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Kalfusová R, Herklotz V, Kumke K, Houben A, Kovařík A, Ritz CM, Lunerová J. Epigenetic histone H3 phosphorylation marks discriminate between univalent- and bivalent-forming chromosomes during canina asymmetrical meiosis. ANNALS OF BOTANY 2024; 133:435-446. [PMID: 38127060 PMCID: PMC11006542 DOI: 10.1093/aob/mcad198] [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: 10/10/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND AND AIMS Dogroses (Rosa sect. Caninae) are mostly pentaploid, bearing 2n = 5x = 35 chromosomes in somatic cells. They evolved a unique form of asymmetrical meiosis characterized by two types of chromosomes: (1) chromosomes forming bivalents and distributed in the normal sexual way; and (2) chromosomes occurring as univalents and transferred by a female gamete only. In the mature pollen of pentaploid species, seven bivalent-derived chromosomes are transmitted to offspring, and 21 unpaired univalent chromosomes are eliminated during microsporogenesis. To discriminate between bivalent- and univalent-forming chromosomes, we studied histone H3 phosphorylation patterns regulating meiotic chromosome condensation and segregation. METHODS We analysed histone modification patterns during male canina meiosis in two representative dogrose species, 5x Rosa canina and 5x Rosa rubiginosa, by immunohistochemical and molecular cytogenetics approaches. Immunostaining of meiotic cells included α-tubulin, histone H3 phosphorylation (H3S10p, H3S28p and H3T3p) and methylation (H3K4me3 and H3K27me3) marks. In addition, fluorescent in situ hybridization was carried out with an 18S rDNA probe. KEY RESULTS In the first meiotic division, univalent chromosomes underwent equational division into chromatids, while homologues in bivalents were segregated as regular dyads. In diakinesis, bivalent chromosomes displayed strong H3 phosphorylation signals in proximal regions, spreading to the rest of the chromosome. In contrast, in univalents, the H3 phosphorylation signals were weaker, occurring mostly outside proximal regions largely overlapping with the H3K4me3 signals. Reduced phosphorylation was associated with relative under-condensation of the univalent chromosomes, particularly at early diakinesis. CONCLUSIONS We hypothesize that the absence of pairing and/or recombination in univalent chromosomes negatively affects the histone H3 phosphorylation of their chromatin and perhaps the loading of meiotic-specific cohesins. This apparently destabilizes cohesion of sister chromatids, leading to their premature split in the first meiotic division.
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Affiliation(s)
- Radka Kalfusová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Veit Herklotz
- Senckenberg Museum of Natural History, Senckenberg – Member of the Leibniz Association, Am Museum 1, 02826 Görlitz, Germany
| | - Katrin Kumke
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, 06466 Stadt Seeland, Germany
| | - Aleš Kovařík
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
| | - Christiane M Ritz
- Senckenberg Museum of Natural History, Senckenberg – Member of the Leibniz Association, Am Museum 1, 02826 Görlitz, Germany
- Chair of Biodiversity of Higher Plants, Technical University Dresden, D-01069, Dresden, Germany
| | - Jana Lunerová
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 00 Brno, Czech Republic
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Heslop-Harrison JS(P, Schwarzacher T, Liu Q. Polyploidy: its consequences and enabling role in plant diversification and evolution. ANNALS OF BOTANY 2023; 131:1-10. [PMID: 36282971 PMCID: PMC9904344 DOI: 10.1093/aob/mcac132] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/24/2022] [Indexed: 05/10/2023]
Abstract
BACKGROUND Most, if not all, green plant (Virdiplantae) species including angiosperms and ferns are polyploids themselves or have ancient polyploid or whole genome duplication signatures in their genomes. Polyploids are not only restricted to our major crop species such as wheat, maize, potato and the brassicas, but also occur frequently in wild species and natural habitats. Polyploidy has thus been viewed as a major driver in evolution, and its influence on genome and chromosome evolution has been at the centre of many investigations. Mechanistic models of the newly structured genomes are being developed that incorporate aspects of sequence evolution or turnover (low-copy genes and regulatory sequences, as well as repetitive DNAs), modification of gene functions, the re-establishment of control of genes with multiple copies, and often meiotic chromosome pairing, recombination and restoration of fertility. SCOPE World-wide interest in how green plants have evolved under different conditions - whether in small, isolated populations, or globally - suggests that gaining further insight into the contribution of polyploidy to plant speciation and adaptation to environmental changes is greatly needed. Forward-looking research and modelling, based on cytogenetics, expression studies, and genomics or genome sequencing analyses, discussed in this Special Issue of the Annals of Botany, consider how new polyploids behave and the pathways available for genome evolution. They address fundamental questions about the advantages and disadvantages of polyploidy, the consequences for evolution and speciation, and applied questions regarding the spread of polyploids in the environment and challenges in breeding and exploitation of wild relatives through introgression or resynthesis of polyploids. CONCLUSION Chromosome number, genome size, repetitive DNA sequences, genes and regulatory sequences and their expression evolve following polyploidy - generating diversity and possible novel traits and enabling species diversification. There is the potential for ever more polyploids in natural, managed and disturbed environments under changing climates and new stresses.
