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Penin AA, Kasianov AS, Klepikova AV, Omelchenko DO, Makarenko MS, Logacheva MD. Origin and diversity of Capsella bursa-pastoris from the genomic point of view. BMC Biol 2024; 22:52. [PMID: 38439107 PMCID: PMC10913212 DOI: 10.1186/s12915-024-01832-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 01/23/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Capsella bursa-pastoris, a cosmopolitan weed of hybrid origin, is an emerging model object for the study of early consequences of polyploidy, being a fast growing annual and a close relative of Arabidopsis thaliana. The development of this model is hampered by the absence of a reference genome sequence. RESULTS We present here a subgenome-resolved chromosome-scale assembly and a genetic map of the genome of Capsella bursa-pastoris. It shows that the subgenomes are mostly colinear, with no massive deletions, insertions, or rearrangements in any of them. A subgenome-aware annotation reveals the lack of genome dominance-both subgenomes carry similar number of genes. While most chromosomes can be unambiguously recognized as derived from either paternal or maternal parent, we also found homeologous exchange between two chromosomes. It led to an emergence of two hybrid chromosomes; this event is shared between distant populations of C. bursa-pastoris. The whole-genome analysis of 119 samples belonging to C. bursa-pastoris and its parental species C. grandiflora/rubella and C. orientalis reveals introgression from C. orientalis but not from C. grandiflora/rubella. CONCLUSIONS C. bursa-pastoris does not show genome dominance. In the earliest stages of evolution of this species, a homeologous exchange occurred; its presence in all present-day populations of C. bursa-pastoris indicates on a single origin of this species. The evidence coming from whole-genome analysis challenges the current view that C. grandiflora/rubella was a direct progenitor of C. bursa-pastoris; we hypothesize that it was an extinct (or undiscovered) species sister to C. grandiflora/rubella.
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Affiliation(s)
- Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia.
| | - Artem S Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Anna V Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Denis O Omelchenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Maksim S Makarenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Maria D Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
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2
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Roux C, Vekemans X, Pannell J. Inferring the Demographic History and Inheritance Mode of Tetraploid Species Using ABC. Methods Mol Biol 2023; 2545:325-348. [PMID: 36720821 DOI: 10.1007/978-1-0716-2561-3_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Genomic patterns of diversity and divergence are impacted by certain life history traits, reproductive systems, and demographic history. The latter is characterized by fluctuations in population sizes over time, as well as by temporal patterns of introgression. For a given organism, identifying a demographic history that deviates from the standard neutral model allows a better understanding of its evolution but also helps to reduce the risk of false positives when screening for molecular targets of natural selection. Tetraploid organisms and beyond have demographic histories that are complicated by the mode of polyploidization, the mode of inheritance, and different scenarios of gene flow between sub-genomes and diploid parental species. Here we provide guidelines for experimenters wishing to address these issues through a flexible statistical framework: approximate Bayesian computation (ABC). The emphasis is on the general philosophy of the approach to encourage future users to exploit the enormous flexibility of ABC beyond the limitations imposed by generalist data analysis pipelines.
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Affiliation(s)
- Camille Roux
- Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, Lille, France.
| | | | - John Pannell
- Department of Ecology and Evolution, Biophore Building, University of Lausanne, Lausanne, Switzerland
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3
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Hörandl E. Novel Approaches for Species Concepts and Delimitation in Polyploids and Hybrids. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11020204. [PMID: 35050093 PMCID: PMC8781807 DOI: 10.3390/plants11020204] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 05/08/2023]
Abstract
Hybridization and polyploidization are important processes for plant evolution. However, classification of hybrid or polyploid species has been notoriously difficult because of the complexity of processes and different evolutionary scenarios that do not fit with classical species concepts. Polyploid complexes are formed via combinations of allopolyploidy, autopolyploidy and homoploid hybridization with persisting sexual reproduction, resulting in many discrete lineages that have been classified as species. Polyploid complexes with facultative apomixis result in complicated net-work like clusters, or rarely in agamospecies. Various case studies illustrate the problems that apply to traditional species concepts to hybrids and polyploids. Conceptual progress can be made if lineage formation is accepted as an inevitable consequence of meiotic sex, which is established already in the first eukaryotes as a DNA restoration tool. The turnaround of the viewpoint that sex forms species as lineages helps to overcome traditional thinking of species as "units". Lineage formation and self-sustainability is the prerequisite for speciation and can also be applied to hybrids and polyploids. Species delimitation is aided by the improved recognition of lineages via various novel -omics methods, by understanding meiosis functions, and by recognizing functional phenotypes by considering morphological-physiological-ecological adaptations.
