PMC9910397 DOI: 10.1093/genetics/iyac132] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/24/2022] [Indexed: 11/14/2022] Open
Abstract
Gene flow between species in the genus Arabidopsis occurs in significant amounts, but how exactly gene flow is achieved is not well understood. Polyploidization may be one avenue to explain gene flow between species. One problem, however, with polyploidization as a satisfying explanation is the occurrence of lethal genomic instabilities in neopolyploids as a result of genomic exchange, erratic meiotic behavior, and genomic shock. We have created an autoallohexaploid by pollinating naturally co-occurring diploid Arabidopsis thaliana with allotetraploid Arabidopsis suecica (an allotetraploid composed of A. thaliana and Arabidopsis arenosa). Its triploid offspring underwent spontaneous genome duplication and was used to generate a multigenerational pedigree. Using genome resequencing, we show that 2 major mechanisms promote stable genomic exchange in this population. Legitimate meiotic recombination and chromosome segregation between the autopolyploid chromosomes of the 2 A. thaliana genomes occur without any obvious bias for the parental origin and combine the A. thaliana haplotypes from the A. thaliana parent with the A. thaliana haplotypes from A. suecica similar to purely autopolyploid plants. In addition, we repeatedly observed that occasional exchanges between regions of the homoeologous chromosomes are tolerated. The combination of these mechanisms may result in gene flow leading to stable introgression in natural populations. Unlike the previously reported resynthesized neoallotetraploid A. suecica, this population of autoallohexaploids contains mostly vigorous, and genetically, cytotypically, and phenotypically variable individuals. We propose that naturally formed autoallohexaploid populations might serve as an intermediate bridge between diploid and polyploid species, which can facilitate gene flow rapidly and efficiently.
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Affiliation(s)
- Vidya Oruganti
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Helena Toegelová
- Institute of Experimental Botany of the Czech Academy of Sciences, 77900 Olomouc, Czech Republic
| | - Aleš Pečinka
- Institute of Experimental Botany of the Czech Academy of Sciences, 77900 Olomouc, Czech Republic
| | - Andreas Madlung
- Department of Biology, University of Puget Sound, Tacoma, WA 98416, USA
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Department of Genetics, Faculty of Biology, Ludwig Maximilian Universität München, 82152 Planegg-Martinsried, Germany
- Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Düsseldorf, Germany
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22
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Brown MR, Becher H, Williams S, Twyford AD. Is there hybridization between diploid and tetraploid Euphrasia in a secondary contact zone? AMERICAN JOURNAL OF BOTANY 2023; 110:e16100. [PMID: 36371731 PMCID: PMC10107515 DOI: 10.1002/ajb2.16100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
PREMISE Strong postzygotic reproductive isolating barriers are usually expected to limit the extent of natural hybridization between species with contrasting ploidy. However, genomic sequencing has revealed previously overlooked examples of natural cross-ploidy hybridization in some flowering plant genera, suggesting that the phenomenon may be more common than once thought. We investigated potential cross-ploidy hybridization in British eyebrights (Euphrasia, Orobanchaceae), a group from which 13 putative cross-ploidy hybrid combinations have been reported based on morphology. METHODS We analyzed a contact zone between diploid Euphrasia rostkoviana and tetraploid E. arctica in Wales. We sequenced part of the internal transcribed spacer (ITS) of nuclear ribosomal DNA and used genotyping by sequencing (GBS) to look for evidence of cross-ploidy hybridization and introgression. RESULTS Common variant sites in the ITS region were fixed between diploids and tetraploids, indicating a strong barrier to hybridization. Clustering analyses of 356 single-nucleotide polymorphisms (SNPs) generated using GBS clearly separated samples by ploidy and revealed strong genetic structure (FST = 0.44). However, the FST distribution across all SNPs was bimodal, indicating potential differential selection on loci between diploids and tetraploids. Demographic inference suggested potential gene flow, limited to around one or fewer migrants per generation. CONCLUSIONS Our results suggest that recent cross-ploidy hybridization is rare or absent in a site of secondary contact in Euphrasia. While a strong ploidy barrier prevents hybridization over ecological timescales, such hybrids may form in stable populations over evolutionary timescales, potentially allowing cross-ploidy introgression to take place.
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Affiliation(s)
- Max R. Brown
- Institute of Ecology and EvolutionUniversity of Edinburgh, Ashworth Laboratories, Charlotte Auerbach RoadEdinburghEH9 3FLUK
- Wellcome Sanger InstituteWellcome Genome Campus, HinxtonCambridgeCB10 1SAUK
| | - Hannes Becher
- Institute of Ecology and EvolutionUniversity of Edinburgh, Ashworth Laboratories, Charlotte Auerbach RoadEdinburghEH9 3FLUK
| | - Sebastian Williams
- Institute of Ecology and EvolutionUniversity of Edinburgh, Ashworth Laboratories, Charlotte Auerbach RoadEdinburghEH9 3FLUK
| | - Alex D. Twyford
- Institute of Ecology and EvolutionUniversity of Edinburgh, Ashworth Laboratories, Charlotte Auerbach RoadEdinburghEH9 3FLUK
- Royal Botanic Garden Edinburgh, 20a Inverleith RowEdinburghEH3 5LRUK
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23
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Duan T, Sicard A, Glémin S, Lascoux M. Expression pattern of resynthesized allotetraploid Capsella is determined by hybridization, not whole-genome duplication. THE NEW PHYTOLOGIST 2023; 237:339-353. [PMID: 36254103 PMCID: PMC10099941 DOI: 10.1111/nph.18542] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Polyploidization, the process leading to the increase in chromosome sets, is a major evolutionary transition in plants. Whole-genome duplication (WGD) within the same species gives rise to autopolyploids, whereas allopolyploids result from a compound process with two distinct components: WGD and interspecific hybridization. To dissect the instant effects of WGD and hybridization on gene expression and phenotype, we created a series of synthetic hybrid and polyploid Capsella plants, including diploid hybrids, autotetraploids of both parental species, and two kinds of resynthesized allotetraploids with different orders of WGD and hybridization. Hybridization played a major role in shaping the relative expression pattern of the neo-allopolyploids, whereas WGD had almost no immediate effect on relative gene expression pattern but, nonetheless, still affected phenotypes. No transposable element-mediated genomic shock scenario was observed in either neo-hybrids or neo-polyploids. Finally, WGD and hybridization interacted and the distorting effects of WGD were less strong in hybrids. Whole-genome duplication may even improve hybrid fertility. In summary, while the initial relative gene expression pattern in neo-allotetraploids was almost entirely determined by hybridization, WGD only had trivial effects on relative expression patterns, both processes interacted and had a strong impact on physical attributes and meiotic behaviors.