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Affiliation(s)
- J S (Pat) Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Leicester, Institute for Environmental Futures, Department of Genetics and Genome Biology, Leicester, LE1 7RH, UK
- South China National Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Trude Schwarzacher
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of Leicester, Institute for Environmental Futures, Department of Genetics and Genome Biology, Leicester, LE1 7RH, UK
- South China National Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
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Schwarzacher T, Liu Q, Pat Heslop-Harrison JS. Plant Cytogenetics: From Chromosomes to Cytogenomics. Methods Mol Biol 2023; 2672:3-21. [PMID: 37335467 DOI: 10.1007/978-1-0716-3226-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Chromosomes have been studied since the late nineteenth century in the disciplines of cytology and cytogenetics. Analyzing their numbers, features, and dynamics has been tightly linked to the technical development of preparation methods, microscopes, and chemicals to stain them, with latest continuing developments described in this volume. At the end of the twentieth and beginning of the twenty-first centuries, DNA technology, genome sequencing, and bioinformatics have revolutionized how we see, use, and analyze chromosomes. The advent of in situ hybridization has shaped our understanding of genome organization and behavior by linking molecular sequence information with the physical location along chromosomes and genomes. Microscopy is the best technique to accurately determine chromosome number. Many features of chromosomes in interphase nuclei or pairing and disjunction at meiosis, involving physical movement of chromosomes, can only be studied by microscopy. In situ hybridization is the method of choice to characterize the abundance and chromosomal distribution of repetitive sequences that make up the majority of most plant genomes. These most variable components of a genome are found to be species- and occasionally chromosome-specific and give information about evolution and phylogeny. Multicolor fluorescence hybridization and large pools of BAC or synthetic probes can paint chromosomes and we can follow them through evolution involving hybridization, polyploidization, and rearrangements, important at a time when structural variations in the genome are being increasingly recognized. This volume discusses many of the most recent developments in the field of plant cytogenetics and gives carefully compiled protocols and useful resources.
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Affiliation(s)
- Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China.
- South China National Botanical Garden, Guangzhou, China.
| | - Qing Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
| | - J S Pat Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- South China National Botanical Garden, Guangzhou, China
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Kazemi-Shahandashti SS, Mann L, El-nagish A, Harpke D, Nemati Z, Usadel B, Heitkam T. Ancient Artworks and Crocus Genetics Both Support Saffron's Origin in Early Greece. FRONTIERS IN PLANT SCIENCE 2022; 13:834416. [PMID: 35283878 PMCID: PMC8913524 DOI: 10.3389/fpls.2022.834416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Saffron crocus (Crocus sativus) is a male-sterile, triploid flower crop, and source of the spice and colorant saffron. For over three millennia, it was cultivated across the Mediterranean, including ancient Greece, Persia, and other cultures, later spreading all over the world. Despite saffron crocus' early omnipresence, its origin has been the matter of a century-old debate, in terms of area and time as well as parental species contribution. While remnants of the ancient arts, crafts, and texts still provide hints on its origin, modern genetics has the potential to efficiently follow these leads, thus shedding light on new possible lines of descent. In this review, we follow ancient arts and recent genetics to trace the evolutionary origin of saffron crocus. We focus on the place and time of saffron domestication and cultivation, and address its presumed autopolyploid origin involving cytotypes of wild Crocus cartwrightianus. Both ancient arts from Greece, Iran, and Mesopotamia as well as recent cytogenetic and comparative next-generation sequencing approaches point to saffron's emergence and domestication in ancient Greece, showing how both disciplines converge in tracing its origin.
