1
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Murphy WJ, Harris AJ. Toward telomere-to-telomere cat genomes for precision medicine and conservation biology. Genome Res 2024; 34:655-664. [PMID: 38849156 PMCID: PMC11216403 DOI: 10.1101/gr.278546.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
Genomic data from species of the cat family Felidae promise to stimulate veterinary and human medical advances, and clarify the coherence of genome organization. We describe how interspecies hybrids have been instrumental in the genetic analysis of cats, from the first genetic maps to propelling cat genomes toward the T2T standard set by the human genome project. Genotype-to-phenotype mapping in cat models has revealed dozens of health-related genetic variants, the molecular basis for mammalian pigmentation and patterning, and species-specific adaptations. Improved genomic surveillance of natural and captive populations across the cat family tree will increase our understanding of the genetic architecture of traits, population dynamics, and guide a future of genome-enabled biodiversity conservation.
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Affiliation(s)
- William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA;
- Department of Biology, Texas A&M University, College Station, Texas 77843-4458, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843-4458, USA
| | - Andrew J Harris
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843-4458, USA
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2
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Rybnikov SR, Frenkel Z, Hübner S, Weissman DB, Korol AB. Modeling the evolution of recombination plasticity: A prospective review. Bioessays 2023; 45:e2200237. [PMID: 37246937 DOI: 10.1002/bies.202200237] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 05/30/2023]
Abstract
Meiotic recombination is one of the main sources of genetic variation, a fundamental factor in the evolutionary adaptation of sexual eukaryotes. Yet, the role of variation in recombination rate and other recombination features remains underexplored. In this review, we focus on the sensitivity of recombination rates to different extrinsic and intrinsic factors. We briefly present the empirical evidence for recombination plasticity in response to environmental perturbations and/or poor genetic background and discuss theoretical models developed to explain how such plasticity could have evolved and how it can affect important population characteristics. We highlight a gap between the evidence, which comes mostly from experiments with diploids, and theory, which typically assumes haploid selection. Finally, we formulate open questions whose solving would help to outline conditions favoring recombination plasticity. This will contribute to answering the long-standing question of why sexual recombination exists despite its costs, since plastic recombination may be evolutionary advantageous even in selection regimes rejecting any non-zero constant recombination.
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Affiliation(s)
- Sviatoslav R Rybnikov
- Institute of Evolution, University of Haifa, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | - Zeev Frenkel
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Sariel Hübner
- Galilee Research Institute (MIGAL), Tel-Hai College, Kiryat Shmona, Israel
| | | | - Abraham B Korol
- Institute of Evolution, University of Haifa, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
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3
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Valero-Regalón FJ, Solé M, López-Jiménez P, Valerio-de Arana M, Martín-Ruiz M, de la Fuente R, Marín-Gual L, Renfree MB, Shaw G, Berríos S, Fernández-Donoso R, Waters PD, Ruiz-Herrera A, Gómez R, Page J. Divergent patterns of meiotic double strand breaks and synapsis initiation dynamics suggest an evolutionary shift in the meiosis program between American and Australian marsupials. Front Cell Dev Biol 2023; 11:1147610. [PMID: 37181752 PMCID: PMC10166821 DOI: 10.3389/fcell.2023.1147610] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/06/2023] [Indexed: 05/16/2023] Open
Abstract
In eutherian mammals, hundreds of programmed DNA double-strand breaks (DSBs) are generated at the onset of meiosis. The DNA damage response is then triggered. Although the dynamics of this response is well studied in eutherian mammals, recent findings have revealed different patterns of DNA damage signaling and repair in marsupial mammals. To better characterize these differences, here we analyzed synapsis and the chromosomal distribution of meiotic DSBs markers in three different marsupial species (Thylamys elegans, Dromiciops gliorides, and Macropus eugenii) that represent South American and Australian Orders. Our results revealed inter-specific differences in the chromosomal distribution of DNA damage and repair proteins, which were associated with differing synapsis patterns. In the American species T. elegans and D. gliroides, chromosomal ends were conspicuously polarized in a bouquet configuration and synapsis progressed exclusively from the telomeres towards interstitial regions. This was accompanied by sparse H2AX phosphorylation, mainly accumulating at chromosomal ends. Accordingly, RAD51 and RPA were mainly localized at chromosomal ends throughout prophase I in both American marsupials, likely resulting in reduced recombination rates at interstitial positions. In sharp contrast, synapsis initiated at both interstitial and distal chromosomal regions in the Australian representative M. eugenii, the bouquet polarization was incomplete and ephemeral, γH2AX had a broad nuclear distribution, and RAD51 and RPA foci displayed an even chromosomal distribution. Given the basal evolutionary position of T. elegans, it is likely that the meiotic features reported in this species represent an ancestral pattern in marsupials and that a shift in the meiotic program occurred after the split of D. gliroides and the Australian marsupial clade. Our results open intriguing questions about the regulation and homeostasis of meiotic DSBs in marsupials. The low recombination rates observed at the interstitial chromosomal regions in American marsupials can result in the formation of large linkage groups, thus having an impact in the evolution of their genomes.
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Affiliation(s)
| | - Mireia Solé
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
- Genetics of Male Fertility Group, Unitat de Biologia Cel·lular, Universitat Autònoma de Barcelona, Spain
| | - Pablo López-Jiménez
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - María Valerio-de Arana
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marta Martín-Ruiz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Roberto de la Fuente
- Department of Experimental Embryology, Institute of Genetics and Animal Biotechnology of The Polish Academy of Sciences, Jastrzębiec, Poland
| | - Laia Marín-Gual
- Departament de Biologia Cel·lular, Universitat Autònoma de Barcelona, Barcelona, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Barcelona, Spain
| | - Marilyn B. Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Geoff Shaw
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Soledad Berríos
- Programa de Genética Humana, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Raúl Fernández-Donoso
- Programa de Genética Humana, Facultad de Medicina, Instituto de Ciencias Biomédicas, Universidad de Chile, Santiago, Chile
| | - Paul D. Waters
- School of Biotechnology and Biomolecular Science, Faculty of Science, University of New South Wales, Sydney, NSW, Australia
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Universitat Autònoma de Barcelona, Barcelona, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Barcelona, Spain
| | - Rocío Gómez
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Jesús Page
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
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4
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Soriano J, Belmonte-Tebar A, de la Casa-Esperon E. Synaptonemal & CO analyzer: A tool for synaptonemal complex and crossover analysis in immunofluorescence images. Front Cell Dev Biol 2023; 11:1005145. [PMID: 36743415 PMCID: PMC9894712 DOI: 10.3389/fcell.2023.1005145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 01/09/2023] [Indexed: 01/20/2023] Open
Abstract
During the formation of ova and sperm, homologous chromosomes get physically attached through the synaptonemal complex and exchange DNA at crossover sites by a process known as meiotic recombination. Chromosomes that do not recombine or have anomalous crossover distributions often separate poorly during the subsequent cell division and end up in abnormal numbers in ova or sperm, which can lead to miscarriage or developmental defects. Crossover numbers and distribution along the synaptonemal complex can be visualized by immunofluorescent microscopy. However, manual analysis of large numbers of cells is very time-consuming and a major bottleneck for recombination studies. Some image analysis tools have been created to overcome this situation, but they are not readily available, do not provide synaptonemal complex data, or do not tackle common experimental difficulties, such as overlapping chromosomes. To overcome these limitations, we have created and validated an open-source ImageJ macro routine that facilitates and speeds up the crossover and synaptonemal complex analyses in mouse chromosome spreads, as well as in other vertebrate species. It is free, easy to use and fulfills the recommendations for enhancing rigor and reproducibility in biomedical studies.
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Affiliation(s)
- Joaquim Soriano
- Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla-La Mancha, Albacete, Spain
| | - Angela Belmonte-Tebar
- Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla-La Mancha, Albacete, Spain
| | - Elena de la Casa-Esperon
- Centro Regional de Investigaciones Biomédicas (CRIB), Universidad de Castilla-La Mancha, Albacete, Spain,Biology of Cell Growth, Differentiation and Activation Group, Department of Inorganic and Organic Chemistry and Biochemistry, School of Pharmacy, Universidad de Castilla-La Mancha, Albacete, Spain,*Correspondence: Elena de la Casa-Esperon,
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5
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Marín-Gual L, González-Rodelas L, M. Garcias M, Kratochvíl L, Valenzuela N, Georges A, Waters PD, Ruiz-Herrera A. Meiotic chromosome dynamics and double strand break formation in reptiles. Front Cell Dev Biol 2022; 10:1009776. [PMID: 36313577 PMCID: PMC9597255 DOI: 10.3389/fcell.2022.1009776] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/23/2022] [Indexed: 11/13/2022] Open
Abstract
During meiotic prophase I, tightly regulated processes take place, from pairing and synapsis of homologous chromosomes to recombination, which are essential for the generation of genetically variable haploid gametes. These processes have canonical meiotic features conserved across different phylogenetic groups. However, the dynamics of meiotic prophase I in non-mammalian vertebrates are poorly known. Here, we compare four species from Sauropsida to understand the regulation of meiotic prophase I in reptiles: the Australian central bearded dragon (Pogona vitticeps), two geckos (Paroedura picta and Coleonyx variegatus) and the painted turtle (Chrysemys picta). We first performed a histological characterization of the spermatogenesis process in both the bearded dragon and the painted turtle. We then analyzed prophase I dynamics, including chromosome pairing, synapsis and the formation of double strand breaks (DSBs). We show that meiosis progression is highly conserved in reptiles with telomeres clustering forming the bouquet, which we propose promotes homologous pairing and synapsis, along with facilitating the early pairing of micro-chromosomes during prophase I (i.e., early zygotene). Moreover, we detected low levels of meiotic DSB formation in all taxa. Our results provide new insights into reptile meiosis.
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Affiliation(s)
- Laia Marín-Gual
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Laura González-Rodelas
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Maria M. Garcias
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, Australia
| | - Paul D. Waters
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW, Sydney, NSW, Australia
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- *Correspondence: Aurora Ruiz-Herrera,
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6
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Booker TR, Payseur BA, Tigano A. Background selection under evolving recombination rates. Proc Biol Sci 2022; 289:20220782. [PMID: 35730151 PMCID: PMC9233929 DOI: 10.1098/rspb.2022.0782] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Background selection (BGS), the effect that purifying selection exerts on sites linked to deleterious alleles, is expected to be ubiquitous across eukaryotic genomes. The effects of BGS reflect the interplay of the rates and fitness effects of deleterious mutations with recombination. A fundamental assumption of BGS models is that recombination rates are invariant over time. However, in some lineages, recombination rates evolve rapidly, violating this central assumption. Here, we investigate how recombination rate evolution affects genetic variation under BGS. We show that recombination rate evolution modifies the effects of BGS in a manner similar to a localized change in the effective population size, potentially leading to underestimation or overestimation of the genome-wide effects of selection. Furthermore, we find evidence that recombination rate evolution in the ancestors of modern house mice may have impacted inferences of the genome-wide effects of selection in that species.