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Affiliation(s)
- Tianlin Duan
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life LaboratoryUppsala University75236UppsalaSweden
| | - Adrien Sicard
- Department of Plant BiologySwedish University of Agricultural Sciences750 07UppsalaSweden
| | - Sylvain Glémin
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life LaboratoryUppsala University75236UppsalaSweden
- UMR CNRS 6553 ECOBIOCampus Beaulieu, bât 14a, p.118, CS 7420535042RennesFrance
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life LaboratoryUppsala University75236UppsalaSweden
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24
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Li Z, Li M, Wu X, Wang J. The characteristics of mRNA m 6A methylomes in allopolyploid Brassica napus and its diploid progenitors. HORTICULTURE RESEARCH 2022; 10:uhac230. [PMID: 36643749 PMCID: PMC9832873 DOI: 10.1093/hr/uhac230] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 09/30/2022] [Indexed: 06/17/2023]
Abstract
Genome duplication events, comprising whole-genome duplication and single-gene duplication, produce a complex genomic context leading to multiple levels of genetic changes. However, the characteristics of m6A modification, the most widespread internal eukaryotic mRNA modification, in polyploid species are still poorly understood. This study revealed the characteristics of m6A methylomes within the early formation and following the evolution of allopolyploid Brassica napus. We found a complex relationship between m6A modification abundance and gene expression level depending on the degree of enrichment or presence/absence of m6A modification. Overall, the m6A genes had lower gene expression levels than the non-m6A genes. Allopolyploidization may change the expression divergence of duplicated gene pairs with identical m6A patterns and diverged m6A patterns. Compared with duplicated genes, singletons with a higher evolutionary rate exhibited higher m6A modification. Five kinds of duplicated genes exhibited distinct distributions of m6A modifications in transcripts and gene expression level. In particular, tandem duplication-derived genes showed unique m6A modification enrichment around the transcript start site. Active histone modifications (H3K27ac and H3K4me3) but not DNA methylation were enriched around genes of m6A peaks. These findings provide a new understanding of the features of m 6A modification and gene expression regulation in allopolyploid plants with sophisticated genomic architecture.
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Affiliation(s)
- Zeyu Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, China
| | - Mengdi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, 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
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25
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Scarlett VT, Lovell JT, Shao M, Phillips J, Shu S, Lusinska J, Goodstein DM, Jenkins J, Grimwood J, Barry K, Chalhoub B, Schmutz J, Hasterok R, Catalán P, Vogel JP. Multiple origins, one evolutionary trajectory: gradual evolution characterizes distinct lineages of allotetraploid Brachypodium. Genetics 2022; 223:6758249. [PMID: 36218464 PMCID: PMC9910409 DOI: 10.1093/genetics/iyac146] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
The "genomic shock" hypothesis posits that unusual challenges to genome integrity such as whole genome duplication may induce chaotic genome restructuring. Decades of research on polyploid genomes have revealed that this is often, but not always the case. While some polyploids show major chromosomal rearrangements and derepression of transposable elements in the immediate aftermath of whole genome duplication, others do not. Nonetheless, all polyploids show gradual diploidization over evolutionary time. To evaluate these hypotheses, we produced a chromosome-scale reference genome for the natural allotetraploid grass Brachypodium hybridum, accession "Bhyb26." We compared 2 independently derived accessions of B. hybridum and their deeply diverged diploid progenitor species Brachypodium stacei and Brachypodium distachyon. The 2 B. hybridum lineages provide a natural timecourse in genome evolution because one formed 1.4 million years ago, and the other formed 140 thousand years ago. The genome of the older lineage reveals signs of gradual post-whole genome duplication genome evolution including minor gene loss and genome rearrangement that are missing from the younger lineage. In neither B. hybridum lineage do we find signs of homeologous recombination or pronounced transposable element activation, though we find evidence supporting steady post-whole genome duplication transposable element activity in the older lineage. Gene loss in the older lineage was slightly biased toward 1 subgenome, but genome dominance was not observed at the transcriptomic level. We propose that relaxed selection, rather than an abrupt genomic shock, drives evolutionary novelty in B. hybridum, and that the progenitor species' similarity in transposable element load may account for the subtlety of the observed genome dominance.
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Affiliation(s)
- Virginia T Scarlett
- U.S. Dept. of Energy Joint Genome Institute, Berkeley, CA 94720, USA,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - John T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Mingqin Shao
- U.S. Dept. of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Jeremy Phillips
- U.S. Dept. of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Shengqiang Shu
- U.S. Dept. of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | | | - David M Goodstein
- U.S. Dept. of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kerrie Barry
- U.S. Dept. of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | | | - Jeremy Schmutz
- U.S. Dept. of Energy Joint Genome Institute, Berkeley, CA 94720, USA,Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | | | - John P Vogel
- Corresponding author: U.S. Dept. of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA.
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26
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Becker FW, Oberlander KC, Trávníček P, Dreyer LL. Inconsistent expression of the gigas effect in polyploid Oxalis. AMERICAN JOURNAL OF BOTANY 2022; 109:1607-1621. [PMID: 36193941 DOI: 10.1002/ajb2.16077] [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: 03/31/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
PREMISE It is well-known that whole genome duplication (WGD) has played a significant role in the evolution of plants. The best-known phenotypic effect of WGD is the gigas effect, or the enlargement of polyploid plant traits. WGD is often linked with increased weediness, which could be a result of fitness advantages conferred by the gigas effect. As a result, the gigas effect could potentially explain polyploid persistence and abundance. We test whether a gigas effect is present in the polyploid-rich geophyte Oxalis, at both organ and cellular scales. METHODS We measured traits in conspecific diploid and polyploid accessions of 24 species across the genus. In addition, we measured the same and additional traits in 20 populations of the weedy and highly ploidy-variable species Oxalis purpurea L., including measures of clonality and selfing as a proxy for weediness. Ploidy level was determined using flow cytometry. RESULTS We found substantial variation and no consistent ploidy-related size difference, both between and within species, and across traits. Oxalis purpurea polyploids did, however, produce significantly more underground biomass and more bulbils than diploids, consistent with a potential role of WGD in the weediness of this species. CONCLUSIONS Our results suggest a more nuanced role for the gigas effect, at least in Oxalis. It may be temporary, short-lived, and inconsistently expressed and retained on evolutionary time scales, but in the short term can contribute to lineage success via increased vegetative reproduction.