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Affiliation(s)
- Seyyedeh-Sanam Kazemi-Shahandashti
- Institute of Biological Data Science, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
- IBG-4 Bioinformatics, Forschungszentrum Jülich, Jülich, Germany
| | - Ludwig Mann
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Abdullah El-nagish
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
- Botany and Microbiology Department, Faculty of Science, Sohag University, Sohag, Egypt
| | - Dörte Harpke
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Zahra Nemati
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Björn Usadel
- Institute of Biological Data Science, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany
- IBG-4 Bioinformatics, Forschungszentrum Jülich, Jülich, Germany
| | - Tony Heitkam
- Faculty of Biology, Institute of Botany, Technische Universität Dresden, Dresden, Germany
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Zhong MC, Jiang XD, Yang GQ, Cui WH, Suo ZQ, Wang WJ, Sun YB, Wang D, Cheng XC, Li XM, Dong X, Tang KX, Li DZ, Hu JY. Rose without prickle: genomic insights linked to moisture adaptation. Natl Sci Rev 2022; 8:nwab092. [PMID: 34987840 PMCID: PMC8694671 DOI: 10.1093/nsr/nwab092] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 04/21/2021] [Accepted: 05/07/2021] [Indexed: 11/14/2022] Open
Abstract
Prickles act against herbivores, pathogens or mechanical injury, while also preventing water loss. However, whether prickles have new function and the molecular genetics of prickle patterning remain poorly explored. Here, we generated a high-quality reference genome assembly for ‘Basye's Thornless’ (BT), a prickle-free cultivar of Rosa wichuraiana, to identify genetic elements related to stem prickle development. The BT genome harbors a high level of sequence diversity in itself and with cultivar ‘Old Blush’ (R. chinensis), a founder genotype in rose domestication. Inheritance of stem prickle density was determined and two QTL were identified. Differentially expressed genes in QTL were involved in water-related functions, suggesting that prickle density may hitchhike with adaptations to moist environments. While the prickle-related gene-regulatory-network (GRN) was highly conserved, the expression variation of key candidate genes was associated with prickle density. Our study provides fundamental resources and insights for genome evolution in the Rosaceae. Ongoing efforts on identification of the molecular bases for key rose traits may lead to improvements for horticultural markets.
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Affiliation(s)
- Mi-Cai Zhong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiao-Dong Jiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Guo-Qian Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Wei-Hua Cui
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Zhi-Quan Suo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Wei-Jia Wang
- Flower Research Institute, Yunnan Agricultural Academy of Sciences, Kunming 650231, China
| | - Yi-Bo Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Dan Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xin-Chao Cheng
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Xu-Ming Li
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Xue Dong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Kai-Xue Tang
- Flower Research Institute, Yunnan Agricultural Academy of Sciences, Kunming 650231, China
| | - De-Zhu Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jin-Yong Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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Herklotz V, Kovařík A, Wissemann V, Lunerová J, Vozárová R, Buschmann S, Olbricht K, Groth M, Ritz CM. Power and Weakness of Repetition - Evaluating the Phylogenetic Signal From Repeatomes in the Family Rosaceae With Two Case Studies From Genera Prone to Polyploidy and Hybridization ( Rosa and Fragaria). FRONTIERS IN PLANT SCIENCE 2021; 12:738119. [PMID: 34950159 PMCID: PMC8688825 DOI: 10.3389/fpls.2021.738119] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
Plant genomes consist, to a considerable extent, of non-coding repetitive DNA. Several studies showed that phylogenetic signals can be extracted from such repeatome data by using among-species dissimilarities from the RepeatExplorer2 pipeline as distance measures. Here, we advanced this approach by adjusting the read input for comparative clustering indirectly proportional to genome size and by summarizing all clusters into a main distance matrix subjected to Neighbor Joining algorithms and Principal Coordinate Analyses. Thus, our multivariate statistical method works as a "repeatomic fingerprint," and we proved its power and limitations by exemplarily applying it to the family Rosaceae at intrafamilial and, in the genera Fragaria and Rosa, at the intrageneric level. Since both taxa are prone to hybridization events, we wanted to show whether repeatome data are suitable to unravel the origin of natural and synthetic hybrids. In addition, we compared the results based on complete repeatomes with those from ribosomal DNA clusters only, because they represent one of the most widely used barcoding markers. Our results demonstrated that repeatome data contained a clear phylogenetic signal supporting the current subfamilial classification within Rosaceae. Accordingly, the well-accepted major evolutionary lineages within Fragaria were distinguished, and hybrids showed intermediate positions between parental species in data sets retrieved from both complete repeatomes and rDNA clusters. Within the taxonomically more complicated and particularly frequently hybridizing genus Rosa, we detected rather weak phylogenetic signals but surprisingly found a geographic pattern at a population scale. In sum, our method revealed promising results at larger taxonomic scales as well as within taxa with manageable levels of reticulation, but success remained rather taxon specific. Since repeatomes can be technically easy and comparably inexpensively retrieved even from samples of rather poor DNA quality, our phylogenomic method serves as a valuable alternative when high-quality genomes are unavailable, for example, in the case of old museum specimens.