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Affiliation(s)
- Tom R. Booker
- Department of Zoology, University of British Columbia, Vancouver Campus, Vancouver, BC, Canada
| | - Bret A. Payseur
- Laboratory of Genetics, University of Wisconsin - Madison, Madison, WI, USA
| | - Anna Tigano
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, Canada
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7
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Ruiz-Herrera A, Waters PD. Fragile, unfaithful and persistent Ys-on how meiosis can shape sex chromosome evolution. Heredity (Edinb) 2022; 129:22-30. [PMID: 35459933 PMCID: PMC9273583 DOI: 10.1038/s41437-022-00532-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 12/28/2022] Open
Abstract
Sex-linked inheritance is a stark exception to Mendel's Laws of Heredity. Here we discuss how the evolution of heteromorphic sex chromosomes (mainly the Y) has been shaped by the intricacies of the meiotic programme. We propose that persistence of Y chromosomes in distantly related mammalian phylogroups can be explained in the context of pseudoautosomal region (PAR) size, meiotic pairing strategies, and the presence of Y-borne executioner genes that regulate meiotic sex chromosome inactivation. We hypothesise that variation in PAR size can be an important driver for the evolution of recombination frequencies genome wide, imposing constraints on Y fate. If small PAR size compromises XY segregation during male meiosis, the stress of producing aneuploid gametes could drive function away from the Y (i.e., a fragile Y). The Y chromosome can avoid fragility either by acquiring an achiasmatic meiotic XY pairing strategy to reduce aneuploid gamete production, or gain meiotic executioner protection (a persistent Y). Persistent Ys will then be under strong pressure to maintain high recombination rates in the PAR (and subsequently genome wide), as improper segregation has fatal consequences for germ cells. In the event that executioner protection is lost, the Y chromosome can be maintained in the population by either PAR rejuvenation (extension by addition of autosome material) or gaining achiasmatic meiotic pairing, the alternative is Y loss. Under this dynamic cyclic evolutionary scenario, understanding the meiotic programme in vertebrate and invertebrate species will be crucial to further understand the plasticity of the rise and fall of heteromorphic sex chromosomes.
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Affiliation(s)
- Aurora Ruiz-Herrera
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193, Spain. .,Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona (UAB), Cerdanyola del Vallès, 08193, Spain.
| | - Paul D Waters
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Sydney, NSW, 2052, Australia.
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8
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Marín-Gual L, González-Rodelas L, Pujol G, Vara C, Martín-Ruiz M, Berríos S, Fernández-Donoso R, Pask A, Renfree MB, Page J, Waters PD, Ruiz-Herrera A. Strategies for meiotic sex chromosome dynamics and telomeric elongation in Marsupials. PLoS Genet 2022; 18:e1010040. [PMID: 35130272 PMCID: PMC8853506 DOI: 10.1371/journal.pgen.1010040] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 02/17/2022] [Accepted: 01/14/2022] [Indexed: 01/30/2023] Open
Abstract
During meiotic prophase I, homologous chromosomes pair, synapse and recombine in a tightly regulated process that ensures the generation of genetically variable haploid gametes. Although the mechanisms underlying meiotic cell division have been well studied in model species, our understanding of the dynamics of meiotic prophase I in non-traditional model mammals remains in its infancy. Here, we reveal key meiotic features in previously uncharacterised marsupial species (the tammar wallaby and the fat-tailed dunnart), plus the fat-tailed mouse opossum, with a focus on sex chromosome pairing strategies, recombination and meiotic telomere homeostasis. We uncovered differences between phylogroups with important functional and evolutionary implications. First, sex chromosomes, which lack a pseudo-autosomal region in marsupials, had species specific pairing and silencing strategies, with implications for sex chromosome evolution. Second, we detected two waves of γH2AX accumulation during prophase I. The first wave was accompanied by low γH2AX levels on autosomes, which correlated with the low recombination rates that distinguish marsupials from eutherian mammals. In the second wave, γH2AX was restricted to sex chromosomes in all three species, which correlated with transcription from the X in tammar wallaby. This suggests non-canonical functions of γH2AX on meiotic sex chromosomes. Finally, we uncover evidence for telomere elongation in primary spermatocytes of the fat-tailed dunnart, a unique strategy within mammals. Our results provide new insights into meiotic progression and telomere homeostasis in marsupials, highlighting the importance of capturing the diversity of meiotic strategies within mammals. The generation of haploid gametes is a hallmark of sexual reproduction. And this is accomplished by a complex, albeit tightly regulated, reductional cell division called meiosis. Although meiosis has been extensively studied in eutherian mammal model species, our understanding of the mechanisms regulating chromosome synapsis, recombination and segregation during meiosis progression is still incomplete especially in non-eutherian mammals. To fill this gap and capture the diversity of meiotic strategies among mammals, we study previously uncharacterised representative marsupial species, an evolutionary assemblage that last shared a common ancestry more than 80 million years ago. We uncover novel, hence non-canonical, strategies for sex chromosome pairing, DNA repair, recombination and transcription. Most importantly, we reveal the uniqueness of marsupial meiosis, which includes the unprecedented detection of alternative mechanism (ALT) for the paternal control of telomere length during prophase I. Our findings suggest that ALT (previously only associated to cancer cells) could play a role in telomere homeostasis in mammalian germ cells.
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Affiliation(s)
- Laia Marín-Gual
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Laura González-Rodelas
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Gala Pujol
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Covadonga Vara
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Marta Martín-Ruiz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Soledad Berríos
- Programa de Genética Humana, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Raúl Fernández-Donoso
- Programa de Genética Humana, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Andrew Pask
- School of BioSciences, The University of Melbourne, Melbourne, Australia
| | - Marilyn B. Renfree
- School of BioSciences, The University of Melbourne, Melbourne, Australia
| | - Jesús Page
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Paul D. Waters
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, UNSW Sydney, Australia
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- * E-mail:
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9
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Malinovskaya LP, Tishakova KV, Bikchurina TI, Slobodchikova AY, Torgunakov NY, Torgasheva AA, Tsepilov YA, Volkova NA, Borodin PM. Negative heterosis for meiotic recombination rate in spermatocytes of the domestic chicken Gallus gallus. Vavilovskii Zhurnal Genet Selektsii 2021; 25:661-668. [PMID: 34782886 PMCID: PMC8558918 DOI: 10.18699/vj21.075] [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: 04/23/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 11/24/2022] Open
Abstract
Benef its and costs of meiotic recombination are a matter of discussion. Because recombination breaks
allele combinations already tested by natural selection and generates new ones of unpredictable f itness, a high
recombination rate is generally benef icial for the populations living in a f luctuating or a rapidly changing environment
and costly in a stable environment. Besides genetic benef its and costs, there are cytological effects of recombination,
both positive and negative. Recombination is necessary for chromosome synapsis and segregation. However,
it involves a massive generation of double-strand DNA breaks, erroneous repair of which may lead to germ
cell death or various mutations and chromosome rearrangements. Thus, the benef its of recombination (generation
of new allele combinations) would prevail over its costs (occurrence of deleterious mutations) as long as the population
remains suff iciently heterogeneous. Using immunolocalization of MLH1, a mismatch repair protein, at the
synaptonemal complexes, we examined the number and distribution of recombination nodules in spermatocytes
of two chicken breeds with high (Pervomai) and low (Russian Crested) recombination rates and their F1 hybrids and
backcrosses. We detected negative heterosis for recombination rate in the F1 hybrids. Backcrosses to the Pervomai
breed were rather homogenous and showed an intermediate recombination rate. The differences in overall recombination
rate between the breeds, hybrids and backcrosses were mainly determined by the differences in the crossing
over number in the seven largest macrochromosomes. The decrease in recombination rate in F1 is probably
determined by diff iculties in homology matching between the DNA sequences of genetically divergent breeds. The
suppression of recombination in the hybrids may impede gene f low between parapatric populations and therefore
accelerate their genetic divergence.
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Affiliation(s)
- L P Malinovskaya
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | - T I Bikchurina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A Yu Slobodchikova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N Yu Torgunakov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Torgasheva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Y A Tsepilov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N A Volkova
- L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Moscow region, Russia
| | - P M Borodin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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10
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Peterson AL, Payseur BA. Sex-specific variation in the genome-wide recombination rate. Genetics 2021; 217:1-11. [PMID: 33683358 DOI: 10.1093/genetics/iyaa019] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/19/2020] [Indexed: 01/13/2023] Open
Abstract
In most species that reproduce sexually, successful gametogenesis requires recombination during meiosis. The number and placement of crossovers (COs) vary among individuals, with females and males often presenting the most striking contrasts. Despite the recognition that the sexes recombine at different rates (heterochiasmy), existing data fail to answer the question of whether patterns of genetic variation in recombination rate are similar in the two sexes. To fill this gap, we measured the genome-wide recombination rate in both sexes from a panel of wild-derived inbred strains from multiple subspecies of house mice (Mus musculus) and from a few additional species of Mus. To directly compare recombination rates in females and males from the same genetic backgrounds, we applied established methods based on immunolocalization of recombination proteins to inbred strains. Our results reveal discordant patterns of genetic variation in the two sexes. Whereas male genome-wide recombination rates vary substantially among strains, female recombination rates measured in the same strains are more static. The direction of heterochiasmy varies within two subspecies, Mus musculus molossinus and Mus musculus musculus. The direction of sex differences in the length of the synaptonemal complex and CO positions is consistent across strains and does not track sex differences in genome-wide recombination rate. In males, contrasts between strains with high recombination rate and strains with low recombination rate suggest more recombination is associated with stronger CO interference and more double-strand breaks. The sex-specific patterns of genetic variation we report underscore the importance of incorporating sex differences into recombination research.
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Affiliation(s)
- April L Peterson
- Laboratory of Genetics, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin - Madison, Madison, WI 53706, USA
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11
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Johnsson M, Whalen A, Ros-Freixedes R, Gorjanc G, Chen CY, Herring WO, de Koning DJ, Hickey JM. Genetic variation in recombination rate in the pig. Genet Sel Evol 2021; 53:54. [PMID: 34171988 PMCID: PMC8235837 DOI: 10.1186/s12711-021-00643-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/02/2021] [Indexed: 11/10/2022] Open
Abstract
Background Meiotic recombination results in the exchange of genetic material between homologous chromosomes. Recombination rate varies between different parts of the genome, between individuals, and is influenced by genetics. In this paper, we assessed the genetic variation in recombination rate along the genome and between individuals in the pig using multilocus iterative peeling on 150,000 individuals across nine genotyped pedigrees. We used these data to estimate the heritability of recombination and perform a genome-wide association study of recombination in the pig. Results Our results confirmed known features of the recombination landscape of the pig genome, including differences in genetic length of chromosomes and marked sex differences. The recombination landscape was repeatable between lines, but at the same time, there were differences in average autosome-wide recombination rate between lines. The heritability of autosome-wide recombination rate was low but not zero (on average 0.07 for females and 0.05 for males). We found six genomic regions that are associated with recombination rate, among which five harbour known candidate genes involved in recombination: RNF212, SHOC1, SYCP2, MSH4 and HFM1. Conclusions Our results on the variation in recombination rate in the pig genome agree with those reported for other vertebrates, with a low but nonzero heritability, and the identification of a major quantitative trait locus for recombination rate that is homologous to that detected in several other species. This work also highlights the utility of using large-scale livestock data to understand biological processes. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00643-0.