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Affiliation(s)
- Frederik W Becker
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Kenneth C Oberlander
- H. G. W. J. Schweickerdt Herbarium, Department of Plant and Soil Sciences, Plant Sciences Complex, University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa
| | - Pavel Trávníček
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic, and Department of Botany, Charles University, Praha, Czech Republic
| | - Léanne L Dreyer
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
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27
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Wu T, Zhao X, Yang S, Yang J, Zhu J, Kou Y, Yu X, Ge H, Jia R. Induction of 2n pollen with colchicine during microsporogenesis in Phalaenopsis. BREEDING SCIENCE 2022; 72:275-284. [PMID: 36699823 PMCID: PMC9868330 DOI: 10.1270/jsbbs.21100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/24/2022] [Indexed: 06/17/2023]
Abstract
The induction of 2n pollen is an important technique for breeding polyploid plants. Here, we observed meiosis in the pollen mother cells (PMCs) of six Phalaenopsis cultivars and attempted to induce 2n pollen. The meiotic stage was related to flower bud length. During meiosis, Phalaenopsis cultivars with flower widths of approximately 20-40 mm and 50-60 mm had bud lengths of approximately 3-8 mm and 5-13 mm, respectively. The duration of meiosis ranged from 4.2 to 14 d. This was the first study to characterize meiosis of the PMCs of Phalaenopsis. The natural generation frequency of 2n pollen varied from 0.68% to 1.78%. Meiotic stage and colchicine concentration significantly affected the induction of 2n pollen. The most effective treatment for obtaining 2n pollen was 0.05% colchicine in the leptotene to zygotene stage for 3 d, which achieved a 2n pollen frequency of 10.04%.
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Affiliation(s)
- Ting Wu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Beijing Forestry University, Beijing 100081, China
| | - Xin Zhao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuhua Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiahui Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jun Zhu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yaping Kou
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaonan Yu
- Beijing Forestry University, Beijing 100081, China
| | - Hong Ge
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ruidong Jia
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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28
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Sabooni N, Gharaghani A. Induced polyploidy deeply influences reproductive life cycles, related phytochemical features, and phytohormonal activities in blackberry species. FRONTIERS IN PLANT SCIENCE 2022; 13:938284. [PMID: 36035697 PMCID: PMC9412943 DOI: 10.3389/fpls.2022.938284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
In some cases, polyploidy is an important phenomenon in the evolution of fruit crops. Polyploidy can be used in fruit breeding programs to develop varieties with higher yields and better fruit quality, as well as better adaptation to adverse environmental conditions. In this study, three wild species of blackberry were subjected to different degrees of induced polyploidy, and the effects of which were evaluated on morphological, physiological, and phytohormonal traits. With the aim of gaining a deep insight into the generative phase of plant growth and development, different levels of induced polyploidy were evaluated on the three blackberry species, i.e., Rubus persicus Bioss. (2x, 4x, and 8x), R. caesius L. (2x and 4x), and R. hirtus Schreb. (2x and 4x). The results showed that the polyploid plants performed significantly better than their diploid counterparts in terms of morphological traits such as flower count per spike and berry weight, as well as biochemical traits such as total soluble solids in the leaves. Induced polyploidy increased berry weight and drupe count per fruit. Microscopic examinations revealed a smaller number of viable pollen in the polyploids, compared to the diploids. Electron microscopy showed that the octaploid R. persicus had larger conical cells on the flower surface, compared to the diploid R. persicus. Correlation analysis showed that the ratio of indoleacetic acid to jasmonic acid changed synergistically with the total soluble solids in the leaves during the fruit set. The ploidy level correlated significantly with the number of pistils, leaf green index, total soluble solids in the leaves, and glucose content in floral nectar. Overall, induced polyploidy allowed Rubus to develop advantageous traits that can benefit future breeding programs and expand reproductive research in blackberries.
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29
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Clo J. Polyploidization: Consequences of genome doubling on the evolutionary potential of populations. AMERICAN JOURNAL OF BOTANY 2022; 109:1213-1220. [PMID: 35862788 DOI: 10.1002/ajb2.16029] [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: 03/17/2022] [Revised: 06/19/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Whole-genome duplication is common in plants and is considered to have a broad range of effects on individuals' phenotypes and genomes and to be an important driver of plant adaptation and speciation. Despite their increased capacity to cope with challenging environments, polyploid lineages are generally as prone to extinction, and sometimes more prone, than their diploid progenitors. Although several explanations have been proposed to explain the short- and long-term disadvantages of polyploidy on the survival probability of populations, the consequences of whole-genome doubling on the heritable variance remain poorly studied. Whole-genome doubling can have major effects not only on the genetics, but also on the ecology and life history of the populations. Modifications of other properties of populations can reverse the effects of polyploidization per se on heritable variance. In this synthesis, I summarize the empirical and theoretical knowledge about the multifarious consequences of genome doubling on the heritable variance of quantitative traits and on the evolutionary potential of polyploid populations compared to their diploid progenitors. I propose several ways to decipher the consequences of whole-genome doubling on survival probability and to study the further consequences of shifting the ecological niche and life-history traits of a population. I also highlight some practical considerations for comparing the heritable variance of a trait among different cytotypes. Such investigations appear to be timely and necessary to understand more about the paradoxical aspects of polyploidization and to understand the evolutionary potential of polyploid lineages in a global warming context.
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Affiliation(s)
- Josselin Clo
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, CZ-128 01, Prague, Czech Republic
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30
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Li Z, Li M, Wang J. Asymmetric subgenomic chromatin architecture impacts on gene expression in resynthesized and natural allopolyploid Brassica napus. Commun Biol 2022; 5:762. [PMID: 35906482 PMCID: PMC9338098 DOI: 10.1038/s42003-022-03729-7] [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: 02/16/2022] [Accepted: 07/15/2022] [Indexed: 11/26/2022] Open
Abstract
Although asymmetric subgenomic epigenetic modification and gene expression have been revealed in the successful establishment of allopolyploids, the changes in chromatin accessibility and their relationship with epigenetic modifications and gene expression are poorly understood. Here, we synthetically analyzed chromatin accessibility, four epigenetic modifications and gene expression in natural allopolyploid Brassica napus, resynthesized allopolyploid B. napus, and diploid progenitors (B. rapa and B. oleracea). “Chromatin accessibility shock” occurred in both allopolyploidization and natural evolutionary processes, and genic accessible chromatin regions (ACRs) increased after allopolyploidization. ACRs associated with H3K27me3 modifications were more accessible than those with H3K27ac or H3K4me3. Although overall chromatin accessibility may be defined by H3K27me3, the enrichment of H3K4me3 and H3K27ac and depletion of DNA methylation around transcriptional start sites up-regulated gene expression. Moreover, we found that subgenome Cn exhibited higher chromatin accessibility than An, which depended on the higher chromatin accessibility of Cn-unique genes but not homologous genes. Changes in chromatin accessibility occuring during the process of allopolyploidization of Brassica napus are analysed using ATAC and ChIPseq, with differences in asymmetric chromatin accessibility between subgenomes of B. napus investigated.
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Affiliation(s)
- Zeyu Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Mengdi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China.