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Affiliation(s)
- Veit Herklotz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Volker Wissemann
- Institute of Botany, Systematic Botany Group, Justus-Liebig-University, Gießen, Germany
| | - Jana Lunerová
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Radka Vozárová
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Sebastian Buschmann
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | | | - Marco Groth
- CF DNA Sequencing, Leibniz Institute on Aging – Fritz Lipmann Institute, Jena, Germany
| | - Christiane M. Ritz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
- Chair of Biodiversity of Higher Plants, Technische Universität Dresden, International Institute (IHI) Zittau, Zittau, Germany
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Vozárová R, Herklotz V, Kovařík A, Tynkevich YO, Volkov RA, Ritz CM, Lunerová J. Ancient Origin of Two 5S rDNA Families Dominating in the Genus Rosa and Their Behavior in the Canina-Type Meiosis. FRONTIERS IN PLANT SCIENCE 2021; 12:643548. [PMID: 33763100 PMCID: PMC7984461 DOI: 10.3389/fpls.2021.643548] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/15/2021] [Indexed: 05/02/2023]
Abstract
The genus Rosa comprises more than 100 woody species characterized by intensive hybridization, introgression, and an overall complex evolutionary history. Besides many diploid species (2n = 2x = 14) polyploids ranging from 3x to 10x are frequently found. Here we analyzed 5S ribosomal DNA in 19 species covering two subgenera and the major sections within subg. Rosa. In addition to diploids and polyploids with regular meiosis, we focused on 5x dogroses (Rosa sect. Caninae), which exhibit an asymmetric meiosis differentiating between bivalent- and univalent-forming chromosomes. Using genomic resources, we reconstructed 5S rDNA units to reveal their phylogenetic relationships. Additionally, we designed locus-specific probes derived from intergenic spacers (IGSs) and determined the position and number of 5S rDNA families on chromosomes. Two major 5S rDNA families (termed 5S_A and 5S_B, respectively) were found at variable ratios in both diploid and polyploid species including members of the early diverging subgenera, Rosa persica and Rosa minutifolia. Within subg. Rosa species of sect. Rosa amplified the 5S_A variant only, while taxa of other sections contained both variants at variable ratios. The 5S_B family was often co-localized with 35S rDNA at the nucleolar organizer regions (NOR) chromosomes, whereas the co-localization of the 5S_A family with NOR was only exceptionally observed. The allo-pentaploid dogroses showed a distinct distribution of 5S rDNA families between bivalent- and univalent-forming chromosomes. In conclusion, two divergent 5S rDNA families dominate rose genomes. Both gene families apparently arose in the early history of the genus, already 30 myrs ago, and apparently survived numerous speciation events thereafter. These observations are consistent with a relatively slow genome turnover in the Rosa genus.