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Affiliation(s)
- Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, 37073 Göttingen, Germany
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4
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Booker WW, Gerhardt HC, Lemmon AR, Ptacek MB, Hassinger ATB, Schul J, Lemmon EM. The complex history of genome duplication and hybridization in North American gray treefrogs. Mol Biol Evol 2021; 39:6427635. [PMID: 34791374 PMCID: PMC8826561 DOI: 10.1093/molbev/msab316] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Polyploid speciation has played an important role in evolutionary history across the tree of life, yet there remain large gaps in our understanding of how polyploid species form and persist. Although systematic studies have been conducted in numerous polyploid complexes, recent advances in sequencing technology have demonstrated that conclusions from data-limited studies may be spurious and misleading. The North American gray treefrog complex, consisting of the diploid Hyla chrysoscelis and the tetraploid H. versicolor, has long been used as a model system in a variety of biological fields, yet all taxonomic studies to date were conducted with only a few loci from nuclear and mitochondrial genomes. Here, we utilized anchored hybrid enrichment and high-throughput sequencing to capture hundreds of loci along with whole mitochondrial genomes to investigate the evolutionary history of this complex. We used several phylogenetic and population genetic methods, including coalescent simulations and testing of polyploid speciation models with approximate Bayesian computation, to determine that H. versicolor was most likely formed via autopolyploidization from a now extinct lineage of H. chrysoscelis. We also uncovered evidence of significant hybridization between diploids and tetraploids where they co-occur, and show that historical hybridization between these groups led to the re-formation of distinct polyploid lineages following the initial whole-genome duplication event. Our study indicates that a wide variety of methods and explicit model testing of polyploid histories can greatly facilitate efforts to uncover the evolutionary history of polyploid complexes.
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Affiliation(s)
- William W Booker
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306-4295, USA
| | - H Carl Gerhardt
- Division of Biological Sciences, University of Missouri, Columbia, USA, 65211-7400, MO
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL, 32306-4192, USA
| | - Margaret B Ptacek
- Department of Biological Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Alyssa T B Hassinger
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH, 43210, USA
| | - Johannes Schul
- Division of Biological Sciences, University of Missouri, Columbia, USA, 65211-7400, MO
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306-4295, USA
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5
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Burge D. Conservation genomics and pollination biology of an endangered, edaphic-endemic, octoploid herb: El Dorado bedstraw ( Galium californicum subsp. sierrae; Rubiaceae). PeerJ 2020; 8:e10042. [PMID: 33173616 PMCID: PMC7594638 DOI: 10.7717/peerj.10042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 09/04/2020] [Indexed: 01/25/2023] Open
Abstract
El Dorado bedstraw (Galium californicum subsp. sierrae) is a federally endangered dioecious, octoploid, perennial herb found only in the Pine Hill region of El Dorado County, CA, USA. Like many species of Galium, El Dorado bedstraw is capable of both sexual and asexual reproduction, spreading via stem-layering as well as seeds. El Dorado bedstraw is also dioecious, and thus dependent on pollinators to transfer pollen from male to female stems. The capacity for asexual reproduction has conservation implications for this plant, due to the potential for populations to become dominated by a small number of clones in the absence of recruitment from seeds. No previous work has examined either the population genetics or pollination biology of this plant. Here, double-digest restriction site-associated DNA sequencing was used to develop a genetic dataset for a sample of El Dorado bedstraw (12 individuals from each of seven locations). Genomic data was used to calculate population genetic statistics and quantify the degree to which clonality affects the sampled populations. Visual observation of insect visitors at every sampling location was used to assess the potential for pollen transfer within and among locations. A total of 23 clonal colonies were detected across 82 successfully sequenced stems, consisting of an average of 2.4 individuals (range: 2–6). Significant isolation by distance among locations was detected using a Mantel test. Insect pollinators were from eleven families, consisting mainly of small species with weak flight. It is recommended that clonality and small-scale population differentiation be taken into account in conservation measures.