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31
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Moraes AP, Engel TBJ, Forni-Martins ER, de Barros F, Felix LP, Cabral JS. Are chromosome number and genome size associated with habit and environmental niche variables? Insights from the Neotropical orchids. ANNALS OF BOTANY 2022; 130:11-25. [PMID: 35143612 PMCID: PMC9295925 DOI: 10.1093/aob/mcac021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS The entangled relationship of chromosome number and genome size with species distribution has been the subject of study for almost a century, but remains an open question due to previous ecological and phylogenetic knowledge constraints. To better address this subject, we used the clade Maxillariinae, a widely distributed and karyotypically known orchid group, as a model system to infer such relationships in a robust methodological framework. METHODS Based on the literature and new data, we gathered the chromosome number and genome size for 93 and 64 species, respectively. We built a phylogenetic hypothesis and assessed the best macroevolutionary model for both genomic traits. Additionally, we collected together ecological data (preferences for bioclimatic variables, elevation and habit) used as explanatory variables in multivariate phylogenetic models explaining genomic traits. Finally, the impact of polyploidy was estimated by running the analyses with and without polyploids in the sample. KEY RESULTS The association between genomic and ecological data varied depending on whether polyploids were considered or not. Without polyploids, chromosome number failed to present consistent associations with ecological variables. With polyploids, there was a tendency to waive epiphytism and colonize new habitats outside humid forests. The genome size showed association with ecological variables: without polyploids, genome increase was associated with flexible habits, with higher elevation and with drier summers; with polyploids, genome size increase was associated with colonizing drier environments. CONCLUSIONS The chromosome number and genome size variations, essential but neglected traits in the ecological niche, are shaped in the Maxillariinae by both neutral and adaptive evolution. Both genomic traits are partially correlated to bioclimatic variables and elevation, even when controlling for phylogenetic constraints. While polyploidy was associated with shifts in the environmental niche, the genome size emerges as a central trait in orchid evolution by the association between small genome size and epiphytism, a key innovation to Neotropical orchid diversification.
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Affiliation(s)
| | - Thaissa Brogliato Junqueira Engel
- Universidade de Campinas – UNICAMP, Instituto de Biologia, Departamento de Biologia Vegetal, Programa de Pós Graduação em Biologia Vegetal, Campinas, 13083-970, São Paulo, Brazil
| | - Eliana R Forni-Martins
- Universidade de Campinas – UNICAMP, Instituto de Biologia, Departamento de Biologia Vegetal, Programa de Pós Graduação em Biologia Vegetal, Campinas, 13083-970, São Paulo, Brazil
| | - Fábio de Barros
- Instituto de Botânica, Núcleo de Pesquisa Orquidário do Estado, São Paulo, 04045-972, São Paulo, Brazil
| | - Leonardo P Felix
- Universidade Federal da Paraíba – UFPB, Campus II, Departamento de Ciências Biológicas, Areia, 58397-000, Paraíba, Brazil
| | - Juliano Sarmento Cabral
- University of Würzburg, Ecosystem Modeling, Center for Computational and Theoretical Biology (CCTB), Klara-Oppenheimer-Weg 32, D-97074, Würzburg, Germany
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32
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Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. PLoS Genet 2022; 18:e1010226. [PMID: 35793353 PMCID: PMC9292114 DOI: 10.1371/journal.pgen.1010226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 07/18/2022] [Accepted: 04/29/2022] [Indexed: 11/19/2022] Open
Abstract
Polyploidization may precipitate dramatic changes to the genome, including chromosome rearrangements, gene loss, and changes in gene expression. In dioecious plants, the sex-determining mechanism may also be disrupted by polyploidization, with the potential evolution of hermaphroditism. However, while dioecy appears to have persisted through a ploidy transition in some species, it is unknown whether the newly formed polyploid maintained its sex-determining system uninterrupted, or whether dioecy re-evolved after a period of hermaphroditism. Here, we develop a bioinformatic pipeline using RNA-sequencing data from natural populations to demonstrate that the allopolyploid plant Mercurialis canariensis directly inherited its sex-determining region from one of its diploid progenitor species, M. annua, and likely remained dioecious through the transition. The sex-determining region of M. canariensis is smaller than that of its diploid progenitor, suggesting that the non-recombining region of M. annua expanded subsequent to the polyploid origin of M. canariensis. Homeologous pairs show partial sexual subfunctionalization. We discuss the possibility that gene duplicates created by polyploidization might contribute to resolving sexual antagonism.
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33
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Van Drunen WE, Johnson MTJ. Polyploidy in urban environments. Trends Ecol Evol 2022; 37:507-516. [PMID: 35246321 DOI: 10.1016/j.tree.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 10/19/2022]
Abstract
Polyploidy is a major driver of evolutionary change in plants, but many aspects of polyploidy in natural systems remain enigmatic. We argue that urban landscapes present an unprecedented opportunity to observe polyploidy in action. Integrating polyploid biology and urban evolutionary ecology, we discuss multiple factors expected to promote polyploid formation, establishment, and persistence in urban systems. We develop a predictive framework for the contemporary ecology and evolution of polyploid plants in cities, and through this novel perspective propose that studying polyploidy in an urban context could lead to breakthroughs in understanding fundamental processes in polyploid evolution. We conclude by highlighting the potential consequences of polyploidy in urban environments, and outline a roadmap for research into this currently unexplored field.
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Affiliation(s)
- Wendy E Van Drunen
- Department of Biology, Queen's University, Kingston, Ontario K7L 3N6, Canada; Department of Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada; Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.
| | - Marc T J Johnson
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada; Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada
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34
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Clo J. The evolution of the additive variance of a trait under stabilizing selection after autopolyploidization. J Evol Biol 2022; 35:891-897. [PMID: 35506572 PMCID: PMC9322463 DOI: 10.1111/jeb.14010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/21/2022] [Accepted: 04/10/2022] [Indexed: 12/22/2022]
Abstract
Whole‐genome duplication is a common mutation in eukaryotes with far‐reaching phenotypic effects. The resulting morphological, physiological and fitness consequences and how they affect the survival probability of polyploid lineages are intensively studied, but little is known about the effect of genome doubling on the evolutionary potential of populations. Historically, it has been argued polyploids should be less able to adapt because gene duplication dilutes the effects of alleles, such that polyploids are less likely to evolve new adaptive gene complexes compared with diploids. In this paper, I investigate the short‐ and long‐term consequences of genome doubling on the additive genetic variance of populations. To do so, I extended the classical models of quantitative traits under stabilizing selection to study the evolution of the additive variance of the trait under study after a shift from diploidy to tetraploidy. I found that, for realistic allele‐dosage effects, polyploidization is associated with an initial decrease in adaptive potential. In the long term, the better masking of recessive deleterious mutations associated with polyploidy compensates for the initial decrease in additive variance. The time for the tetraploid populations to reach or exceed the additive variance of their diploid progenitors is generally lower than 200 generations. These results highlight that polyploidization per se has a negligible negative effect on the adaptive potential of populations in the short term, and a substantial positive effect in the long term.