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Affiliation(s)
- Radka Vozárová
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Veit Herklotz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Yuri O. Tynkevich
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
| | - Roman A. Volkov
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
| | - Christiane M. Ritz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
- Chair of Biodiversity of Higher Plants, International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany
| | - Jana Lunerová
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
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Lunerová J, Herklotz V, Laudien M, Vozárová R, Groth M, Kovařík A, Ritz CM. Asymmetrical canina meiosis is accompanied by the expansion of a pericentromeric satellite in non-recombining univalent chromosomes in the genus Rosa. ANNALS OF BOTANY 2020; 125:1025-1038. [PMID: 32095807 PMCID: PMC7262465 DOI: 10.1093/aob/mcaa028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 02/24/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS Despite their abundant odd-ploidy (2n = 5x = 35), dogroses (Rosa sect. Caninae) are capable of sexual reproduction due to their unique meiosis. During canina meiosis, two sets of chromosomes form bivalents and are transmitted by male and female gametes, whereas the remaining chromosomes form univalents and are exclusively transmitted by the egg cells. Thus, the evolution of chromosomes is expected to be driven by their behaviour during meiosis. METHODS To gain insight into differential chromosome evolution, fluorescence in situ hybridization was conducted for mitotic and meiotic chromosomes in four dogroses (two subsections) using satellite and ribosomal DNA probes. By exploiting high-throughput sequencing data, we determined the abundance and diversity of the satellite repeats in the genus Rosa by analysing 20 pentaploid, tetraploid and diploid species in total. KEY RESULTS A pericentromeric satellite repeat, CANR4, was found in all members of the genus Rosa, including the basal subgenera Hulthemia and Hesperhodos. The satellite was distributed across multiple chromosomes (5-20 sites per mitotic cell), and its genomic abundance was higher in pentaploid dogroses (2.3 %) than in non-dogrose species (1.3 %). In dogrose meiosis, univalent chromosomes were markedly enriched in CANR4 repeats based on both the number and the intensity of the signals compared to bivalent-forming chromosomes. Single-nucleotide polymorphisms and cluster analysis revealed high intragenomic homogeneity of the satellite in dogrose genomes. CONCLUSIONS The CANR4 satellite arose early in the evolution of the genus Rosa. Its high content and extraordinary homogeneity in dogrose genomes is explained by its recent amplification in non-recombining chromosomes. We hypothesize that satellite DNA expansion may contribute to the divergence of univalent chromosomes in Rosa species with non-symmetrical meiosis.
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Affiliation(s)
- Jana Lunerová
- Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
| | - Veit Herklotz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Melanie Laudien
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
- Technical University Dresden, International Institute Zittau (IHI), Chair of Biodiversity of Higher Plants, Zittau, Germany
| | - Radka Vozárová
- Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
- Masaryk University, Faculty of Science, Brno, Czech Republic
| | - Marco Groth
- Leibniz Institute on Ageing – Fritz Lipmann Institute, Jena, Germany
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic
| | - Christiane M Ritz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
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Rovná K, Ivanišová E, Žiarovská J, Ferus P, Terentjeva M, Kowalczewski PŁ, Kačániová M. Characterization of Rosa canina Fruits Collected in Urban Areas of Slovakia. Genome Size, iPBS Profiles and Antioxidant and Antimicrobial Activities. Molecules 2020; 25:E1888. [PMID: 32325812 PMCID: PMC7221986 DOI: 10.3390/molecules25081888] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/13/2020] [Accepted: 04/17/2020] [Indexed: 11/17/2022] Open
Abstract
The studies of plant bacterial endophytes, colonizing the plant tissues without any signs of diseases, are essential for understanding of ecological interactions. The aim of our study is to detect microbiological contamination and to assess the antimicrobial, antioxidant activity, total phenolic, carotenoid content, genome size, and ploidy of non-cultivated Rosa canina sampled from urban areas. Samples of Rosa canina fruits were collected in three locations in Slovakia. The highest total viable count and the Enterobacteriaceae count in fruits were 4.32 log CFU/g and 4.29 log CFU/g, respectively. Counts of the mesophilic anaerobic sporulating bacteria, Pseudomonas spp., and of the microscopic fungi and yeasts were 3.00, 2.15 log CFU/g, 3.65 log CFU/g, and 2.76 log CFU/g, respectively. Regarding the antimicrobial activity, Escherichia coli and Klebsiela oxytoca were the most sensitive species among the assayed microorganisms to the treatment with the ethanolic extracts of Rosa canina fruits. The fruits were rich in bioactive compounds, polyphenols, and carotenoids, that could be related to their antioxidant activity. Genome sizes of analyzed samples ranged from 2.3 to 2.96. DNA-based fingerprinting obtained by iPBS markers of the Rosa canina var. lapidicola Heinr. Braun., was characterized by some distinctive inserted loci. An interdisciplinary study was performed for the dog roses from different parts of Slovakia that resulted in deeper characterization of this species.