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Affiliation(s)
- Dylan Burge
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
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6
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Eriksson JS, de Sousa F, Bertrand YJK, Antonelli A, Oxelman B, Pfeil BE. Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae). BMC Evol Biol 2018; 18:9. [PMID: 29374461 PMCID: PMC5787288 DOI: 10.1186/s12862-018-1127-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 01/22/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Whole genome duplication plays a central role in plant evolution. There are two main classes of polyploid formation: autopolyploids which arise within one species by doubling of similar homologous genomes; in contrast, allopolyploidy (hybrid polyploidy) arise via hybridization and subsequent doubling of nonhomologous (homoeologous) genomes. The distinction between polyploid origins can be made using gene phylogenies, if alleles from each genome can be correctly retrieved. We examined whether two closely related tetraploid Mediterranean shrubs (Medicago arborea and M. strasseri) have an allopolyploid origin - a question that has remained unsolved despite substantial previous research. We sequenced and analyzed ten low-copy nuclear genes from these and related species, phasing all alleles. To test the efficacy of allele phasing on the ability to recover the evolutionary origin of polyploids, we compared these results to analyses using unphased sequences. RESULTS In eight of the gene trees the alleles inferred from the tetraploids formed two clades, in a non-sister relationship. Each of these clades was more closely related to alleles sampled from other species of Medicago, a pattern typical of allopolyploids. However, we also observed that alleles from one of the remaining genes formed two clades that were sister to one another, as is expected for autopolyploids. Trees inferred from unphased sequences were very different, with the tetraploids often placed in poorly supported and different positions compared to results obtained using phased alleles. CONCLUSIONS The complex phylogenetic history of M. arborea and M. strasseri is explained predominantly by shared allotetraploidy. We also observed that an increase in woodiness is correlated with polyploidy in this group of species and present a new possibility that woodiness could be a transgressive phenotype. Correctly phased homoeologues are likely to be critical for inferring the hybrid origin of allopolyploid species, when most genes retain more than one homoeologue. Ignoring homoeologous variation by merging the homoeologues can obscure the signal of hybrid polyploid origins and produce inaccurate results.
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Affiliation(s)
- Jonna S Eriksson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 40530, Gothenburg, Sweden. .,Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Göteborg, Sweden.
| | - Filipe de Sousa
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 40530, Gothenburg, Sweden
| | - Yann J K Bertrand
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 40530, Gothenburg, Sweden
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 40530, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Göteborg, Sweden.,Gothenburg Botanical Garden, SE-41319, Göteborg, Sweden
| | - Bengt Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 40530, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Göteborg, Sweden
| | - Bernard E Pfeil
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 40530, Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre, Box 461, SE-405 30, Göteborg, Sweden
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7
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Kasianov AS, Klepikova AV, Kulakovskiy IV, Gerasimov ES, Fedotova AV, Besedina EG, Kondrashov AS, Logacheva MD, Penin AA. High-quality genome assembly of Capsella bursa-pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:278-291. [PMID: 28387959 DOI: 10.1111/tpj.13563] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 03/01/2017] [Accepted: 03/31/2017] [Indexed: 05/22/2023]
Abstract
Polyploidization and subsequent sub- and neofunctionalization of duplicated genes represent a major mechanism of plant genome evolution. Capsella bursa-pastoris, a widespread ruderal plant, is a recent allotetraploid and, thus, is an ideal model organism for studying early changes following polyploidization. We constructed a high-quality assembly of C. bursa-pastoris genome and a transcriptome atlas covering a broad sample of organs and developmental stages (available online at http://travadb.org/browse/Species=Cbp). We demonstrate that expression of homeologs is mostly symmetric between subgenomes, and identify a set of homeolog pairs with discordant expression. Comparison of promoters within such pairs revealed emerging asymmetry of regulatory elements. Among them there are multiple binding sites for transcription factors controlling the regulation of photosynthesis and plant development by light (PIF3, HY5) and cold stress response (CBF). These results suggest that polyploidization in C. bursa-pastoris enhanced its plasticity of response to light and temperature, and allowed substantial expansion of its distribution range.