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Affiliation(s)
- Martin Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK. .,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 750 07, Uppsala, Sweden.
| | - Andrew Whalen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK
| | - Roger Ros-Freixedes
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK.,Departament de Ciència Animal, Universitat de Lleida-Agrotecnio-CERCA Center, Lleida, Spain
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK
| | - Ching-Yi Chen
- Pig Improvement Company, Genus plc, 100 Bluegrass Commons Blvd., Ste2200, Hendersonville, TN, 37075, USA
| | - William O Herring
- Pig Improvement Company, Genus plc, 100 Bluegrass Commons Blvd., Ste2200, Hendersonville, TN, 37075, USA
| | - Dirk-Jan de Koning
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 750 07, Uppsala, Sweden
| | - John M Hickey
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG, Scotland, UK
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12
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The impact of chromosomal fusions on 3D genome folding and recombination in the germ line. Nat Commun 2021; 12:2981. [PMID: 34016985 PMCID: PMC8137915 DOI: 10.1038/s41467-021-23270-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 04/16/2021] [Indexed: 02/08/2023] Open
Abstract
The spatial folding of chromosomes inside the nucleus has regulatory effects on gene expression, yet the impact of genome reshuffling on this organization remains unclear. Here, we take advantage of chromosome conformation capture in combination with single-nucleotide polymorphism (SNP) genotyping and analysis of crossover events to study how the higher-order chromatin organization and recombination landscapes are affected by chromosomal fusions in the mammalian germ line. We demonstrate that chromosomal fusions alter the nuclear architecture during meiosis, including an increased rate of heterologous interactions in primary spermatocytes, and alterations in both chromosome synapsis and axis length. These disturbances in topology were associated with changes in genomic landscapes of recombination, resulting in detectable genomic footprints. Overall, we show that chromosomal fusions impact the dynamic genome topology of germ cells in two ways: (i) altering chromosomal nuclear occupancy and synapsis, and (ii) reshaping landscapes of recombination.
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13
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Bredemeyer KR, Harris AJ, Li G, Zhao L, Foley NM, Roelke-Parker M, O'Brien SJ, Lyons LA, Warren WC, Murphy WJ. Ultracontinuous Single Haplotype Genome Assemblies for the Domestic Cat (Felis catus) and Asian Leopard Cat (Prionailurus bengalensis). J Hered 2021; 112:165-173. [PMID: 33305796 PMCID: PMC8006817 DOI: 10.1093/jhered/esaa057] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/08/2020] [Indexed: 12/11/2022] Open
Abstract
In addition to including one of the most popular companion animals, species from the cat family Felidae serve as a powerful system for genetic analysis of inherited and infectious disease, as well as for the study of phenotypic evolution and speciation. Previous diploid-based genome assemblies for the domestic cat have served as the primary reference for genomic studies within the cat family. However, these versions suffered from poor resolution of complex and highly repetitive regions, with substantial amounts of unplaced sequence that is polymorphic or copy number variable. We sequenced the genome of a female F1 Bengal hybrid cat, the offspring of a domestic cat (Felis catus) x Asian leopard cat (Prionailurus bengalensis) cross, with PacBio long sequence reads and used Illumina sequence reads from the parents to phase >99.9% of the reads into the 2 species' haplotypes. De novo assembly of the phased reads produced highly continuous haploid genome assemblies for the domestic cat and Asian leopard cat, with contig N50 statistics exceeding 83 Mb for both genomes. Whole-genome alignments reveal the Felis and Prionailurus genomes are colinear, and the cytogenetic differences between the homologous F1 and E4 chromosomes represent a case of centromere repositioning in the absence of a chromosomal inversion. Both assemblies offer significant improvements over the previous domestic cat reference genome, with a 100% increase in contiguity and the capture of the vast majority of chromosome arms in 1 or 2 large contigs. We further demonstrated that comparably accurate F1 haplotype phasing can be achieved with members of the same species when one or both parents of the trio are not available. These novel genome resources will empower studies of feline precision medicine, adaptation, and speciation.
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Affiliation(s)
- Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX.,Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX
| | - Andrew J Harris
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX.,Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Le Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, China
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
| | - Melody Roelke-Parker
- Frederick National Laboratory of Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD
| | - Stephen J O'Brien
- Laboratory of Genomic Diversity-Center for Computer Technologies, ITMO University, Saint Petersburg, Russian Federation.,Guy Harvey Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL
| | - Leslie A Lyons
- Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO
| | - Wesley C Warren
- Bond Life Science Center, University of Missouri, Columbia, MO
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX.,Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX
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14
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Matveevsky S, Tretiakov A, Kashintsova A, Bakloushinskaya I, Kolomiets O. Meiotic Nuclear Architecture in Distinct Mole Vole Hybrids with Robertsonian Translocations: Chromosome Chains, Stretched Centromeres, and Distorted Recombination. Int J Mol Sci 2020; 21:E7630. [PMID: 33076404 PMCID: PMC7589776 DOI: 10.3390/ijms21207630] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 10/13/2020] [Indexed: 11/24/2022] Open
Abstract
Genome functioning in hybrids faces inconsistency. This mismatch is manifested clearly in meiosis during chromosome synapsis and recombination. Species with chromosomal variability can be a model for exploring genomic battles with high visibility due to the use of advanced immunocytochemical methods. We studied synaptonemal complexes (SC) and prophase I processes in 44-chromosome intraspecific (Ellobius tancrei × E. tancrei) and interspecific (Ellobius talpinus × E. tancrei) hybrid mole voles heterozygous for 10 Robertsonian translocations. The same pachytene failures were found for both types of hybrids. In the intraspecific hybrid, the chains were visible in the pachytene stage, then 10 closed SC trivalents formed in the late pachytene and diplotene stage. In the interspecific hybrid, as a rule, SC trivalents composed the SC chains and rarely could form closed configurations. Metacentrics involved with SC trivalents had stretched centromeres in interspecific hybrids. Linkage between neighboring SC trivalents was maintained by stretched centromeric regions of acrocentrics. This centromeric plasticity in structure and dynamics of SC trivalents was found for the first time. We assume that stretched centromeres were a marker of altered nuclear architecture in heterozygotes due to differences in the ancestral chromosomal territories of the parental species. Restructuring of the intranuclear organization and meiotic disturbances can contribute to the sterility of interspecific hybrids, and lead to the reproductive isolation of studied species.
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Affiliation(s)
- Sergey Matveevsky
- Laboratory of Cytogenetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.T.); (A.K.); (O.K.)
| | - Artemii Tretiakov
- Laboratory of Cytogenetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.T.); (A.K.); (O.K.)
| | - Anna Kashintsova
- Laboratory of Cytogenetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.T.); (A.K.); (O.K.)
| | - Irina Bakloushinskaya
- Laboratory of Genome Evolution and Mechanisms of Speciation, Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Oxana Kolomiets
- Laboratory of Cytogenetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia; (A.T.); (A.K.); (O.K.)
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15
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del Priore L, Pigozzi MI. MLH1 focus mapping in the guinea fowl (Numida meleagris) give insights into the crossover landscapes in birds. PLoS One 2020; 15:e0240245. [PMID: 33017431 PMCID: PMC7535058 DOI: 10.1371/journal.pone.0240245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/22/2020] [Indexed: 11/21/2022] Open
Abstract
Crossover rates and localization are not homogeneous throughout the genomes. Along the chromosomes of almost all species, domains with high crossover rates alternate with domains where crossover rates are significantly lower than the genome-wide average. The distribution of crossovers along chromosomes constitutes the recombination landscape of a given species and can be analyzed at broadscale using immunostaining of the MLH1 protein, a component of mature recombination nodules found on synaptonemal complexes during pachytene. We scored the MLH1 foci in oocytes of the chicken and the guinea fowl and compared their frequencies in the largest bivalents. The average autosomal number of foci is 62 in the chicken and 44 in the guinea fowl. The lower number in the guinea fowl responds to the occurrence of fewer crossovers in the six largest bivalents, where most MLH1 foci occur within one-fifth of the chromosome length with high polarization towards opposite ends. The skewed distribution of foci in the guinea fowl contrast with the more uniform distribution of numerous foci in the chicken, especially in the four largest bivalents. The crossover distribution observed in the guinea fowl is unusual among Galloanserae and also differs from other, more distantly related birds. We discussed the current evidence showing that the shift towards crossover localization, as observed in the guinea fowl, was not a unique event but also occurred at different moments of bird evolution. A comparative analysis of genome-wide average recombination rates in birds shows variations within narrower limits compared to mammals and the absence of a phylogenetic trend.
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Affiliation(s)
- Lucía del Priore
- INBIOMED (CONICET-UBA), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Inés Pigozzi
- INBIOMED (CONICET-UBA), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
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16
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Abstract
Through recombination, genes are freed to evolve more independently of one another, unleashing genetic variance hidden in the linkage disequilibrium that accumulates through selection combined with drift. Yet crossover numbers are evolutionarily constrained, with at least one and not many more than one crossover per bivalent in most taxa. Crossover interference, whereby a crossover reduces the probability of a neighboring crossover, contributes to this homogeneity. The mechanisms by which interference is achieved and crossovers are regulated are a major current subject of inquiry, facilitated by novel methods to visualize crossovers and to pinpoint recombination events. Here, we review patterns of crossover interference and the models built to describe this process. We then discuss the selective forces that have likely shaped interference and the regulation of crossover numbers.
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Affiliation(s)
- Sarah P Otto
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada;
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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17
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Dapper AL, Payseur BA. Molecular evolution of the meiotic recombination pathway in mammals. Evolution 2019; 73:2368-2389. [PMID: 31579931 DOI: 10.1111/evo.13850] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 09/07/2019] [Indexed: 02/06/2023]
Abstract
Meiotic recombination shapes evolution and helps to ensure proper chromosome segregation in most species that reproduce sexually. Recombination itself evolves, with species showing considerable divergence in the rate of crossing-over. However, the genetic basis of this divergence is poorly understood. Recombination events are produced via a complicated, but increasingly well-described, cellular pathway. We apply a phylogenetic comparative approach to a carefully selected panel of genes involved in the processes leading to crossovers-spanning double-strand break formation, strand invasion, the crossover/non-crossover decision, and resolution-to reconstruct the evolution of the recombination pathway in eutherian mammals and identify components of the pathway likely to contribute to divergence between species. Eleven recombination genes, predominantly involved in the stabilization of homologous pairing and the crossover/non-crossover decision, show evidence of rapid evolution and positive selection across mammals. We highlight TEX11 and associated genes involved in the synaptonemal complex and the early stages of the crossover/non-crossover decision as candidates for the evolution of recombination rate. Evolutionary comparisons to MLH1 count, a surrogate for the number of crossovers, reveal a positive correlation between genome-wide recombination rate and the rate of evolution at TEX11 across the mammalian phylogeny. Our results illustrate the power of viewing the evolution of recombination from a pathway perspective.