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Affiliation(s)
- Josselin Clo
- Department of Botany, Charles University, Prague, Czech Republic
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35
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Fernández P, Hidalgo O, Juan A, Leitch IJ, Leitch AR, Palazzesi L, Pegoraro L, Viruel J, Pellicer J. Genome Insights into Autopolyploid Evolution: A Case Study in Senecio doronicum (Asteraceae) from the Southern Alps. PLANTS 2022; 11:plants11091235. [PMID: 35567236 PMCID: PMC9099586 DOI: 10.3390/plants11091235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022]
Abstract
Polyploidy is a widespread phenomenon across angiosperms, and one of the main drivers of diversification. Whilst it frequently involves hybridisation, autopolyploidy is also an important feature of plant evolution. Minority cytotypes are frequently overlooked due to their lower frequency in populations, but the development of techniques such as flow cytometry, which enable the rapid screening of cytotype diversity across large numbers of individuals, is now providing a more comprehensive understanding of cytotype diversity within species. Senecio doronicum is a relatively common daisy found throughout European mountain grasslands from subalpine to almost nival elevations. We have carried out a population-level cytotype screening of 500 individuals from Tête Grosse (Alpes-de-Haute-Provence, France), confirming the coexistence of tetraploid (28.2%) and octoploid cytotypes (71.2%), but also uncovering a small number of hexaploid individuals (0.6%). The analysis of repetitive elements from short-read genome-skimming data combined with nuclear (ITS) and whole plastid DNA sequences support an autopolyploid origin of the polyploid S. doronicum individuals and provide molecular evidence regarding the sole contribution of tetraploids in the formation of hexaploid individuals. The evolutionary impact and resilience of the new cytotype have yet to be determined, although the coexistence of different cytotypes may indicate nascent speciation.
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Affiliation(s)
- Pol Fernández
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, 08038 Barcelona, Spain;
- Correspondence: (P.F.); (J.P.); Tel.: +34-932890611 (P.F. & J.P.)
| | - Oriane Hidalgo
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, 08038 Barcelona, Spain;
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK; (I.J.L.); (J.V.)
| | - Ana Juan
- Departamento de Ciencias Ambientales y Recursos Naturales, Universidad de Alicante, 03080 Alicante, Spain;
| | - Ilia J. Leitch
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK; (I.J.L.); (J.V.)
| | - Andrew R. Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK;
| | - Luis Palazzesi
- Museo Argentino de Ciencias Naturales, CONICET, División Paleobotánica, Buenos Aires C1405DJR, Argentina;
| | - Luca Pegoraro
- Biodiversity and Conservation Biology Research Unit, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Bimensdorf, Switzerland;
| | - Juan Viruel
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK; (I.J.L.); (J.V.)
| | - Jaume Pellicer
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia s.n., Parc de Montjuïc, 08038 Barcelona, Spain;
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK; (I.J.L.); (J.V.)
- Correspondence: (P.F.); (J.P.); Tel.: +34-932890611 (P.F. & J.P.)
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Cheng A, Mohd Hanafiah N, Harikrishna JA, Eem LP, Baisakh N, Mispan MS. A Reappraisal of Polyploidy Events in Grasses (Poaceae) in a Rapidly Changing World. BIOLOGY 2022; 11:biology11050636. [PMID: 35625365 PMCID: PMC9138248 DOI: 10.3390/biology11050636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 11/16/2022]
Abstract
Around 80% of megaflora species became extinct at the Cretaceous–Paleogene (K–Pg) boundary. Subsequent polyploidy events drove the survival of thousands of plant species and played a significant historical role in the development of the most successful modern cereal crops. However, current and rapid global temperature change poses an urgent threat to food crops worldwide, including the world’s big three cereals: rice, wheat, and maize, which are members of the grass family, Poaceae. Some minor cereals from the same family (such as teff) have grown in popularity in recent years, but there are important knowledge gaps regarding the similarities and differences between major and minor crops, including how polyploidy affects their biological processes under natural and (a)biotic stress conditions and thus the potential to harness polyploidization attributes for improving crop climate resilience. This review focuses on the impact of polyploidy events on the Poaceae family, which includes the world’s most important food sources, and discusses the past, present, and future of polyploidy research for major and minor crops. The increasing accessibility to genomes of grasses and their wild progenitors together with new tools and interdisciplinary research on polyploidy can support crop improvement for global food security in the face of climate change.
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Affiliation(s)
- Acga Cheng
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.C.); (N.M.H.); (J.A.H.)
| | - Noraikim Mohd Hanafiah
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.C.); (N.M.H.); (J.A.H.)
| | - Jennifer Ann Harikrishna
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.C.); (N.M.H.); (J.A.H.)
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Lim Phaik Eem
- Institute of Ocean and Earth Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
| | - Niranjan Baisakh
- School of Plant, Environmental, and Soil Science, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
- Correspondence: (N.B.); (M.S.M.)
| | - Muhamad Shakirin Mispan
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.C.); (N.M.H.); (J.A.H.)
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Correspondence: (N.B.); (M.S.M.)
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Baranow P, Rojek J, Dudek M, Szlachetko D, Bohdanowicz J, Kapusta M, Jedrzejczyk I, Rewers M, Moraes AP. Chromosome Number and Genome Size Evolution in Brasolia and Sobralia (Sobralieae, Orchidaceae). Int J Mol Sci 2022; 23:ijms23073948. [PMID: 35409308 PMCID: PMC8999598 DOI: 10.3390/ijms23073948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 11/24/2022] Open
Abstract
Despite the clear circumscription of tribe Sobralieae (Orchidaceae), its internal relationships are still dubious. The recently delimited genus Brasolia, based on previous Sobralia species, is now assumed to be paraphyletic, with a third genus, Elleanthus, nested in it. The morphology of these three genera is significantly different, indicating the necessity of new data for a better genera delimitation. Though morphology and molecular data are available, cytogenetics data for Sobralieae is restricted to two Sobralia and one Elleanthus species. Aiming to evaluate the potential of cytogenetic data for Brasolia-Elleanthus-Sobralia genera delimitation, we present chromosome number and genome size data for 21 and 20 species, respectively, and used such data to infer the pattern of karyotype evolution in these genera. The analysis allowed us to infer x = 24 as the base chromosome number and genome size of average 1C-value of 5.0 pg for the common ancestor of Brasolia-Elleanthus-Sobralia. The recurrent descending dysploidy in Sobralieae and the punctual genome upsize suggest a recent diversification in Sobralieae but did not allow differing between Brasolia and Sobralia. However, the basal position of tribe Sobralieae in the subfamily Epidendroideae makes this tribe of interest to further studies clarifying the internal delimitation and pattern of karyotype evolution.
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Affiliation(s)
- Przemysław Baranow
- Department of Plant Taxonomy & Nature Conservation, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (P.B.); (M.D.); (D.S.)
| | - Joanna Rojek
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (J.B.); (M.K.)