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Affiliation(s)
- Artem S Kasianov
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina str, Moscow, 119333, Russia
| | - Anna V Klepikova
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
| | - Ivan V Kulakovskiy
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina str, Moscow, 119333, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow, 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Building 3, Moscow, 143026, Russia
| | - Evgeny S Gerasimov
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Anna V Fedotova
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Elizaveta G Besedina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Alexey S Kondrashov
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Department of Ecology and Evolution, University of Michigan, 830 North University, Ann Arbor, MI 48109-1048, MI, USA
| | - Maria D Logacheva
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlevskaya str, Kazan, 420008, Russia
| | - Aleksey A Penin
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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8
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Tsuda Y, Semerikov V, Sebastiani F, Vendramin GG, Lascoux M. Multispecies genetic structure and hybridization in theBetulagenus across Eurasia. Mol Ecol 2016; 26:589-605. [DOI: 10.1111/mec.13885] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 09/19/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Yoshiaki Tsuda
- Department of Ecology and Genetics; Evolutionary Biology Centre; Science for Life Laboratory; Uppsala University; Norbyvägen 18D 75236 Uppsala Sweden
- Institute of Biosciences and Bioresources; Division of Florence; National Research Council; Via Madonna del Piano 10 50019 Sesto Fiorentino (Firenze) Italy
| | - Vladimir Semerikov
- Institute of Plant and Animal Ecology; Ural Branch of Russian Academy of Science; Ekaterinburg 620144 Russia
| | - Federico Sebastiani
- Institute of Biosciences and Bioresources; Division of Florence; National Research Council; Via Madonna del Piano 10 50019 Sesto Fiorentino (Firenze) Italy
| | - Giovanni Giuseppe Vendramin
- Institute of Biosciences and Bioresources; Division of Florence; National Research Council; Via Madonna del Piano 10 50019 Sesto Fiorentino (Firenze) Italy
| | - Martin Lascoux
- Department of Ecology and Genetics; Evolutionary Biology Centre; Science for Life Laboratory; Uppsala University; Norbyvägen 18D 75236 Uppsala Sweden
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9
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Liu F, Si H, Wang C, Sun G, Zhou E, Chen C, Ma C. Molecular evolution of Wcor15 gene enhanced our understanding of the origin of A, B and D genomes in Triticum aestivum. Sci Rep 2016; 6:31706. [PMID: 27526862 PMCID: PMC4985644 DOI: 10.1038/srep31706] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/25/2016] [Indexed: 11/29/2022] Open
Abstract
The allohexaploid bread wheat originally derived from three closely related species with A, B and D genome. Although numerous studies were performed to elucidate its origin and phylogeny, no consensus conclusion has reached. In this study, we cloned and sequenced the genes Wcor15-2A, Wcor15-2B and Wcor15-2D in 23 diploid, 10 tetraploid and 106 hexaploid wheat varieties and analyzed their molecular evolution to reveal the origin of the A, B and D genome in Triticum aestivum. Comparative analyses of sequences in diploid, tetraploid and hexaploid wheats suggest that T. urartu, Ae. speltoides and Ae. tauschii subsp. strangulata are most likely the donors of the Wcor15-2A, Wcor15-2B and Wcor15-2D locus in common wheat, respectively. The Wcor15 genes from subgenomes A and D were very conservative without insertion and deletion of bases during evolution of diploid, tetraploid and hexaploid. Non-coding region of Wcor15-2B gene from B genome might mutate during the first polyploidization from Ae. speltoides to tetraploid wheat, however, no change has occurred for this gene during the second allopolyploidization from tetraploid to hexaploid. Comparison of the Wcor15 gene shed light on understanding of the origin of the A, B and D genome of common wheat.