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Affiliation(s)
- Amy L Dapper
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin, 53706.,Department of Biological Sciences, Mississippi State University, Mississippi, 39762
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin, 53706
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18
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CENP-A binding domains and recombination patterns in horse spermatocytes. Sci Rep 2019; 9:15800. [PMID: 31676881 PMCID: PMC6825197 DOI: 10.1038/s41598-019-52153-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/11/2019] [Indexed: 02/07/2023] Open
Abstract
Centromeres exert an inhibitory effect on meiotic recombination, but the possible contribution of satellite DNA to this "centromere effect" is under debate. In the horse, satellite DNA is present at all centromeres with the exception of the one from chromosome 11. This organization of centromeres allowed us to investigate the role of satellite DNA on recombination suppression in horse spermatocytes at the stage of pachytene. To this aim we analysed the distribution of the MLH1 protein, marker of recombination foci, relative to CENP-A, marker of centromeric function. We demonstrated that the satellite-less centromere of chromosome 11 causes crossover suppression, similarly to satellite-based centromeres. These results suggest that the centromere effect does not depend on satellite DNA. During this analysis, we observed a peculiar phenomenon: while, as expected, the centromere of the majority of meiotic bivalent chromosomes was labelled with a single immunofluorescence centromeric signal, double-spotted or extended signals were also detected. Their number varied from 0 to 7 in different cells. This observation can be explained by positional variation of the centromeric domain on the two homologs and/or misalignment of pericentromeric satellite DNA arrays during homolog pairing confirming the great plasticity of equine centromeres.
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19
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Conservation of the genome-wide recombination rate in white-footed mice. Heredity (Edinb) 2019; 123:442-457. [PMID: 31366913 PMCID: PMC6781155 DOI: 10.1038/s41437-019-0252-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 07/05/2019] [Accepted: 07/09/2019] [Indexed: 11/09/2022] Open
Abstract
Despite being linked to the fundamental processes of chromosome segregation and offspring diversification, meiotic recombination rates vary within and between species. Recent years have seen progress in quantifying recombination rate evolution across multiple temporal and genomic scales. Nevertheless, the level of variation in recombination rate within wild populations-a key determinant of evolution in this trait-remains poorly documented on the genomic scale. To address this notable gap, we used immunofluorescent cytology to quantify genome-wide recombination rates in males from a wild population of the white-footed mouse, Peromyscus leucopus. For comparison, we measured recombination rates in a second population of male P. leucopus raised in the laboratory and in male deer mice from the subspecies Peromyscus maniculatus bairdii. Although we found differences between individuals in the genome-wide recombination rate, levels of variation were low-within populations, between populations, and between species. Quantification of synaptonemal complex length and crossover positions along chromosome 1 using a novel automated approach also revealed conservation in broad-scale crossover patterning, including strong crossover interference. We propose stabilizing selection targeting recombination or correlated processes as the explanation for these patterns.
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20
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Malinovskaya L, Tishakova K, Volkova N, Torgasheva A, Tsepilov Y, Borodin P. Interbreed variation in meiotic recombination rate and distribution in the domestic chicken Gallus gallus. Arch Anim Breed 2019; 62:403-411. [PMID: 31807651 PMCID: PMC6859913 DOI: 10.5194/aab-62-403-2019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/21/2019] [Indexed: 11/11/2022] Open
Abstract
The efficiency of natural and artificial selection is critically dependent on the recombination rate. However, interbreed and individual variation in recombination rate in poultry remains unknown. Conventional methods of analysis of recombination such as genetic linkage analysis, sperm genotyping and chiasma count at lampbrush chromosomes are expensive and time-consuming. In this study, we analyzed the number and distribution of recombination nodules in spermatocytes of the roosters of six chicken breeds using immunolocalization of key proteins involved in chromosome pairing and recombination. We revealed significant effects of breed (R 2 = 0.17 ; p < 0.001 ) and individual (R 2 = 0.28 ; p < 0.001 ) on variation in the number of recombination nodules. Both interbreed and individual variations in recombination rate were almost entirely determined by variation in recombination density on macrochromosomes, because almost all microchromosomes in each breed had one recombination nodule. Despite interbreed differences in the density of recombination nodules, the patterns of their distribution along homologous chromosomes were similar. The breeds examined in this study showed a correspondence between the age of the breed and its recombination rate. Those with high recombination rates (Pervomai, Russian White and Brahma) are relatively young breeds created by crossing several local breeds. The breeds displaying low recombination rate are ancient local breeds: Cochin (Indo-China), Brown Leghorn (Tuscany, Italy) and Russian Crested (the European part of Russia).
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Affiliation(s)
- Lyubov P. Malinovskaya
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090,
Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Katerina V. Tishakova
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090,
Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Natalia A. Volkova
- L. K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy, 142132, Russia
| | - Anna A. Torgasheva
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090,
Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Yakov A. Tsepilov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090,
Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Pavel M. Borodin
- Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090,
Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
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21
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Aggarwal DD, Rybnikov S, Cohen I, Frenkel Z, Rashkovetsky E, Michalak P, Korol AB. Desiccation-induced changes in recombination rate and crossover interference in Drosophila melanogaster: evidence for fitness-dependent plasticity. Genetica 2019; 147:291-302. [PMID: 31240599 DOI: 10.1007/s10709-019-00070-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 06/18/2019] [Indexed: 12/31/2022]
Abstract
Meiotic recombination is evolutionarily ambiguous, as being associated with both benefits and costs to its bearers, with the resultant dependent on a variety of conditions. While existing theoretical models explain the emergence and maintenance of recombination, some of its essential features remain underexplored. Here we focus on one such feature, recombination plasticity, and test whether recombination response to stress is fitness-dependent. We compare desiccation stress effects on recombination rate and crossover interference in chromosome 3 between desiccation-sensitive and desiccation-tolerant Drosophila lines. We show that relative to desiccation-tolerant genotypes, desiccation-sensitive genotypes exhibit a significant segment-specific increase in single- and double-crossover frequencies across the pericentromeric region of chromosome 3. Significant changes (relaxation) in crossover interference were found for the interval pairs flanking the centromere and extending to the left arm of the chromosome. These results indicate that desiccation is a recombinogenic factor and that desiccation-induced changes in both recombination rate and crossover interference are fitness-dependent, with a tendency of less fitted individuals to produce more variable progeny. Such dependence may play an important role in the regulation of genetic variation in populations experiencing environmental challenges.
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Affiliation(s)
- Dau Dayal Aggarwal
- Institute of Evolution, University of Haifa, 3498838, Haifa, Israel.,Department of Zoology, Banaras Hindu University, Varanasi, 221005, India
| | - Sviatoslav Rybnikov
- Institute of Evolution, University of Haifa, 3498838, Haifa, Israel.,Department of Evolutionary and Environmental Biology, University of Haifa, 3498838, Haifa, Israel
| | - Irit Cohen
- Institute of Evolution, University of Haifa, 3498838, Haifa, Israel.,Department of Evolutionary and Environmental Biology, University of Haifa, 3498838, Haifa, Israel
| | - Zeev Frenkel
- Department of Mathematics and Computational Science, Ariel University, 40700, Ariel, Israel
| | | | - Pawel Michalak
- Institute of Evolution, University of Haifa, 3498838, Haifa, Israel.,Edward Via College of Osteopathic Medicine, Blacksburg, VA, 24060, USA.,Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, 24060, USA
| | - Abraham B Korol
- Institute of Evolution, University of Haifa, 3498838, Haifa, Israel. .,Department of Evolutionary and Environmental Biology, University of Haifa, 3498838, Haifa, Israel.
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22
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Wang S, Veller C, Sun F, Ruiz-Herrera A, Shang Y, Liu H, Zickler D, Chen Z, Kleckner N, Zhang L. Per-Nucleus Crossover Covariation and Implications for Evolution. Cell 2019; 177:326-338.e16. [PMID: 30879787 PMCID: PMC6472931 DOI: 10.1016/j.cell.2019.02.021] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 12/17/2018] [Accepted: 02/13/2019] [Indexed: 12/25/2022]
Abstract
Crossing over is a nearly universal feature of sexual reproduction. Here, analysis of crossover numbers on a per-chromosome and per-nucleus basis reveals a fundamental, evolutionarily conserved feature of meiosis: within individual nuclei, crossover frequencies covary across different chromosomes. This effect results from per-nucleus covariation of chromosome axis lengths. Crossovers can promote evolutionary adaptation. However, the benefit of creating favorable new allelic combinations must outweigh the cost of disrupting existing favorable combinations. Covariation concomitantly increases the frequencies of gametes with especially high, or especially low, numbers of crossovers, and thus might concomitantly enhance the benefits of crossing over while reducing its costs. A four-locus population genetic model suggests that such an effect can pertain in situations where the environment fluctuates: hyper-crossover gametes are advantageous when the environment changes while hypo-crossover gametes are advantageous in periods of environmental stasis. These findings reveal a new feature of the basic meiotic program and suggest a possible adaptive advantage.
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Affiliation(s)
- Shunxin Wang
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China.
| | - Carl Veller
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA
| | - Fei Sun
- School of Medicine, Institute of Reproductive Medicine, Nantong University, Nantong, Jiangsu, China
| | - Aurora Ruiz-Herrera
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain; Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Yongliang Shang
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
| | - Hongbin Liu
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
| | - Denise Zickler
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex 91198, France
| | - Zijiang Chen
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Liangran Zhang
- Center for Reproductive Medicine, Shandong University, National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Key Laboratory of Reproductive Endocrinology of Ministry of Education, Jinan, Shandong 250001, China; Advanced Medical Research Institute, Shandong University, Jinan, Shandong 250014, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
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23
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Veller C, Kleckner N, Nowak MA. A rigorous measure of genome-wide genetic shuffling that takes into account crossover positions and Mendel's second law. Proc Natl Acad Sci U S A 2019; 116:1659-1668. [PMID: 30635424 PMCID: PMC6358705 DOI: 10.1073/pnas.1817482116] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Comparative studies in evolutionary genetics rely critically on evaluation of the total amount of genetic shuffling that occurs during gamete production. Such studies have been hampered by the absence of a direct measure of this quantity. Existing measures consider crossing-over by simply counting the average number of crossovers per meiosis. This is qualitatively inadequate, because the positions of crossovers along a chromosome are also critical: a crossover toward the middle of a chromosome causes more shuffling than a crossover toward the tip. Moreover, traditional measures fail to consider shuffling from independent assortment of homologous chromosomes (Mendel's second law). Here, we present a rigorous measure of genome-wide shuffling that does not suffer from these limitations. We define the parameter [Formula: see text] as the probability that the alleles at two randomly chosen loci are shuffled during gamete production. This measure can be decomposed into separate contributions from crossover number and position and from independent assortment. Intrinsic implications of this metric include the fact that [Formula: see text] is larger when crossovers are more evenly spaced, which suggests a selective advantage of crossover interference. Utilization of [Formula: see text] is enabled by powerful emergent methods for determining crossover positions either cytologically or by DNA sequencing. Application of our analysis to such data from human male and female reveals that (i) [Formula: see text] in humans is close to its maximum possible value of 1/2 and that (ii) this high level of shuffling is due almost entirely to independent assortment, the contribution of which is ∼30 times greater than that of crossovers.
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Affiliation(s)
- Carl Veller
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138
| | - Nancy Kleckner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138;
| | - Martin A Nowak
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138
- Department of Mathematics, Harvard University, Cambridge, MA 02138
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24
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Slomka S, Pilpel Y. Meiotic Recombination: Genetics' Good Old Scalpel. Cell 2018; 172:391-392. [PMID: 29373827 DOI: 10.1016/j.cell.2018.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In the era of genome engineering, a new study returns to classical genetics to decipher genotype-phenotype relationships in unprecedented throughput and with unprecedented accuracy. Capitalizing on natural variation in yeast strains and frequent meiotic recombination, She and Jarosz (2018) dissect and map to nucleotide resolution, simple and complex determinants of diverse phenotypic traits.
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Affiliation(s)
- Shai Slomka
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel.