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Affiliation(s)
- Katarína Rovná
- Department of Planting Design and Maintenance, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, Tr. A. Hlinku 2, 94976 Nitra, Slovakia;
| | - Eva Ivanišová
- Department of Technology and Quality of Plant Products, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture, Tr. A. Hlinku 2, SK-94976 Nitra, Slovakia;
| | - Jana Žiarovská
- Department of Plant Genetics and Breeding, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, Tr. A. Hlinku 2, 94976 Nitra, Slovakia;
| | - Peter Ferus
- Department of Dendrobiology, Institute of Forest Ecology, Slovak Academy of Sciences, Ľ. Štúra 2, 96053 Zvolen, Slovakia;
| | - Margarita Terentjeva
- Institute of Food and Environmental Hygiene, Faculty of Veterinary Medicine, Latvia University of Life Sciences and Technologies, K. Helmaņaiela 8, LV-3004, Jelgava, Latvia;
| | - Przemysław Łukasz Kowalczewski
- Institute of Food Technology of Plant Origin, Poznań University of Life Sciences, 31 Wojska Polskiego St., 60-624 Poznań, Poland;
| | - Miroslava Kačániová
- Department of Fruit Sciences, Viticulture and Enology, Faculty of Horticulture and Landscape Engineering, Slovak University of Agriculture, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
- Department of Bioenergy, Food Technology and Microbiology, Institute of Agriculture Sciences, Land Management and Environmental Protection, University of Rzeszow, 4 Zelwerowicza St., 35601 Rzeszow, Poland
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10
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Debray K, Marie-Magdelaine J, Ruttink T, Clotault J, Foucher F, Malécot V. Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae). BMC Evol Biol 2019; 19:152. [PMID: 31340752 PMCID: PMC6657147 DOI: 10.1186/s12862-019-1479-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/16/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND With an ever-growing number of published genomes, many low levels of the Tree of Life now contain several species with enough molecular data to perform shallow-scale phylogenomic studies. Moving away from using just a few universal phylogenetic markers, we can now target thousands of other loci to decipher taxa relationships. Making the best possible selection of informative sequences regarding the taxa studied has emerged as a new issue. Here, we developed a general procedure to mine genomic data, looking for orthologous single-copy loci capable of deciphering phylogenetic relationships below the generic rank. To develop our strategy, we chose the genus Rosa, a rapid-evolving lineage of the Rosaceae family in which several species genomes have recently been sequenced. We also compared our loci to conventional plastid markers, commonly used for phylogenetic inference in this genus. RESULTS We generated 1856 sequence tags in putative single-copy orthologous nuclear loci. Associated in silico primer pairs can potentially amplify fragments able to resolve a wide range of speciation events within the genus Rosa. Analysis of parsimony-informative site content showed the value of non-coding genomic regions to obtain variable sequences despite the fact that they may be more difficult to target in less related species. Dozens of nuclear loci outperform the conventional plastid phylogenetic markers in terms of phylogenetic informativeness, for both recent and ancient evolutionary divergences. However, conflicting phylogenetic signals were found between nuclear gene tree topologies and the species-tree topology, shedding light on the many patterns of hybridization and/or incomplete lineage sorting that occur in the genus Rosa. CONCLUSIONS With recently published genome sequence data, we developed a set of single-copy orthologous nuclear loci to resolve species-level phylogenomics in the genus Rosa. This genome-wide scale dataset contains hundreds of highly variable loci which phylogenetic interest was assessed in terms of phylogenetic informativeness and topological conflict. Our target identification procedure can easily be reproduced to identify new highly informative loci for other taxonomic groups and ranks.
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Affiliation(s)
- Kevin Debray
- IRHS, Agrocampus-Ouest, INRA, UNIV Angers, SFR 4207 QuaSaV, Beaucouzé, France.
| | | | - Tom Ruttink
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - Jérémy Clotault
- IRHS, Agrocampus-Ouest, INRA, UNIV Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Fabrice Foucher
- IRHS, Agrocampus-Ouest, INRA, UNIV Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Valéry Malécot
- IRHS, Agrocampus-Ouest, INRA, UNIV Angers, SFR 4207 QuaSaV, Beaucouzé, France.