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Affiliation(s)
- Fangfang Liu
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.,Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow &Huai River Valley, Ministry of Agriculture, Hefei 230036, China
| | - Hongqi Si
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.,Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow &Huai River Valley, Ministry of Agriculture, Hefei 230036, China
| | - Chengcheng Wang
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.,Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow &Huai River Valley, Ministry of Agriculture, Hefei 230036, China
| | - Genlou Sun
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.,Biology Department, Saint Mary's University, Halifax, NS, B3H 3C3 Canada
| | - Erting Zhou
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Can Chen
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Chuanxi Ma
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.,Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow &Huai River Valley, Ministry of Agriculture, Hefei 230036, China.,National United Engineering Laboratory for Crop Stress Resistance Breeding, Hefei 230036, China.,Anhui Key Laboratory of Crop Biology, Hefei 230036, China
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10
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Divergent sorting of a balanced ancestral polymorphism underlies the establishment of gene-flow barriers in Capsella. Nat Commun 2015; 6:7960. [PMID: 26268845 PMCID: PMC4539569 DOI: 10.1038/ncomms8960] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 07/01/2015] [Indexed: 11/13/2022] Open
Abstract
In the Bateson–Dobzhansky–Muller model of genetic incompatibilities post-zygotic gene-flow barriers arise by fixation of novel alleles at interacting loci in separated populations. Many such incompatibilities are polymorphic in plants, implying an important role for genetic drift or balancing selection in their origin and evolution. Here we show that NPR1 and RPP5 loci cause a genetic incompatibility between the incipient species Capsella grandiflora and C. rubella, and the more distantly related C. rubella and C. orientalis. The incompatible RPP5 allele results from a mutation in C. rubella, while the incompatible NPR1 allele is frequent in the ancestral C. grandiflora. Compatible and incompatible NPR1 haplotypes are maintained by balancing selection in C. grandiflora, and were divergently sorted into the derived C. rubella and C. orientalis. Thus, by maintaining differentiated alleles at high frequencies, balancing selection on ancestral polymorphisms can facilitate establishing gene-flow barriers between derived populations through lineage sorting of the alternative alleles. A hybrid incompatibility between Capsella plant species is due to an interaction between two immune regulators. Here, the authors show that highly divergent haplotypes result from balancing selection in the ancestral lineage and their sorting into derived lineages facilitated the evolution of the incompatibility.
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11
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Perley DS, Jesson LK. Hybridization is associated with changes in sexual system in the bryophyte genus Atrichum. AMERICAN JOURNAL OF BOTANY 2015; 102:555-565. [PMID: 25878089 DOI: 10.3732/ajb.1400494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 03/07/2015] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY Over 50% of bryophytes have separate sexes, and numerous transitions have occurred between combined and separate sexes. Polyploidy and hybridization is one proximate mechanism hypothesized to cause evolutionary transitions to hermaphroditism in bryophytes because sex is expressed at the haploid stage and in nonpolyploid dioecious species males have a single V chromosome and females a U. Hermaphroditism can arise if gametophytes of allopolyploids have both U and V chromosomes. We examined the association between polyploidy and hermaphroditism in the bryophyte genus Atrichum, which has species where gametophytes can be haploid, diploid, or triploid, and some species have hermaphroditic individuals. METHODS We generated phylogenies of Atrichum from sequences of three plastid regions (rbcL, rps4, and trnL-trnF) and the second intron for the nuclear gene Leafy/Floricaula to further understand the relationships among haploid, diploid, and triploid species, and those with combined or separate sexes. KEY RESULTS The existence of multiple sequences of Leafy/Floricaula in diploid and triploid, but not haploid, individuals is consistent with independent allopolyploid origins of the diploid and triploid species. Allopolyploidy was associated with a likely gain in hermaphroditism in triploid Atrichum undulatum and possibly diploid A. altecristatum, but not in the allopolyploid A. crispulum (diploid at the gametophyte level). CONCLUSIONS These results highlight a role for hybridization and polyploidy in sexual system evolution, but the presence of diploid (allopolyploid) dioecious species suggest that other factors may influence the maintenance of sexual systems after an evolutionary transition.