- Correspondence:
| | - Magdalena Dudek
- Department of Plant Taxonomy & Nature Conservation, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (P.B.); (M.D.); (D.S.)
| | - Dariusz Szlachetko
- Department of Plant Taxonomy & Nature Conservation, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (P.B.); (M.D.); (D.S.)
| | - Jerzy Bohdanowicz
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (J.B.); (M.K.)
| | - Małgorzata Kapusta
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (J.B.); (M.K.)
| | - Iwona Jedrzejczyk
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, Bydgoszcz University of Science and Technology, Kaliskiego Ave 7, 85-796 Bydgoszcz, Poland; (I.J.); (M.R.)
| | - Monika Rewers
- Laboratory of Molecular Biology and Cytometry, Department of Agricultural Biotechnology, Bydgoszcz University of Science and Technology, Kaliskiego Ave 7, 85-796 Bydgoszcz, Poland; (I.J.); (M.R.)
| | - Ana Paula Moraes
- Laboratory of Cytogenomic and Evolution of Plants, Center of Natural and Human Science, Federal University of ABC (UFABC), Sao Bernardo do Campo 09606-045, SP, Brazil;
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Cheng J, Zhang G, Xu L, Liu C, Jiang H. Altered H3K27 trimethylation contributes to flowering time variations in polyploid Arabidopsis thaliana ecotypes. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1402-1414. [PMID: 34698830 DOI: 10.1093/jxb/erab470] [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: 07/26/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Polyploidy is a widespread phenomenon in flowering plant species. Polyploid plants frequently exhibit considerable transcriptomic alterations after whole-genome duplication (WGD). It is known that the transcriptomic response to tetraploidization is ecotype-dependent in Arabidopsis; however, the biological significance and the underlying mechanisms are unknown. In this study, we found that 4x Col-0 presents a delayed flowering time whereas 4x Ler does not. The expression of FLOWERING LOCUS C (FLC), the major repressor of flowering, was significantly increased in 4x Col-0 but only a subtle change was present in 4x Ler. Moreover, the level of a repressive epigenetic mark, trimethylation of histone H3 at lysine 27 (H3K27me3), was significantly decreased in 4x Col-0 but not in 4x Ler, potentially leading to the differences in FLC transcription levels and flowering times. Hundreds of other genes in addition to FLC showed H3K27me3 alterations in 4x Col-0 and 4x Ler. LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) and transcription factors required for H3K27me3 deposition presented transcriptional changes between the two ecotypes, potentially accounting for the different H3K27me3 alterations. We also found that the natural 4x Arabidopsis ecotype Wa-1 presented an early flowering time, which was associated with low expression of FLC. Taken together, our results demonstrate a role of H3K27me3 alterations in response to genome duplication in Arabidopsis autopolyploids, and that variation in flowering time potentially functions in autopolyploid speciation.
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Affiliation(s)
- Jinping Cheng
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Guiqian Zhang
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Linhao Xu
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Chang Liu
- Department of Epigenetics, Institute of Biology, University of Hohenheim, Garbenstrasse 30, 70599 Stuttgart, Germany
| | - Hua Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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Margarido GRA, Correr FH, Furtado A, Botha FC, Henry RJ. Limited allele-specific gene expression in highly polyploid sugarcane. Genome Res 2022; 32:297-308. [PMID: 34949669 PMCID: PMC8805727 DOI: 10.1101/gr.275904.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/19/2021] [Indexed: 12/04/2022]
Abstract
Polyploidy is widespread in plants, allowing the different copies of genes to be expressed differently in a tissue-specific or developmentally specific way. This allele-specific expression (ASE) has been widely reported, but the proportion and nature of genes showing this characteristic have not been well defined. We now report an analysis of the frequency and patterns of ASE at the whole-genome level in the highly polyploid sugarcane genome. Very high depth whole-genome sequencing and RNA sequencing revealed strong correlations between allelic proportions in the genome and in expressed sequences. This level of sequencing allowed discrimination of each of the possible allele doses in this 12-ploid genome. Most genes were expressed in direct proportion to the frequency of the allele in the genome with examples of polymorphisms being found with every possible discrete level of dose from 1:11 for single-copy alleles to 12:0 for monomorphic sites. The rarer cases of ASE were more frequent in the expression of defense-response genes, as well as in some processes related to the biosynthesis of cell walls. ASE was more common in genes with variants that resulted in significant disruption of function. The low level of ASE may reflect the recent origin of polyploid hybrid sugarcane. Much of the ASE present can be attributed to strong selection for resistance to diseases in both nature and domestication.
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Affiliation(s)
- Gabriel Rodrigues Alves Margarido
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba 13418-900, Brazil
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
| | - Fernando Henrique Correr
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Piracicaba 13418-900, Brazil
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
| | - Frederik C Botha
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
| | - Robert James Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane 4072, Australia
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40
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Williams JH. Consequences of whole genome duplication for 2n pollen performance. PLANT REPRODUCTION 2021; 34:321-334. [PMID: 34302535 DOI: 10.1007/s00497-021-00426-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
The vegetative cell of the angiosperm male gametophyte (pollen) functions as a free-living, single-celled organism that both produces and transports sperm to egg. Whole-genome duplication (WGD) should have strong effects on pollen because of the haploid to diploid transition and because of both genetic and epigenetic effects on cell-level phenotypes. To disentangle historical effects of WGD on pollen performance, studies can compare 1n pollen from diploids to neo-2n pollen from diploids and synthetic autotetraploids to older 2n pollen from established neo-autotetraploids. WGD doubles both gene number and bulk nuclear DNA mass, and a substantial proportion of diploid and autotetraploid heterozygosity can be transmitted to 2n pollen. Relative to 1n pollen, 2n pollen can exhibit heterosis due to higher gene dosage, higher heterozygosity and new allelic interactions. Doubled genome size also has consequences for gene regulation and expression as well as epigenetic effects on cell architecture. Pollen volume doubling is a universal effect of WGD, whereas an increase in aperture number is common among taxa with simultaneous microsporogenesis and pored apertures, mostly eudicots. WGD instantly affects numerous evolved compromises among mature pollen functional traits and these are rapidly shaped by highly diverse tissue interactions and pollen competitive environments in the early post-WGD generations. 2n pollen phenotypes generally incur higher performance costs, and the degree to which these are met or evolve by scaling up provisioning and metabolic vigor needs further study.
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Affiliation(s)
- Joseph H Williams
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA.
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41
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Li M, Sun W, Wang F, Wu X, Wang J. Asymmetric epigenetic modification and homoeolog expression bias in the establishment and evolution of allopolyploid Brassica napus. THE NEW PHYTOLOGIST 2021; 232:898-913. [PMID: 34265096 DOI: 10.1111/nph.17621] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/09/2021] [Indexed: 05/26/2023]
Abstract
This study explores how allopolyploidization reshapes the biased expression and asymmetric epigenetic modification of homoeologous gene pairs, and examines the regulation types and epigenetic basis of expression bias. We analyzed the gene expression and four epigenetic modifications (DNA methylation, H3K4me3, H3K27me3 and H3K27ac) of 29 976 homoeologous gene pairs in resynthesized, natural allopolyploid Brassica napus and an in silico 'hybrid'. We comprehensively elucidated the biased gene expression, asymmetric epigenetic modifications and the generational transmission characteristics of these homoeologous gene pairs in B. napus. We analyzed cis/trans effects and the epigenetic basis of homoeolog expression bias. There was a significant positive correlation between two active histone modifications and biased gene expression. We revealed that parental legacy was the dominant principle in the remodeling of homoeolog expression bias and asymmetric epigenetic modifications in B. napus, and further clarified that this depends on whether there were differences in the expression/epigenetic modifications of gene pairs in parents/progenitors. The maternal genome was dominant in the homoeolog expression bias of resynthesized B. napus, and this phenomenon was attenuated in natural B. napus. Furthermore, cis rather than trans effects were dominant when epigenetic modifications potentially affected biased expression of gene pairs in B. napus.