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25
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Dapper AL, Payseur BA. Connecting theory and data to understand recombination rate evolution. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0469. [PMID: 29109228 DOI: 10.1098/rstb.2016.0469] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2017] [Indexed: 02/03/2023] Open
Abstract
Meiotic recombination is necessary for successful gametogenesis in most sexually reproducing organisms and is a fundamental genomic parameter, influencing the efficacy of selection and the fate of new mutations. The molecular and evolutionary functions of recombination should impose strong selective constraints on the range of recombination rates. Yet, variation in recombination rate is observed on a variety of genomic and evolutionary scales. In the past decade, empirical studies have described variation in recombination rate within genomes, between individuals, between sexes, between populations and between species. At the same time, theoretical work has provided an increasingly detailed picture of the evolutionary advantages to recombination. Perhaps surprisingly, the causes of natural variation in recombination rate remain poorly understood. We argue that empirical and theoretical approaches to understand the evolution of recombination have proceeded largely independently of each other. Most models that address the evolution of recombination rate were created to explain the evolutionary advantage of recombination rather than quantitative differences in rate among individuals. Conversely, most empirical studies aim to describe variation in recombination rate, rather than to test evolutionary hypotheses. In this Perspective, we argue that efforts to integrate the rich bodies of empirical and theoretical work on recombination rate are crucial to moving this field forward. We provide new directions for the development of theory and the production of data that will jointly close this gap.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'.
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Affiliation(s)
- Amy L Dapper
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin, Madison, WI 53706, USA
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26
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Rybnikov SR, Frenkel ZM, Korol AB. What drives the evolution of condition-dependent recombination in diploids? Some insights from simulation modelling. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0460. [PMID: 29109223 DOI: 10.1098/rstb.2016.0460] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2017] [Indexed: 12/15/2022] Open
Abstract
While the evolutionary advantages of non-zero recombination rates have prompted diverse theoretical explanations, the evolution of essential recombination features remains underexplored. We focused on one such feature, the condition dependence of recombination, viewed as the variation in within-generation sensitivity of recombination to external (environment) and/or internal (genotype) conditions. Limited empirical evidence for its existence comes mainly from diploids, whereas theoretical models show that it only easily evolves in haploids. The evolution of condition-dependent recombination can be explained by its advantage for the selected system (indirect effect), or by benefits to modifier alleles, ensuring this strategy regardless of effects on the selected system (direct effect). We considered infinite panmictic populations of diploids exposed to a cyclical two-state environment. Each organism had three selected loci. Examining allele dynamics at a fourth, selectively neutral recombination modifier locus, we frequently observed that a modifier allele conferring condition-dependent recombination between the selected loci displaced the allele conferring the optimal constant recombination rate. Our simulations also confirm the results of theoretical studies showing that condition-dependent recombination cannot evolve in diploids on the basis of direct fitness-dependent effects alone. Therefore, the evolution of condition-dependent recombination in diploids can be driven by indirect effects alone, i.e. by modifier effects on the selected system.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'.
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Affiliation(s)
| | - Zeev M Frenkel
- Institute of Evolution, University of Haifa, Haifa, Israel
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27
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Matveevsky S, Ivanitskaya E, Spangenberg V, Bakloushinskaya I, Kolomiets O. Reorganization of the Y Chromosomes Enhances Divergence in Israeli Mole Rats Nannospalax ehrenbergi (Spalacidae, Rodentia): Comparative Analysis of Meiotic and Mitotic Chromosomes. Genes (Basel) 2018; 9:genes9060272. [PMID: 29794981 PMCID: PMC6027163 DOI: 10.3390/genes9060272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/18/2018] [Accepted: 05/22/2018] [Indexed: 12/14/2022] Open
Abstract
The Y chromosome in mammals is variable, even in closely related species. Middle East blind mole rats Nannospalax ehrenbergi demonstrate autosomal variability, which probably leads to speciation. Here, we compare the mitotic and meiotic chromosomes of mole rats. For the first time, we studied the behavior of their sex chromosomes in the meiotic prophase I using electron microscopy and immunocytochemical analysis. Unexpectedly, the sex chromosomes of the 52- and 60-chromosome forms of mole rats showed different synaptic and recombination patterns due to distinct locations of the centromeres on the Y chromosomes. The absence of recombination in the 60-chromosome form, the asymmetric synapsis, and the short-term disturbance in the synaptic co-orientation of the telomeric regions of the X and Y chromosomes were revealed as specific features of mole rat sex bivalents. We suggest several scenarios of Y chromosome alteration in connection with species differentiation in mole rats.
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Affiliation(s)
- Sergey Matveevsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.
| | | | - Victor Spangenberg
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.
| | - Irina Bakloushinskaya
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow 119334, Russia.
| | - Oxana Kolomiets
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia.
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28
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Bikchurina TI, Tishakova KV, Kizilova EA, Romanenko SA, Serdyukova NA, Torgasheva AA, Borodin PM. Chromosome Synapsis and Recombination in Male-Sterile and Female-Fertile Interspecies Hybrids of the Dwarf Hamsters ( Phodopus, Cricetidae). Genes (Basel) 2018; 9:genes9050227. [PMID: 29693587 PMCID: PMC5977167 DOI: 10.3390/genes9050227] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/09/2018] [Accepted: 04/18/2018] [Indexed: 02/06/2023] Open
Abstract
Hybrid sterility is an important step in the speciation process. Hybrids between dwarf hamsters Phodopus sungorus and P.campbelli provide a good model for studies in cytological and genetic mechanisms of hybrid sterility. Previous studies in hybrids detected multiple abnormalities of spermatogenesis and a high frequency of dissociation between the X and Y chromosomes at the meiotic prophase. In this study, we found that the autosomes of the hybrid males and females underwent paring and recombination as normally as their parental forms did. The male hybrids showed a significantly higher frequency of asynapsis and recombination failure between the heterochromatic arms of the X and Y chromosomes than the males of the parental species. Female hybrids as well as the females of the parental species demonstrated a high incidence of centromere misalignment at the XX bivalent and partial asynapsis of the ends of its heterochromatic arms. In all three karyotypes, recombination was completely suppressed in the heterochromatic arm of the X chromosome, where the pseudoautosomal region is located. We propose that this recombination pattern speeds up divergence of the X- and Y-linked pseudoautosomal regions between the parental species and results in their incompatibility in the male hybrids.
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Affiliation(s)
- Tatiana I Bikchurina
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
- Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Katerina V Tishakova
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
- Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Elena A Kizilova
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
- Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Svetlana A Romanenko
- Novosibirsk State University, Novosibirsk 630090, Russia.
- Institute of Cell and Molecular Biology, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
| | - Natalya A Serdyukova
- Institute of Cell and Molecular Biology, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
| | - Anna A Torgasheva
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
- Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Pavel M Borodin
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Department, Novosibirsk 630090, Russia.
- Novosibirsk State University, Novosibirsk 630090, Russia.
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29
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Capilla L, Sánchez-Guillén RA, Farré M, Paytuví-Gallart A, Malinverni R, Ventura J, Larkin DM, Ruiz-Herrera A. Mammalian Comparative Genomics Reveals Genetic and Epigenetic Features Associated with Genome Reshuffling in Rodentia. Genome Biol Evol 2018; 8:3703-3717. [PMID: 28175287 PMCID: PMC5521730 DOI: 10.1093/gbe/evw276] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2016] [Indexed: 12/16/2022] Open
Abstract
Understanding how mammalian genomes have been reshuffled through structural changes is fundamental to the dynamics of its composition, evolutionary relationships between species and, in the long run, speciation. In this work, we reveal the evolutionary genomic landscape in Rodentia, the most diverse and speciose mammalian order, by whole-genome comparisons of six rodent species and six representative outgroup mammalian species. The reconstruction of the evolutionary breakpoint regions across rodent phylogeny shows an increased rate of genome reshuffling that is approximately two orders of magnitude greater than in other mammalian species here considered. We identified novel lineage and clade-specific breakpoint regions within Rodentia and analyzed their gene content, recombination rates and their relationship with constitutive lamina genomic associated domains, DNase I hypersensitivity sites and chromatin modifications. We detected an accumulation of protein-coding genes in evolutionary breakpoint regions, especially genes implicated in reproduction and pheromone detection and mating. Moreover, we found an association of the evolutionary breakpoint regions with active chromatin state landscapes, most probably related to gene enrichment. Our results have two important implications for understanding the mechanisms that govern and constrain mammalian genome evolution. The first is that the presence of genes related to species-specific phenotypes in evolutionary breakpoint regions reinforces the adaptive value of genome reshuffling. Second, that chromatin conformation, an aspect that has been often overlooked in comparative genomic studies, might play a role in modeling the genomic distribution of evolutionary breakpoints.
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Affiliation(s)
- Laia Capilla
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Rosa Ana Sánchez-Guillén
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Apartado, Mexico
| | - Marta Farré
- Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Apartado, Mexico
| | - Andreu Paytuví-Gallart
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, London, UK.,Sequentia Biotech S.L. Calle Comte d'Urgell, Barcelona, Spain
| | - Roberto Malinverni
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Jacint Ventura
- Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Denis M Larkin
- Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Apartado, Mexico
| | - Aurora Ruiz-Herrera
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Sequentia Biotech S.L. Calle Comte d'Urgell, Barcelona, Spain
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30
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She R, Jarosz DF. Mapping Causal Variants with Single-Nucleotide Resolution Reveals Biochemical Drivers of Phenotypic Change. Cell 2018; 172:478-490.e15. [PMID: 29373829 PMCID: PMC5788306 DOI: 10.1016/j.cell.2017.12.015] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 10/21/2017] [Accepted: 12/06/2017] [Indexed: 12/13/2022]
Abstract
Understanding the sequence determinants that give rise to diversity among individuals and species is the central challenge of genetics. However, despite ever greater numbers of sequenced genomes, most genome-wide association studies cannot distinguish causal variants from linked passenger mutations spanning many genes. We report that this inherent challenge can be overcome in model organisms. By pushing the advantages of inbred crossing to its practical limit in Saccharomyces cerevisiae, we improved the statistical resolution of linkage analysis to single nucleotides. This "super-resolution" approach allowed us to map 370 causal variants across 26 quantitative traits. Missense, synonymous, and cis-regulatory mutations collectively gave rise to phenotypic diversity, providing mechanistic insight into the basis of evolutionary divergence. Our data also systematically unmasked complex genetic architectures, revealing that multiple closely linked driver mutations frequently act on the same quantitative trait. Single-nucleotide mapping thus complements traditional deletion and overexpression screening paradigms and opens new frontiers in quantitative genetics.