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Affiliation(s)
- Danielle S Perley
- Department of Biology, University of New Brunswick, 10 Bailey Dr, Fredericton, Canada E3B5A3
| | - Linley K Jesson
- Department of Biology, University of New Brunswick, 10 Bailey Dr, Fredericton, Canada E3B5A3 Faculty of Biology, University of Marburg, Karl-von-Frisch-Str. 8, D-35043 Marburg, Germany
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12
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Han TS, Wu Q, Hou XH, Li ZW, Zou YP, Ge S, Guo YL. Frequent introgressions from diploid species contribute to the adaptation of the tetraploid Shepherd's purse (Capsella bursa-pastoris). MOLECULAR PLANT 2015; 8:427-438. [PMID: 25661060 DOI: 10.1016/j.molp.2014.11.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 11/19/2014] [Accepted: 11/30/2014] [Indexed: 06/04/2023]
Abstract
Adaptation is the most important ability for organisms to survive in diverse habitats. Animals have the option to escape from stressful environments, but plants do not. In plants, polyploids consist of about 30%-70% angiosperms and 95% ferns, of which some are important crops such as cotton and wheat. How polyploid plants adapt to various habitats has been a fundamental question remained largely unanswered. The tetraploid Shepherd's purse (Capsella bursa-pastoris) is one of the most successful plants on earth and has been distributed across the world, thus being an ideal model system for studying the adaptation of polyploids. We found that there are frequent introgressions from congeneric diploids to Shepherd's purse. Ecological niche modeling suggests that ecological differentiation is evident between the introgressed and non-introgressed C. bursa-pastoris, and the introgressions are a source of adaptation. This result links an evolutionary process to the adaptation of polyploids, and sheds light on the breeding strategy of polyploids as well. We conclude that frequent introgressions from congeneric diploids contributed to the acquisition of adequate genetic variations, thereby allowing C. bursa-pastoris to adapt to various habitats across the world. Our results highlight how a polyploid could have successfully established after it originated.
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Affiliation(s)
- Ting-Shen Han
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiong Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xing-Hui Hou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zi-Wen Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yu-Pan Zou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris. Proc Natl Acad Sci U S A 2015; 112:2806-11. [PMID: 25691747 DOI: 10.1073/pnas.1412277112] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Whole-genome duplication (WGD) events have occurred repeatedly during flowering plant evolution, and there is growing evidence for predictable patterns of gene retention and loss following polyploidization. Despite these important insights, the rate and processes governing the earliest stages of diploidization remain poorly understood, and the relative importance of genetic drift, positive selection, and relaxed purifying selection in the process of gene degeneration and loss is unclear. Here, we conduct whole-genome resequencing in Capsella bursa-pastoris, a recently formed tetraploid with one of the most widespread species distributions of any angiosperm. Whole-genome data provide strong support for recent hybrid origins of the tetraploid species within the past 100,000-300,000 y from two diploid progenitors in the Capsella genus. Major-effect inactivating mutations are frequent, but many were inherited from the parental species and show no evidence of being fixed by positive selection. Despite a lack of large-scale gene loss, we observe a decrease in the efficacy of natural selection genome-wide due to the combined effects of demography, selfing, and genome redundancy from WGD. Our results suggest that the earliest stages of diploidization are associated with quantitative genome-wide decreases in the strength and efficacy of selection rather than rapid gene loss, and that nonfunctionalization can receive a "head start" through a legacy of deleterious variants and differential expression originating in parental diploid populations.