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Affiliation(s)
- Mengdi Li
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Weiqi Sun
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Fan Wang
- 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
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
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42
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Sharma G, Barney JN, Westwood JH, Haak DC. Into the weeds: new insights in plant stress. TRENDS IN PLANT SCIENCE 2021; 26:1050-1060. [PMID: 34238685 DOI: 10.1016/j.tplants.2021.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 06/03/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
Weeds, plants that thrive in the face of disturbance, have eluded human's attempts at control for >12 000 years, positioning them as a unique group of extreme stress tolerators. The most successful weeds have a suite of traits that enable them to rapidly adapt to environments typified by stress, growing in hostile conditions or subject to massive destruction from agricultural practices. Through their ability to persist and adapt, weeds illuminate principles of evolution and provide insights into weed management and crop improvement. Here we highlight why the time is right to move beyond traditional model systems and leverage weeds to gain a deeper understanding of the mechanisms, adaptations, and genetic and physiological bases for stress tolerance.
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Affiliation(s)
- Gourav Sharma
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Jacob N Barney
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - James H Westwood
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA.
| | - David C Haak
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA.
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Parallel adaptation in autopolyploid Arabidopsis arenosa is dominated by repeated recruitment of shared alleles. Nat Commun 2021; 12:4979. [PMID: 34404804 PMCID: PMC8370997 DOI: 10.1038/s41467-021-25256-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/21/2021] [Indexed: 01/26/2023] Open
Abstract
Relative contributions of pre-existing vs de novo genomic variation to adaptation are poorly understood, especially in polyploid organisms. We assess this in high resolution using autotetraploid Arabidopsis arenosa, which repeatedly adapted to toxic serpentine soils that exhibit skewed elemental profiles. Leveraging a fivefold replicated serpentine invasion, we assess selection on SNPs and structural variants (TEs) in 78 resequenced individuals and discover significant parallelism in candidate genes involved in ion homeostasis. We further model parallel selection and infer repeated sweeps on a shared pool of variants in nearly all these loci, supporting theoretical expectations. A single striking exception is represented by TWO PORE CHANNEL 1, which exhibits convergent evolution from independent de novo mutations at an identical, otherwise conserved site at the calcium channel selectivity gate. Taken together, this suggests that polyploid populations can rapidly adapt to environmental extremes, calling on both pre-existing variation and novel polymorphisms. Relative contributions of pre-existing versus de novo genomic variation to adaptation remain unclear. Here, the authors address this problem by examining the adaptation of autotetraploid Arabidopsis arenosa to serpentine soils and find that both types of variations contribute to rapid adaptation.
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44
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Bowers JE, Paterson AH. Chromosome number is key to longevity of polyploid lineages. THE NEW PHYTOLOGIST 2021; 231:19-28. [PMID: 33772797 DOI: 10.1111/nph.17361] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
Polyploidy is ubiquitous and often recursive in plant lineages, most frequently resulting in extinction but occasionally associated with great evolutionary success. However, instead of chromosome numbers exponentially increasing due to recurrent polyploidy, most angiosperm species have fewer than 14 chromosome pairs. Following genome duplication, diploidisation can render one copy of essential genes nonfunctional without fitness cost. In isolated subpopulations, alternate (homoeologous) gene copies can be lost, creating incompatibilities that reduce fitness of hybrids between subpopulations, constraining exchange of favourable genetic changes and reducing species fitness. When multiple sets of incompatible genes are genetically linked, their deleterious effects are not independent. The effective number of independently acting sets of incompatible loci in hybrids is limited by chromosome number and recombination. Therefore, species with many chromosomes are subject to a higher fitness penalty during diploidisation. Karyotypic changes, especially fusions, that reduce gene flow are normally fitness disadvantages, but during the diploidisation process, can increase fitness by reducing mixing of differentially diploidised alleles. Fitness penalties caused by diploidisation favour accelerated karyotypic change, with each change increasing barriers to gene flow, contributing to speciation. Lower chromosome numbers and increased chromosome fusions confer advantages to surviving the diploidisation process following polyploid formation, by independent mechanisms.
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Affiliation(s)
- John E Bowers
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
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45
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Li Z, McKibben MTW, Finch GS, Blischak PD, Sutherland BL, Barker MS. Patterns and Processes of Diploidization in Land Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:387-410. [PMID: 33684297 DOI: 10.1146/annurev-arplant-050718-100344] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Most land plants are now known to be ancient polyploids that have rediploidized. Diploidization involves many changes in genome organization that ultimately restore bivalent chromosome pairing and disomic inheritance, and resolve dosage and other issues caused by genome duplication. In this review, we discuss the nature of polyploidy and its impact on chromosome pairing behavior. We also provide an overview of two major and largely independent processes of diploidization: cytological diploidization and genic diploidization/fractionation. Finally, we compare variation in gene fractionation across land plants and highlight the differences in diploidization between plants and animals. Altogether, we demonstrate recent advancements in our understanding of variation in the patterns and processes of diploidization in land plants and provide a road map for future research to unlock the mysteries of diploidization and eukaryotic genome evolution.
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Affiliation(s)
- Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Michael T W McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Geoffrey S Finch
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Paul D Blischak
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Brittany L Sutherland
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
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46
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Rothfels CJ. Polyploid phylogenetics. THE NEW PHYTOLOGIST 2021; 230:66-72. [PMID: 33491778 DOI: 10.1111/nph.17105] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/27/2020] [Indexed: 05/23/2023]
Abstract
Polyploidy is a dominant feature of extant plant diversity. However, major research questions, including whether polyploidy is important to long-term evolution or is just 'evolutionary noise', remain unresolved due to difficulties associated with the generation and analysis of data from polyploid lineages. Many of these difficulties have been recently overcome, such that it is now often relatively straightforward to infer the full and often reticulate phylogenetic history of groups with recently formed polyploids. This nascent field of 'polyploid phylogenetics' allows researchers to tackle long-standing questions of polyploid macroevolution, supplies the foundation for mechanistic models of ploidy change, and provides the opportunity to include a more complete and representative sample of plant taxa in our analyses in general.