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Affiliation(s)
- Richard She
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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31
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del Priore L, Pigozzi MI. Broad-scale recombination pattern in the primitive bird Rhea americana (Ratites, Palaeognathae). PLoS One 2017; 12:e0187549. [PMID: 29095930 PMCID: PMC5667853 DOI: 10.1371/journal.pone.0187549] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/20/2017] [Indexed: 12/02/2022] Open
Abstract
Birds have genomic and chromosomal features that make them an attractive group to analyze the evolution of recombination rate and the distribution of crossing over. Yet, analyses are biased towards certain species, especially domestic poultry and passerines. Here we analyze for the first time the recombination rate and crossover distribution in the primitive ratite bird, Rhea americana (Rheiformes, Palaeognathae). Using a cytogenetic approach for in situ mapping of crossovers we found that the total genetic map is 3050 cM with a global recombination rate of 2.1 cM/Mb for female rheas. In the five largest macrobivalents there were 3 or more crossovers in most bivalents. Recombination rates for macrobivalents ranges between 1.8-2.1 cM/Mb and the physical length of their synaptonemal complexes is highly predictive of their genetic lengths. The crossover rate at the pseudoautosomal region is 2.1 cM/Mb, similar to those of autosomal pairs 5 and 6 and only slightly higher compared to other macroautosomes. It is suggested that the presence of multiple crossovers on the largest macrobivalents is a feature common to many avian groups, irrespective of their position throughout phylogeny. These data provide new insights to analyze the heterogeneous recombination landscape of birds.
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Affiliation(s)
- Lucía del Priore
- INBIOMED Instituto de Investigaciones Biomédicas UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Inés Pigozzi
- INBIOMED Instituto de Investigaciones Biomédicas UBA-CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
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32
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Chromosome Synapsis and Recombination in Male Hybrids between Two Chromosome Races of the Common Shrew (Sorex araneus L., Soricidae, Eulipotyphla). Genes (Basel) 2017; 8:genes8100282. [PMID: 29053571 PMCID: PMC5664132 DOI: 10.3390/genes8100282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/08/2017] [Accepted: 10/17/2017] [Indexed: 11/17/2022] Open
Abstract
Hybrid zones between chromosome races of the common shrew (Sorex araneus) provide exceptional models to study the potential role of chromosome rearrangements in the initial steps of speciation. The Novosibirsk and Tomsk races differ by a series of Robertsonian fusions with monobrachial homology. They form a narrow hybrid zone and generate hybrids with both simple (chain of three chromosomes) and complex (chain of eight or nine) synaptic configurations. Using immunolocalisation of the meiotic proteins, we examined chromosome pairing and recombination in males from the hybrid zone. Homozygotes and simple heterozygotes for Robertsonian fusions showed a low frequency of synaptic aberrations (<10%). The carriers of complex synaptic configurations showed multiple pairing abnormalities, which might lead to reduced fertility. The recombination frequency in the proximal regions of most chromosomes of all karyotypes was much lower than in the other regions. The strong suppression of recombination in the pericentromeric regions and co-segregation of race specific chromosomes involved in the long chains would be expected to lead to linkage disequilibrium between genes located there. Genic differentiation, together with the high frequency of pairing aberrations in male carriers of the long chains, might contribute to maintenance of the narrow hybrid zone.
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33
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Sun L, Wang J, Sang M, Jiang L, Zhao B, Cheng T, Zhang Q, Wu R. Landscaping Crossover Interference Across a Genome. TRENDS IN PLANT SCIENCE 2017; 22:894-907. [PMID: 28822625 DOI: 10.1016/j.tplants.2017.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 06/09/2017] [Accepted: 06/12/2017] [Indexed: 05/14/2023]
Abstract
The evolutionary success of eukaryotic organisms crucially depends on the capacity to produce genetic diversity through reciprocal exchanges of each chromosome pair, or crossovers (COs), during meiosis. It has been recognized that COs arise more evenly across a given chromosome than at random. This phenomenon, termed CO interference, occurs pervasively in eukaryotes and may confer a selective advantage. We describe here a multipoint linkage analysis procedure for segregating families to quantify the strength of CO interference over the genome, and extend this procedure to illustrate the landscape of CO interference in natural populations. We further discuss the crucial role of CO interference in amplifying and maintaining genetic diversity through sex-, stress-, and age-induced differentiation.
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Affiliation(s)
- Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
| | - Jing Wang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Mengmeng Sang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Libo Jiang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
| | - Bingyu Zhao
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061, USA
| | - Tangran Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing 100083, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; Center for Statistical Genetics, Pennsylvania State University, Hershey, PA 17033, USA.
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34
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Ruiz-Herrera A, Vozdova M, Fernández J, Sebestova H, Capilla L, Frohlich J, Vara C, Hernández-Marsal A, Sipek J, Robinson TJ, Rubes J. Recombination correlates with synaptonemal complex length and chromatin loop size in bovids-insights into mammalian meiotic chromosomal organization. Chromosoma 2017; 126:615-631. [PMID: 28101670 DOI: 10.1007/s00412-016-0624-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 11/14/2016] [Accepted: 12/12/2016] [Indexed: 11/25/2022]
Abstract
Homologous chromosomes exchange genetic information through recombination during meiosis, a process that increases genetic diversity, and is fundamental to sexual reproduction. In an attempt to shed light on the dynamics of mammalian recombination and its implications for genome organization, we have studied the recombination characteristics of 112 individuals belonging to 28 different species in the family Bovidae. In particular, we analyzed the distribution of RAD51 and MLH1 foci during the meiotic prophase I that serve, respectively, as proxies for double-strand breaks (DSBs) which form in early stages of meiosis and for crossovers. In addition, synaptonemal complex length and meiotic DNA loop size were estimated to explore how genome organization determines DSBs and crossover patterns. We show that although the number of meiotic DSBs per cell and recombination rates observed vary between individuals of the same species, these are correlated with diploid number as well as with synaptonemal complex and DNA loop sizes. Our results illustrate that genome packaging, DSB frequencies, and crossover rates tend to be correlated, while meiotic chromosomal axis length and DNA loop size are inversely correlated in mammals. Moreover, axis length, DSB frequency, and crossover frequencies all covary, suggesting that these correlations are established in the early stages of meiosis.
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Affiliation(s)
- Aurora Ruiz-Herrera
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Barcelona, Spain. .,Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Miluse Vozdova
- Central European Institute of Technology - Veterinary Research Institute, Brno, Czech Republic
| | - Jonathan Fernández
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Hana Sebestova
- Central European Institute of Technology - Veterinary Research Institute, Brno, Czech Republic
| | - Laia Capilla
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jan Frohlich
- Central European Institute of Technology - Veterinary Research Institute, Brno, Czech Republic
| | - Covadonga Vara
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Adrià Hernández-Marsal
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jaroslav Sipek
- Central European Institute of Technology - Veterinary Research Institute, Brno, Czech Republic
| | - Terence J Robinson
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Stellenbosch, South Africa
| | - Jiri Rubes
- Central European Institute of Technology - Veterinary Research Institute, Brno, Czech Republic
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35
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Wang RJ, Gray MM, Parmenter MD, Broman KW, Payseur BA. Recombination rate variation in mice from an isolated island. Mol Ecol 2016; 26:457-470. [PMID: 27864900 DOI: 10.1111/mec.13932] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 11/09/2016] [Accepted: 11/14/2016] [Indexed: 01/14/2023]
Abstract
Recombination rate is a heritable trait that varies among individuals. Despite the major impact of recombination rate on patterns of genetic diversity and the efficacy of selection, natural variation in this phenotype remains poorly characterized. We present a comparison of genetic maps, sampling 1212 meioses, from a unique population of wild house mice (Mus musculus domesticus) that recently colonized remote Gough Island. Crosses to a mainland reference strain (WSB/EiJ) reveal pervasive variation in recombination rate among Gough Island mice, including subchromosomal intervals spanning up to 28% of the genome. In spite of this high level of polymorphism, the genomewide recombination rate does not significantly vary. In general, we find that recombination rate varies more when measured in smaller genomic intervals. Using the current standard genetic map of the laboratory mouse to polarize intervals with divergent recombination rates, we infer that the majority of evolutionary change occurred in one of the two tested lines of Gough Island mice. Our results confirm that natural populations harbour a high level of recombination rate polymorphism and highlight the disparities in recombination rate evolution across genomic scales.
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Affiliation(s)
- Richard J Wang
- Laboratory of Genetics, University of Wisconsin - Madison, 425-G Henry Mall, 2428 Genetics, Madison, WI, 53706, USA
| | - Melissa M Gray
- Laboratory of Genetics, University of Wisconsin - Madison, 425-G Henry Mall, 2428 Genetics, Madison, WI, 53706, USA
| | - Michelle D Parmenter
- Laboratory of Genetics, University of Wisconsin - Madison, 425-G Henry Mall, 2428 Genetics, Madison, WI, 53706, USA
| | - Karl W Broman
- Department of Biostatistics & Medical Informatics, University of Wisconsin - Madison, Madison, WI, 53706, USA
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin - Madison, 425-G Henry Mall, 2428 Genetics, Madison, WI, 53706, USA
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Variation and Evolution of the Meiotic Requirement for Crossing Over in Mammals. Genetics 2016; 205:155-168. [PMID: 27838628 PMCID: PMC5223500 DOI: 10.1534/genetics.116.192690] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 11/03/2016] [Indexed: 01/08/2023] Open
Abstract
The segregation of homologous chromosomes at the first meiotic division is dependent on the presence of at least one well-positioned crossover per chromosome. In some mammalian species, however, the genomic distribution of crossovers is consistent with a more stringent baseline requirement of one crossover per chromosome arm. Given that the meiotic requirement for crossing over defines the minimum frequency of recombination necessary for the production of viable gametes, determining the chromosomal scale of this constraint is essential for defining crossover profiles predisposed to aneuploidy and understanding the parameters that shape patterns of recombination rate evolution across species. Here, I use cytogenetic methods for in situ imaging of crossovers in karyotypically diverse house mice (Mus musculus domesticus) and voles (genus Microtus) to test how chromosome number and configuration constrain the distribution of crossovers in a genome. I show that the global distribution of crossovers in house mice is thresholded by a minimum of one crossover per chromosome arm, whereas the crossover landscape in voles is defined by a more relaxed requirement of one crossover per chromosome. I extend these findings in an evolutionary metaanalysis of published recombination and karyotype data for 112 mammalian species and demonstrate that the physical scale of the genomic crossover distribution has undergone multiple independent shifts from one crossover per chromosome arm to one per chromosome during mammalian evolution. Together, these results indicate that the chromosomal scale constraint on crossover rates is itself a trait that evolves among species, a finding that casts light on an important source of crossover rate variation in mammals.
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Anderson C, Khan MA, Catanzariti AM, Jack CA, Nemri A, Lawrence GJ, Upadhyaya NM, Hardham AR, Ellis JG, Dodds PN, Jones DA. Genome analysis and avirulence gene cloning using a high-density RADseq linkage map of the flax rust fungus, Melampsora lini. BMC Genomics 2016; 17:667. [PMID: 27550217 PMCID: PMC4994203 DOI: 10.1186/s12864-016-3011-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/11/2016] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Rust fungi are an important group of plant pathogens that cause devastating losses in agricultural, silvicultural and natural ecosystems. Plants can be protected from rust disease by resistance genes encoding receptors that trigger a highly effective defence response upon recognition of specific pathogen avirulence proteins. Identifying avirulence genes is crucial for understanding how virulence evolves in the field. RESULTS To facilitate avirulence gene cloning in the flax rust fungus, Melampsora lini, we constructed a high-density genetic linkage map using single nucleotide polymorphisms detected in restriction site-associated DNA sequencing (RADseq) data. The map comprises 13,412 RADseq markers in 27 linkage groups that together span 5860 cM and contain 2756 recombination bins. The marker sequences were used to anchor 68.9 % of the M. lini genome assembly onto the genetic map. The map and anchored assembly were then used to: 1) show that M. lini has a high overall meiotic recombination rate, but recombination distribution is uneven and large coldspots exist; 2) show that substantial genome rearrangements have occurred in spontaneous loss-of-avirulence mutants; and 3) identify the AvrL2 and AvrM14 avirulence genes by map-based cloning. AvrM14 is a dual-specificity avirulence gene that encodes a predicted nudix hydrolase. AvrL2 is located in the region of the M. lini genome with the lowest recombination rate and encodes a small, highly-charged proline-rich protein. CONCLUSIONS The M. lini high-density linkage map has greatly advanced our understanding of virulence mechanisms in this pathogen by providing novel insights into genome variability and enabling identification of two new avirulence genes.