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14
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Roux C, Pannell JR. Inferring the mode of origin of polyploid species from next-generation sequence data. Mol Ecol 2015; 24:1047-59. [DOI: 10.1111/mec.13078] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 01/06/2015] [Accepted: 01/08/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Camille Roux
- Department of Ecology and Evolution; University of Lausanne; Lausanne 1015 Switzerland
| | - John R. Pannell
- Department of Ecology and Evolution; University of Lausanne; Lausanne 1015 Switzerland
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15
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Shafer ABA, Gattepaille LM, Stewart REA, Wolf JBW. Demographic inferences using short-read genomic data in an approximate Bayesian computation framework: in silico evaluation of power, biases and proof of concept in Atlantic walrus. Mol Ecol 2015; 24:328-45. [DOI: 10.1111/mec.13034] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 11/29/2014] [Accepted: 12/03/2014] [Indexed: 01/01/2023]
Affiliation(s)
- Aaron B. A. Shafer
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala SE-75236 Sweden
| | - Lucie M. Gattepaille
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala SE-75236 Sweden
| | - Robert E. A. Stewart
- Fisheries and Oceans Canada; Freshwater Institute; 501 University Crescent Winnipeg Manitoba R3T 2N6 Canada
| | - Jochen B. W. Wolf
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala SE-75236 Sweden
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16
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Liang Q, Hu X, Wu G, Liu J. Cryptic and repeated “allopolyploid” speciation within Allium przewalskianum Regel. (Alliaceae) from the Qinghai-Tibet Plateau. ORG DIVERS EVOL 2014. [DOI: 10.1007/s13127-014-0196-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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17
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Dufresne F, Stift M, Vergilino R, Mable BK. Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools. Mol Ecol 2013; 23:40-69. [DOI: 10.1111/mec.12581] [Citation(s) in RCA: 248] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 12/19/2022]
Affiliation(s)
- France Dufresne
- Département de Biologie; Université du Québec à Rimouski; Québec QC Canada G5L 3A1
| | - Marc Stift
- Department of Biology; University of Konstanz; Konstanz D 78457 Germany
| | - Roland Vergilino
- Department of Integrative Biology; University of Guelph; Guelph ON Canada N1G 2W1
| | - Barbara K. Mable
- Institute of Biodiversity; Animal Health and Comparative Medicine; College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow UK
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18
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Roux C, Tsagkogeorga G, Bierne N, Galtier N. Crossing the species barrier: genomic hotspots of introgression between two highly divergent Ciona intestinalis species. Mol Biol Evol 2013; 30:1574-87. [PMID: 23564941 DOI: 10.1093/molbev/mst066] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Inferring a realistic demographic model from genetic data is an important challenge to gain insights into the historical events during the speciation process and to detect molecular signatures of selection along genomes. Recent advances in divergence population genetics have reported that speciation in face of gene flow occurred more frequently than theoretically expected, but the approaches used did not account for genome-wide heterogeneity (GWH) in introgression rates. Here, we investigate the impact of GWH on the inference of divergence with gene flow between two cryptic species of the marine model Ciona intestinalis by analyzing polymorphism and divergence patterns in 852 protein-coding sequence loci. These morphologically similar entities are highly diverged molecular-wise, but evidence of hybridization has been reported in both laboratory and field studies. We compare various speciation models and test for GWH under the approximate Bayesian computation framework. Our results demonstrate the presence of significant extents of gene flow resulting from a recent secondary contact after >3 My of divergence in isolation. The inferred rates of introgression are relatively low, highly variable across loci and mostly unidirectional, which is consistent with the idea that numerous genetic incompatibilities have accumulated over time throughout the genomes of these highly diverged species. A genomic map of the level of gene flow identified two hotspots of introgression, that is, large genome regions of unidirectional introgression. This study clarifies the history and degree of isolation of two cryptic and partially sympatric model species and provides a methodological framework to investigate GWH at various stages of speciation process.
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Affiliation(s)
- Camille Roux
- Institut des Sciences de l'Évolution, Université Montpellier 2, CNRS, Montpellier, France.