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Affiliation(s)
- Carl J Rothfels
- Department of Integrative Biology, University Herbarium, University of California, Berkeley, CA, 94702, USA
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47
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Qi X, An H, Hall TE, Di C, Blischak PD, McKibben MTW, Hao Y, Conant GC, Pires JC, Barker MS. Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa. THE NEW PHYTOLOGIST 2021; 230:372-386. [PMID: 33452818 DOI: 10.1111/nph.17194] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Many crops are polyploid or have a polyploid ancestry. Recent phylogenetic analyses have found that polyploidy often preceded the domestication of crop plants. One explanation for this observation is that increased genetic diversity following polyploidy may have been important during the strong artificial selection that occurs during domestication. In order to test the connection between domestication and polyploidy, we identified and examined candidate genes associated with the domestication of the diverse crop varieties of Brassica rapa. Like all 'diploid' flowering plants, B. rapa has a diploidized paleopolyploid genome and experienced many rounds of whole genome duplication (WGD). We analyzed transcriptome data of more than 100 cultivated B. rapa accessions. Using a combination of approaches, we identified > 3000 candidate genes associated with the domestication of four major B. rapa crop varieties. Consistent with our expectation, we found that the candidate genes were significantly enriched with genes derived from the Brassiceae mesohexaploidy. We also observed that paleologs were significantly more diverse than non-paleologs. Our analyses find evidence for that genetic diversity derived from ancient polyploidy played a key role in the domestication of B. rapa and provide support for its importance in the success of modern agriculture.
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Affiliation(s)
- Xinshuai Qi
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Hong An
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Tara E Hall
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Chenlu Di
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Paul D Blischak
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Michael T W McKibben
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Yue Hao
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
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48
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Bohutínská M, Alston M, Monnahan P, Mandáková T, Bray S, Paajanen P, Kolář F, Yant L. Novelty and convergence in adaptation to whole genome duplication. Mol Biol Evol 2021; 38:3910-3924. [PMID: 33783509 PMCID: PMC8382928 DOI: 10.1093/molbev/msab096] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/08/2021] [Accepted: 03/29/2021] [Indexed: 12/26/2022] Open
Abstract
Whole genome duplication (WGD) can promote adaptation but is disruptive to conserved processes, especially meiosis. Studies in Arabidopsis arenosa revealed a coordinated evolutionary response to WGD involving interacting proteins controlling meiotic crossovers, which are minimised in an autotetraploid (within-species polyploid) to avoid mis-segregation. Here we test whether this surprising flexibility of a conserved essential process, meiosis, is recapitulated in an independent WGD system, Cardamine amara, 17 million years diverged from A. arenosa. We assess meiotic stability and perform population-based scans for positive selection, contrasting the genomic response to WGD in C. amara with that of A. arenosa. We found in C. amara the strongest selection signals at genes with predicted functions thought important to adaptation to WGD: meiosis, chromosome remodelling, cell cycle, and ion transport. However, genomic responses to WGD in the two species differ: minimal ortholog-level convergence emerged, with none of the meiosis genes found in A. arenosa exhibiting strong signal in C. amara. This is consistent with our observations of lower meiotic stability and occasional clonal spreading in diploid C. amara, suggesting that nascent C. amara autotetraploid lineages were preadapted by their diploid lifestyle to survive while enduring reduced meiotic fidelity. However, in contrast to a lack of ortholog convergence, we see process-level and network convergence in DNA management, chromosome organisation, stress signalling, and ion homeostasis processes. This gives the first insight into the salient adaptations required to meet the challenges of a WGD state and shows that autopolyploids can utilize multiple evolutionary trajectories to adapt to WGD.
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Affiliation(s)
- Magdalena Bohutínská
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic
| | - Mark Alston
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Patrick Monnahan
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Terezie Mandáková
- CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Czech Republic
| | - Sian Bray
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, UK.,School of Biosciences University of Nottingham, Nottingham, UK
| | - Pirita Paajanen
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic.,Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic.,Natural History Museum, University of Oslo, Oslo, Norway
| | - Levi Yant
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, UK.,School of Life Sciences University of Nottingham, Nottingham, UK
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49
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Van de Peer Y, Ashman TL, Soltis PS, Soltis DE. Polyploidy: an evolutionary and ecological force in stressful times. THE PLANT CELL 2021; 33:11-26. [PMID: 33751096 PMCID: PMC8136868 DOI: 10.1093/plcell/koaa015] [Citation(s) in RCA: 238] [Impact Index Per Article: 79.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/07/2020] [Indexed: 05/10/2023]
Abstract
Polyploidy has been hypothesized to be both an evolutionary dead-end and a source for evolutionary innovation and species diversification. Although polyploid organisms, especially plants, abound, the apparent nonrandom long-term establishment of genome duplications suggests a link with environmental conditions. Whole-genome duplications seem to correlate with periods of extinction or global change, while polyploids often thrive in harsh or disturbed environments. Evidence is also accumulating that biotic interactions, for instance, with pathogens or mutualists, affect polyploids differently than nonpolyploids. Here, we review recent findings and insights on the effect of both abiotic and biotic stress on polyploids versus nonpolyploids and propose that stress response in general is an important and even determining factor in the establishment and success of polyploidy.
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Affiliation(s)
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611
- Department of Biology, University of Florida, Gainesville, Florida 32611
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50
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Pérez YDJ, Angulo MB, Honfi A, Dematteis M. Embryology and fertility of the natural tetraploid Lessingianthus plantaginoides (Asteraceae, Vernonieae): taxonomic implications. RODRIGUÉSIA 2021. [DOI: 10.1590/2175-7860202172080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract Lessingianthus plantaginoides (Vernonieae, Asteraceae) is a small natural tetraploid shrub that inhabits rocky highlands from South America. The population studied inhabits and covers an extensive region of a private reserve with high local biodiversity and animal and plant endemisms. With the purpose of providing insights into the cyto-embryology of this tetraploid species, the aims of this study were: to perform an ontogenetic study of the male and female gametophytes of L. plantaginoides; to carry out detailed meiotic analysis and evaluate the fertility of this species; to document and provide highlights on taxonomic implications of their reproductive aspects. Lessingianthus plantaginoides presented the following male and female gametophyte traits: dicotyledonous type of anther wall development, tetrahedral tetrads, 3-celled mature pollen grains; development of the chalazal megaspore, monosporic embryo sac and Polygonum type of megagametophyte development. The meiotic behavior was regular, the spores were tetrads of equal size and the pollen grains were highly stainable. Lessingianthus plantaginoides is a highly diplodized autotetraploid that reproduces sexually and has high meiotic regularity; which is apparently responsible for its colonization potential. It now seems certain that polyploid speciation plays a significant role in the establishment and diversification of the genus.
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Affiliation(s)
| | - Maria Betiana Angulo
- Instituto de Botánica del Nordeste, Argentina; Facultad de Ciencias Exactas y Naturales y Agrimensura (UNNE), Argentina
| | - Ana Honfi
- Universidad Nacional de Misiones, Argentina
| | - Massimiliano Dematteis
- Instituto de Botánica del Nordeste, Argentina; Facultad de Ciencias Exactas y Naturales y Agrimensura (UNNE), Argentina
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