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Affiliation(s)
- Claire Anderson
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601 Australia
| | - Muhammad Adil Khan
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601 Australia
- Current address: ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - Ann-Maree Catanzariti
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601 Australia
| | - Cameron A. Jack
- ANU Bioinformatics Consulting Unit, The John Curtin School of Medical Research, The Australian National University, 131 Garran Road, Acton, ACT 2601 Australia
| | - Adnane Nemri
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601 Australia
- Current address: KWS SAAT SE, Grimsehlstraße 31, Einbeck, 37574 Germany
| | | | | | - Adrienne R. Hardham
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601 Australia
| | | | - Peter N. Dodds
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601 Australia
| | - David A. Jones
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601 Australia
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Matveevsky S, Bakloushinskaya I, Kolomiets O. Unique sex chromosome systems in Ellobius: How do male XX chromosomes recombine and undergo pachytene chromatin inactivation? Sci Rep 2016; 6:29949. [PMID: 27425629 PMCID: PMC4947958 DOI: 10.1038/srep29949] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/27/2016] [Indexed: 01/09/2023] Open
Abstract
Most mammalian species have heteromorphic sex chromosomes in males, except for a few enigmatic groups such as the mole voles Ellobius, which do not have the Y chromosome and Sry gene. The Ellobius (XX ♀♂) system of sex chromosomes has no analogues among other animals. The structure and meiotic behaviour of the two X chromosomes were investigated for males of the sibling species Ellobius talpinus and Ellobius tancrei. Their sex chromosomes, despite their identical G-structure, demonstrate short synaptic fragments and crossover-associated MLH1 foci in both telomeric regions only. The chromatin undergoes modifications in the meiotic sex chromosomes. SUMO-1 marks a small nucleolus-like body of the meiotic XX. ATR and ubiH2A are localized in the asynaptic area and the histone γH2AFX covers the entire XX bivalent. The distribution of some markers of chromatin inactivation differentiates sex chromosomes of mole voles from those of other mammals. Sex chromosomes of both studied species have identical recombination and meiotic inactivation patterns. In Ellobius, similar chromosome morphology masks the functional heteromorphism of the male sex chromosomes, which can be seen at meiosis.
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Affiliation(s)
- Sergey Matveevsky
- Cytogenetics Laboratory, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Irina Bakloushinskaya
- Evolutionary and Developmental Genetics Laboratory, N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Oxana Kolomiets
- Cytogenetics Laboratory, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
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Li G, Hillier LW, Grahn RA, Zimin AV, David VA, Menotti-Raymond M, Middleton R, Hannah S, Hendrickson S, Makunin A, O'Brien SJ, Minx P, Wilson RK, Lyons LA, Warren WC, Murphy WJ. A High-Resolution SNP Array-Based Linkage Map Anchors a New Domestic Cat Draft Genome Assembly and Provides Detailed Patterns of Recombination. G3 (BETHESDA, MD.) 2016; 6:1607-16. [PMID: 27172201 PMCID: PMC4889657 DOI: 10.1534/g3.116.028746] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/23/2016] [Indexed: 01/03/2023]
Abstract
High-resolution genetic and physical maps are invaluable tools for building accurate genome assemblies, and interpreting results of genome-wide association studies (GWAS). Previous genetic and physical maps anchored good quality draft assemblies of the domestic cat genome, enabling the discovery of numerous genes underlying hereditary disease and phenotypes of interest to the biomedical science and breeding communities. However, these maps lacked sufficient marker density to order thousands of shorter scaffolds in earlier assemblies, which instead relied heavily on comparative mapping with related species. A high-resolution map would aid in validating and ordering chromosome scaffolds from existing and new genome assemblies. Here, we describe a high-resolution genetic linkage map of the domestic cat genome based on genotyping 453 domestic cats from several multi-generational pedigrees on the Illumina 63K SNP array. The final maps include 58,055 SNP markers placed relative to 6637 markers with unique positions, distributed across all autosomes and the X chromosome. Our final sex-averaged maps span a total autosomal length of 4464 cM, the longest described linkage map for any mammal, confirming length estimates from a previous microsatellite-based map. The linkage map was used to order and orient the scaffolds from a substantially more contiguous domestic cat genome assembly (Felis catus v8.0), which incorporated ∼20 × coverage of Illumina fragment reads. The new genome assembly shows substantial improvements in contiguity, with a nearly fourfold increase in N50 scaffold size to 18 Mb. We use this map to report probable structural errors in previous maps and assemblies, and to describe features of the recombination landscape, including a massive (∼50 Mb) recombination desert (of virtually zero recombination) on the X chromosome that parallels a similar desert on the porcine X chromosome in both size and physical location.
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Affiliation(s)
- Gang Li
- Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843
| | - LaDeana W Hillier
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Robert A Grahn
- College of Veterinary Medicine, University of Missouri-Columbia, Missouri 65201 Population Health and Reproduction, University of California-Davis, California 95616
| | - Aleksey V Zimin
- Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742
| | - Victor A David
- National Cancer Institute-Frederick, National Institutes of Health, Maryland 21702
| | | | | | - Steven Hannah
- Nestlé Purina PetCare Company, St. Louis, Missouri 63134
| | - Sher Hendrickson
- Department of Biology, Shepherd University, Shepherdstown, West Virginia 25443 Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia
| | - Alex Makunin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia
| | - Stephen J O'Brien
- National Cancer Institute-Frederick, National Institutes of Health, Maryland 21702 Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Russia
| | - Pat Minx
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Leslie A Lyons
- College of Veterinary Medicine, University of Missouri-Columbia, Missouri 65201 Population Health and Reproduction, University of California-Davis, California 95616
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843
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40
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Smeds L, Mugal CF, Qvarnström A, Ellegren H. High-Resolution Mapping of Crossover and Non-crossover Recombination Events by Whole-Genome Re-sequencing of an Avian Pedigree. PLoS Genet 2016; 12:e1006044. [PMID: 27219623 PMCID: PMC4878770 DOI: 10.1371/journal.pgen.1006044] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 04/19/2016] [Indexed: 01/04/2023] Open
Abstract
Recombination is an engine of genetic diversity and therefore constitutes a key process in evolutionary biology and genetics. While the outcome of crossover recombination can readily be detected as shuffled alleles by following the inheritance of markers in pedigreed families, the more precise location of both crossover and non-crossover recombination events has been difficult to pinpoint. As a consequence, we lack a detailed portrait of the recombination landscape for most organisms and knowledge on how this landscape impacts on sequence evolution at a local scale. To localize recombination events with high resolution in an avian system, we performed whole-genome re-sequencing at high coverage of a complete three-generation collared flycatcher pedigree. We identified 325 crossovers at a median resolution of 1.4 kb, with 86% of the events localized to <10 kb intervals. Observed crossover rates were in excellent agreement with data from linkage mapping, were 52% higher in male (3.56 cM/Mb) than in female meiosis (2.28 cM/Mb), and increased towards chromosome ends in male but not female meiosis. Crossover events were non-randomly distributed in the genome with several distinct hot-spots and a concentration to genic regions, with the highest density in promoters and CpG islands. We further identified 267 non-crossovers, whose location was significantly associated with crossover locations. We detected a significant transmission bias (0.18) in favour of 'strong' (G, C) over 'weak' (A, T) alleles at non-crossover events, providing direct evidence for the process of GC-biased gene conversion in an avian system. The approach taken in this study should be applicable to any species and would thereby help to provide a more comprehensive portray of the recombination landscape across organism groups.
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Affiliation(s)
- Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Carina F. Mugal
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Anna Qvarnström
- Department of Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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41
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Meiotic behaviour of evolutionary sex-autosome translocations in Bovidae. Chromosome Res 2016; 24:325-38. [PMID: 27136937 DOI: 10.1007/s10577-016-9524-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 04/12/2016] [Accepted: 04/17/2016] [Indexed: 10/21/2022]
Abstract
The recurrent occurrence of sex-autosome translocations during mammalian evolution suggests common mechanisms enabling a precise control of meiotic synapsis, recombination and inactivation of sex chromosomes. We used immunofluorescence and FISH to study the meiotic behaviour of sex chromosomes in six species of Bovidae with evolutionary sex-autosome translocations (Tragelaphus strepsiceros, Taurotragus oryx, Tragelaphus imberbis, Tragelaphus spekii, Gazella leptoceros and Nanger dama ruficollis). The autosomal regions of fused sex chromosomes showed normal synapsis with their homologous counterparts. Synapsis in the pseudoautosomal region (PAR) leads to the formation of characteristic bivalent (in T. imberbis and T. spekii with X;BTA13/Y;BTA13), trivalent (in T. strepsiceros and T. oryx with X/Y;BTA13 and G. leptoceros with X;BTA5/Y) and quadrivalent (in N. dama ruficollis with X;BTA5/Y;BTA16) structures at pachynema. However, when compared with other mammals, the number of pachynema lacking MLH1 foci in the PAR was relatively high, especially in T. imberbis and T. spekii, species with both sex chromosomes involved in sex autosome translocations. Meiotic transcriptional inactivation of the sex-autosome translocations assessed by γH2AX staining was restricted to their gonosomal regions. Despite intraspecies differences, the evolutionary fixation of sex-autosome translocations among bovids appears to involve general mechanisms ensuring sex chromosome pairing, synapsis, recombination and inactivation.
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42
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Limborg MT, McKinney GJ, Seeb LW, Seeb JE. Recombination patterns reveal information about centromere location on linkage maps. Mol Ecol Resour 2015; 16:655-61. [PMID: 26561199 DOI: 10.1111/1755-0998.12484] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/29/2015] [Accepted: 11/04/2015] [Indexed: 12/22/2022]
Abstract
Linkage mapping is often used to identify genes associated with phenotypic traits and for aiding genome assemblies. Still, many emerging maps do not locate centromeres - an essential component of the genomic landscape. Here, we demonstrate that for genomes with strong chiasma interference, approximate centromere placement is possible by phasing the same data used to generate linkage maps. Assuming one obligate crossover per chromosome arm, information about centromere location can be revealed by tracking the accumulated recombination frequency along linkage groups, similar to half-tetrad analyses. We validate the method on a linkage map for sockeye salmon (Oncorhynchus nerka) with known centromeric regions. Further tests suggest that the method will work well in other salmonids and other eukaryotes. However, the method performed weakly when applied to a male linkage map (rainbow trout; O. mykiss) characterized by low and unevenly distributed recombination - a general feature of male meiosis in many species. Further, a high frequency of double crossovers along chromosome arms in barley reduced resolution for locating centromeric regions on most linkage groups. Despite these limitations, our method should work well for high-density maps in species with strong recombination interference and will enrich many existing and future mapping resources.