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11
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Hibrand Saint-Oyant L, Ruttink T, Hamama L, Kirov I, Lakhwani D, Zhou NN, Bourke PM, Daccord N, Leus L, Schulz D, Van de Geest H, Hesselink T, Van Laere K, Debray K, Balzergue S, Thouroude T, Chastellier A, Jeauffre J, Voisine L, Gaillard S, Borm TJA, Arens P, Voorrips RE, Maliepaard C, Neu E, Linde M, Le Paslier MC, Bérard A, Bounon R, Clotault J, Choisne N, Quesneville H, Kawamura K, Aubourg S, Sakr S, Smulders MJM, Schijlen E, Bucher E, Debener T, De Riek J, Foucher F. A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. NATURE PLANTS 2018; 4:473-484. [PMID: 29892093 DOI: 10.1101/254102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/01/2018] [Indexed: 05/27/2023]
Abstract
Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.
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Affiliation(s)
- L Hibrand Saint-Oyant
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Ruttink
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - L Hamama
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - I Kirov
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
- Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - D Lakhwani
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N N Zhou
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - P M Bourke
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - N Daccord
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Leus
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - D Schulz
- Leibniz Universität, Hannover, Germany
| | - H Van de Geest
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - T Hesselink
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - K Van Laere
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - K Debray
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Balzergue
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Thouroude
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - A Chastellier
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - J Jeauffre
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Voisine
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Gaillard
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T J A Borm
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - P Arens
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - R E Voorrips
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - C Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Neu
- Leibniz Universität, Hannover, Germany
| | - M Linde
- Leibniz Universität, Hannover, Germany
| | - M C Le Paslier
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - A Bérard
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - R Bounon
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - J Clotault
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N Choisne
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - H Quesneville
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - K Kawamura
- Osaka Institute of Technology, Osaka, Japan
| | - S Aubourg
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Sakr
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - M J M Smulders
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Schijlen
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - E Bucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Debener
- Leibniz Universität, Hannover, Germany
| | - J De Riek
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - F Foucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France.
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12
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Hibrand Saint-Oyant L, Ruttink T, Hamama L, Kirov I, Lakhwani D, Zhou NN, Bourke PM, Daccord N, Leus L, Schulz D, Van de Geest H, Hesselink T, Van Laere K, Debray K, Balzergue S, Thouroude T, Chastellier A, Jeauffre J, Voisine L, Gaillard S, Borm TJA, Arens P, Voorrips RE, Maliepaard C, Neu E, Linde M, Le Paslier MC, Bérard A, Bounon R, Clotault J, Choisne N, Quesneville H, Kawamura K, Aubourg S, Sakr S, Smulders MJM, Schijlen E, Bucher E, Debener T, De Riek J, Foucher F. A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. NATURE PLANTS 2018; 4:473-484. [PMID: 29892093 PMCID: PMC6786968 DOI: 10.1038/s41477-018-0166-1] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/01/2018] [Indexed: 05/18/2023]
Abstract
Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.
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Affiliation(s)
- L Hibrand Saint-Oyant
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Ruttink
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - L Hamama
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - I Kirov
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
- Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - D Lakhwani
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N N Zhou
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - P M Bourke
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - N Daccord
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Leus
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - D Schulz
- Leibniz Universität, Hannover, Germany
| | - H Van de Geest
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - T Hesselink
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - K Van Laere
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - K Debray
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Balzergue
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Thouroude
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - A Chastellier
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - J Jeauffre
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Voisine
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Gaillard
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T J A Borm
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - P Arens
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - R E Voorrips
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - C Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Neu
- Leibniz Universität, Hannover, Germany
| | - M Linde
- Leibniz Universität, Hannover, Germany
| | - M C Le Paslier
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - A Bérard
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - R Bounon
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - J Clotault
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N Choisne
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - H Quesneville
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - K Kawamura
- Osaka Institute of Technology, Osaka, Japan
| | - S Aubourg
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Sakr
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - M J M Smulders
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Schijlen
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - E Bucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Debener
- Leibniz Universität, Hannover, Germany
| | - J De Riek
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - F Foucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France.