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Arnold B, Bomblies K, Wakeley J. Extending coalescent theory to autotetraploids. Genetics 2012; 192:195-204. [PMID: 22714411 PMCID: PMC3430536 DOI: 10.1534/genetics.112.140582] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 06/01/2012] [Indexed: 11/18/2022] Open
Abstract
We develop coalescent models for autotetraploid species with tetrasomic inheritance. We show that the ancestral genetic process in a large population without recombination may be approximated using Kingman's standard coalescent, with a coalescent effective population size 4N. Numerical results suggest that this approximation is accurate for population sizes on the order of hundreds of individuals. Therefore, existing coalescent simulation programs can be adapted to study population history in autotetraploids simply by interpreting the timescale in units of 4N generations. We also consider the possibility of double reduction, a phenomenon unique to polysomic inheritance, and show that its effects on gene genealogies are similar to partial self-fertilization.
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Affiliation(s)
- B Arnold
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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20
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Impact of sampling schemes on demographic inference: an empirical study in two species with different mating systems and demographic histories. G3-GENES GENOMES GENETICS 2012; 2:803-14. [PMID: 22870403 PMCID: PMC3385986 DOI: 10.1534/g3.112.002410] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 05/10/2012] [Indexed: 12/12/2022]
Abstract
Most species have at least some level of genetic structure. Recent simulation studies have shown that it is important to consider population structure when sampling individuals to infer past population history. The relevance of the results of these computer simulations for empirical studies, however, remains unclear. In the present study, we use DNA sequence datasets collected from two closely related species with very different histories, the selfing species Capsella rubella and its outcrossing relative C. grandiflora, to assess the impact of different sampling strategies on summary statistics and the inference of historical demography. Sampling strategy did not strongly influence the mean values of Tajima's D in either species, but it had some impact on the variance. The general conclusions about demographic history were comparable across sampling schemes even when resampled data were analyzed with approximate Bayesian computation (ABC). We used simulations to explore the effects of sampling scheme under different demographic models. We conclude that when sequences from modest numbers of loci (<60) are analyzed, the sampling strategy is generally of limited importance. The same is true under intermediate or high levels of gene flow (4Nm > 2-10) in models in which global expansion is combined with either local expansion or hierarchical population structure. Although we observe a less severe effect of sampling than predicted under some earlier simulation models, our results should not be seen as an encouragement to neglect this issue. In general, a good coverage of the natural range, both within and between populations, will be needed to obtain a reliable reconstruction of a species's demographic history, and in fact, the effect of sampling scheme on polymorphism patterns may itself provide important information about demographic history.
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Huang HR, Yan PC, Lascoux M, Ge XJ. Flowering time and transcriptome variation in Capsella bursa-pastoris (Brassicaceae). THE NEW PHYTOLOGIST 2012; 194:676-689. [PMID: 22409515 DOI: 10.1111/j.1469-8137.2012.04101.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
• Flowering is a major developmental transition and its timing in relation to environmental conditions is of crucial importance to plant fitness. Understanding the genetic basis of flowering time variation is important to determining how plants adapt locally. • Here, we investigated flowering time variation of Capsella bursa-pastoris collected from different latitudes in China. We also used a digital gene expression (DGE) system to generate partial gene expression profiles for 12 selected samples. • We found that flowering time was highly variable and most strongly correlated with day length and winter temperature. Significant differences in gene expression between early- and late-flowering samples were detected for 72 candidate genes for flowering time. Genes related to circadian rhythms were significantly overrepresented among the differentially expressed genes. • Our data suggest that circadian rhythms and circadian clock genes play an important role in the evolution of flowering time, and C. bursa-pastoris plants exhibit expression differences for candidate genes likely to affect flowering time across the broad range of environments they face in China.
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Affiliation(s)
- Hui-Run Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou 510650, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
| | - Peng-Cheng Yan
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering and College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
- Laboratory of Evolutionary Genomics, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, the Chinese Academy of Sciences, Shanghai, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou 510650, China
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