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13
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Alix K, Gérard PR, Schwarzacher T, Heslop-Harrison JS(P. Polyploidy and interspecific hybridization: partners for adaptation, speciation and evolution in plants. ANNALS OF BOTANY 2017; 120:183-194. [PMID: 28854567 PMCID: PMC5737848 DOI: 10.1093/aob/mcx079] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 05/31/2017] [Indexed: 05/15/2023]
Abstract
BACKGROUND Polyploidy or whole-genome duplication is now recognized as being present in almost all lineages of higher plants, with multiple rounds of polyploidy occurring in most extant species. The ancient evolutionary events have been identified through genome sequence analysis, while recent hybridization events are found in about half of the world's crops and wild species. Building from this new paradigm for understanding plant evolution, the papers in this Special Issue address questions about polyploidy in ecology, adaptation, reproduction and speciation of wild and cultivated plants from diverse ecosystems. Other papers, including this review, consider genomic aspects of polyploidy. APPROACHES Discovery of the evolutionary consequences of new, evolutionarily recent and ancient polyploidy requires a range of approaches. Large-scale studies of both single species and whole ecosystems, with hundreds to tens of thousands of individuals, sometimes involving 'garden' or transplant experiments, are important for studying adaptation. Molecular studies of genomes are needed to measure diversity in genotypes, showing ancestors, the nature and number of polyploidy and backcross events that have occurred, and allowing analysis of gene expression and transposable element activation. Speciation events and the impact of reticulate evolution require comprehensive phylogenetic analyses and can be assisted by resynthesis of hybrids. In this Special Issue, we include studies ranging in scope from experimental and genomic, through ecological to more theoretical. CONCLUSIONS The success of polyploidy, displacing the diploid ancestors of almost all plants, is well illustrated by the huge angiosperm diversity that is assumed to originate from recurrent polyploidization events. Strikingly, polyploidization often occurred prior to or simultaneously with major evolutionary transitions and adaptive radiation of species, supporting the concept that polyploidy plays a predominant role in bursts of adaptive speciation. Polyploidy results in immediate genetic redundancy and represents, with the emergence of new gene functions, an important source of novelty. Along with recombination, gene mutation, transposon activity and chromosomal rearrangement, polyploidy and whole-genome duplication act as drivers of evolution and divergence in plant behaviour and gene function, enabling diversification, speciation and hence plant evolution.
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Affiliation(s)
- Karine Alix
- GQE – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
- For correspondence. E-mail
| | - Pierre R. Gérard
- GQE – Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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14
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Bourke PM, Arens P, Voorrips RE, Esselink GD, Koning-Boucoiran CFS, Van't Westende WPC, Santos Leonardo T, Wissink P, Zheng C, van Geest G, Visser RGF, Krens FA, Smulders MJM, Maliepaard C. Partial preferential chromosome pairing is genotype dependent in tetraploid rose. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:330-343. [PMID: 28142191 DOI: 10.1111/tpj.13496] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 05/18/2023]
Abstract
It has long been recognised that polyploid species do not always neatly fall into the categories of auto- or allopolyploid, leading to the term 'segmental allopolyploid' to describe everything in between. The meiotic behaviour of such intermediate species is not fully understood, nor is there consensus as to how to model their inheritance patterns. In this study we used a tetraploid cut rose (Rosa hybrida) population, genotyped using the 68K WagRhSNP array, to construct an ultra-high-density linkage map of all homologous chromosomes using methods previously developed for autotetraploids. Using the predicted bivalent configurations in this population we quantified differences in pairing behaviour among and along homologous chromosomes, leading us to correct our estimates of recombination frequency to account for this behaviour. This resulted in the re-mapping of 25 695 SNP markers across all homologues of the seven rose chromosomes, tailored to the pairing behaviour of each chromosome in each parent. We confirmed the inferred differences in pairing behaviour among chromosomes by examining repulsion-phase linkage estimates, which also carry information about preferential pairing and recombination. Currently, the closest sequenced relative to rose is Fragaria vesca. Aligning the integrated ultra-dense rose map with the strawberry genome sequence provided a detailed picture of the synteny, confirming overall co-linearity but also revealing new genomic rearrangements. Our results suggest that pairing affinities may vary along chromosome arms, which broadens our current understanding of segmental allopolyploidy.
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Affiliation(s)
- Peter M Bourke
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Paul Arens
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Roeland E Voorrips
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - G Danny Esselink
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | | | - Wendy P C Van't Westende
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Tiago Santos Leonardo
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Patrick Wissink
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Chaozhi Zheng
- Biometris, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Geert van Geest
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Horticulture and Product Physiology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Frans A Krens
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Marinus J M Smulders
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Chris Maliepaard
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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