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Affiliation(s)
- Morten T Limborg
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195, USA.,National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark
| | - Garrett J McKinney
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195, USA
| | - Lisa W Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195, USA
| | - James E Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195, USA
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43
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Mugal CF, Weber CC, Ellegren H. GC-biased gene conversion links the recombination landscape and demography to genomic base composition. Bioessays 2015; 37:1317-26. [DOI: 10.1002/bies.201500058] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Carina F. Mugal
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Claudia C. Weber
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
- Department of Biology; Center for Computational Genetics and Genomics; Temple University; Philadelphia PA USA
| | - Hans Ellegren
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
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44
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Fröhlich J, Vozdova M, Kubickova S, Cernohorska H, Sebestova H, Rubes J. Variation of Meiotic Recombination Rates and MLH1 Foci Distribution in Spermatocytes of Cattle, Sheep and Goats. Cytogenet Genome Res 2015; 146:211-21. [PMID: 26406935 DOI: 10.1159/000439452] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2015] [Indexed: 11/19/2022] Open
Abstract
Despite similar genome sizes, a great variability in recombination rates is observed in mammals. We used antibodies against SYCP3, MLH1 and centromeres to compare crossover frequency, position along chromosome arms and the effect of crossover interference in spermatocytes of 4 species from the family Bovidae (Bos taurus, 2n = 60, tribe Bovini; Ovis aries, 2n = 54, Capra hircus, 2n = 60 and Ammotragus lervia, 2n = 58, tribe Caprini). Despite significant individual variability, our results also show significant differences in both recombination rates and the total length of autosomal synaptonemal complexes (SC) between cattle (47.53 MLH1 foci/cell, 244.59 µm) and members of the tribe Caprini (61.83 MLH1 foci, 296.19 µm) which can be explained by the length of time that has passed since their evolutionary divergence. Sheep displayed the highest number of MLH1 foci per cell and recombination density, although they have a lower diploid chromosome number caused by centric fusions corresponding to cattle chromosomes 1;3, 2;8 and 5;11. However, the proportion of MLH1 foci observed on the fused chromosomes in sheep (26.14%) was significantly lower than on the orthologous acrocentrics in cattle (27.6%) and goats (28.2%), and their distribution along the SC arms differed significantly. The reduced recombination rate in metacentrics is probably caused by interference acting across the centromere.
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Affiliation(s)
- Jan Fröhlich
- Central European Institute of Technology - Veterinary Research Institute, Brno, Czech Republic
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45
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Limborg MT, Waples RK, Allendorf FW, Seeb JE. Linkage Mapping Reveals Strong Chiasma Interference in Sockeye Salmon: Implications for Interpreting Genomic Data. G3 (BETHESDA, MD.) 2015; 5:2463-73. [PMID: 26384769 PMCID: PMC4632065 DOI: 10.1534/g3.115.020222] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/14/2015] [Indexed: 01/15/2023]
Abstract
Meiotic recombination is fundamental for generating new genetic variation and for securing proper disjunction. Further, recombination plays an essential role during the rediploidization process of polyploid-origin genomes because crossovers between pairs of homeologous chromosomes retain duplicated regions. A better understanding of how recombination affects genome evolution is crucial for interpreting genomic data; unfortunately, current knowledge mainly originates from a few model species. Salmonid fishes provide a valuable system for studying the effects of recombination in nonmodel species. Salmonid females generally produce thousands of embryos, providing large families for conducting inheritance studies. Further, salmonid genomes are currently rediploidizing after a whole genome duplication and can serve as models for studying the role of homeologous crossovers on genome evolution. Here, we present a detailed interrogation of recombination patterns in sockeye salmon (Oncorhynchus nerka). First, we use RAD sequencing of haploid and diploid gynogenetic families to construct a dense linkage map that includes paralogous loci and location of centromeres. We find a nonrandom distribution of paralogs that mainly cluster in extended regions distally located on 11 different chromosomes, consistent with ongoing homeologous recombination in these regions. We also estimate the strength of interference across each chromosome; results reveal strong interference and crossovers are mostly limited to one per arm. Interference was further shown to continue across centromeres, but metacentric chromosomes generally had at least one crossover on each arm. We discuss the relevance of these findings for both mapping and population genomic studies.
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Affiliation(s)
- Morten T Limborg
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington 98195 National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, Silkeborg, Denmark
| | - Ryan K Waples
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington 98195
| | - Fred W Allendorf
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812
| | - James E Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington 98195
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46
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Sebestova H, Vozdova M, Kubickova S, Cernohorska H, Kotrba R, Rubes J. Effect of species-specific differences in chromosome morphology on chromatin compaction and the frequency and distribution of RAD51 and MLH1 foci in two bovid species: cattle (Bos taurus) and the common eland (Taurotragus oryx). Chromosoma 2015; 125:137-49. [PMID: 26194101 DOI: 10.1007/s00412-015-0533-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 06/29/2015] [Accepted: 07/08/2015] [Indexed: 10/23/2022]
Abstract
Meiotic recombination between homologous chromosomes is crucial for their correct segregation into gametes and for generating diversity. We compared the frequency and distribution of MLH1 foci and RAD51 foci, synaptonemal complex (SC) length and DNA loop size in two related Bovidae species that share chromosome arm homology but show an extreme difference in their diploid chromosome number: cattle (Bos taurus, 2n = 60) and the common eland (Taurotragus oryx, 2nmale = 31). Compared to cattle, significantly fewer MLH1 foci per cell were observed in the common eland, which can be attributed to the lower number of initial double-strand breaks (DSBs) detected as RAD51 foci in leptonema. Despite the significantly shorter total autosomal SC length and longer DNA loop size of the common eland bi-armed chromosomes compared to those of bovine acrocentrics, the overall crossover density in the common eland was still lower than in cattle, probably due to the reduction in the number of MLH1 foci in the proximal regions of the bi-armed chromosomes. The formation of centric fusions during karyotype evolution of the common eland accompanied by meiotic chromatin compaction has greater implications in the reduction in the number of DSBs in leptonema than in the decrease of MLH1 foci number in pachynema.
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Affiliation(s)
- Hana Sebestova
- Central European Institute of Technology-Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic
| | - Miluse Vozdova
- Central European Institute of Technology-Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic.
| | - Svatava Kubickova
- Central European Institute of Technology-Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic
| | - Halina Cernohorska
- Central European Institute of Technology-Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic
| | - Radim Kotrba
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 21, Prague, Czech Republic
| | - Jiri Rubes
- Central European Institute of Technology-Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic
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47
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Ross CR, DeFelice DS, Hunt GJ, Ihle KE, Amdam GV, Rueppell O. Genomic correlates of recombination rate and its variability across eight recombination maps in the western honey bee (Apis mellifera L.). BMC Genomics 2015; 16:107. [PMID: 25765996 PMCID: PMC4339005 DOI: 10.1186/s12864-015-1281-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 01/26/2015] [Indexed: 12/02/2022] Open
Abstract
Background Meiotic recombination has traditionally been explained based on the structural requirement to stabilize homologous chromosome pairs to ensure their proper meiotic segregation. Competing hypotheses seek to explain the emerging findings of significant heterogeneity in recombination rates within and between genomes, but intraspecific comparisons of genome-wide recombination patterns are rare. The honey bee (Apis mellifera) exhibits the highest rate of genomic recombination among multicellular animals with about five cross-over events per chromatid. Results Here, we present a comparative analysis of recombination rates across eight genetic linkage maps of the honey bee genome to investigate which genomic sequence features are correlated with recombination rate and with its variation across the eight data sets, ranging in average marker spacing ranging from 1 Mbp to 120 kbp. Overall, we found that GC content explained best the variation in local recombination rate along chromosomes at the analyzed 100 kbp scale. In contrast, variation among the different maps was correlated to the abundance of microsatellites and several specific tri- and tetra-nucleotides. Conclusions The combined evidence from eight medium-scale recombination maps of the honey bee genome suggests that recombination rate variation in this highly recombining genome might be due to the DNA configuration instead of distinct sequence motifs. However, more fine-scale analyses are needed. The empirical basis of eight differing genetic maps allowed for robust conclusions about the correlates of the local recombination rates and enabled the study of the relation between DNA features and variability in local recombination rates, which is particularly relevant in the honey bee genome with its exceptionally high recombination rate. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1281-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Caitlin R Ross
- Department of Computer Sciences, The University of North Carolina at Greensboro, Greensboro, NC, 27402, USA.
| | - Dominick S DeFelice
- Department of Biology, 312 Eberhart Building, The University of North Carolina at Greensboro, 321 McIver Street, Greensboro, NC, 27402, USA.
| | - Greg J Hunt
- Department of Entomology, Purdue University, West Lafayette, IN, 47907, USA.
| | - Kate E Ihle
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA.
| | - Gro V Amdam
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA. .,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Aas, Norway.
| | - Olav Rueppell
- Department of Biology, 312 Eberhart Building, The University of North Carolina at Greensboro, 321 McIver Street, Greensboro, NC, 27402, USA.
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48
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Del Priore L, Pigozzi MI. Sex-specific recombination maps for individual macrochromosomes in the Japanese quail (Coturnix japonica). Chromosome Res 2015; 23:199-210. [PMID: 25596820 DOI: 10.1007/s10577-014-9448-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/25/2014] [Accepted: 11/26/2014] [Indexed: 11/29/2022]
Abstract
Meiotic recombination in the Japanese quail was directly studied by immunolocalization of mutL homolog 1 (MLH1), a mismatch repair protein of mature recombination nodules. In total, 15,862 crossovers were scored along the autosomal synaptonemal complexes in 308 meiotic nuclei from males and females. Crossover frequencies calculated from MLH1 foci show wide similitude between males and females with slightly higher number of foci in females. From this analysis, we predict that the sex-averaged map length of the Japanese quail is 2580 cM, with a genome-wide recombination rate of 1.9 cM/Mb. MLH1 focus mapping along the six largest bivalents showed few intersex differences in the distribution of crossovers along with variant patterns in metacentric and acrocentric macrobivalents. These results provide valuable information to complement linkage map analysis in the species while providing insight into our understanding of the mechanisms of crossover distribution along chromosome arms.
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Affiliation(s)
- Lucía Del Priore
- INBIOMED (CONICET-UBA), Facultad de Medicina, Universidad de Buenos Aires, Paraguay 2155 Piso 10, C1121ABG, Buenos Aires, Argentina
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49
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Capilla L, Medarde N, Alemany-Schmidt A, Oliver-Bonet M, Ventura J, Ruiz-Herrera A. Genetic recombination variation in wild Robertsonian mice: on the role of chromosomal fusions and Prdm9 allelic background. Proc Biol Sci 2015; 281:rspb.2014.0297. [PMID: 24850922 DOI: 10.1098/rspb.2014.0297] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Despite the existence of formal models to explain how chromosomal rearrangements can be fixed in a population in the presence of gene flow, few empirical data are available regarding the mechanisms by which genome shuffling contributes to speciation, especially in mammals. In order to shed light on this intriguing evolutionary process, here we present a detailed empirical study that shows how Robertsonian (Rb) fusions alter the chromosomal distribution of recombination events during the formation of the germline in a Rb system of the western house mouse (Mus musculus domesticus). Our results indicate that both the total number of meiotic crossovers and the chromosomal distribution of recombination events are reduced in mice with Rb fusions and that this can be related to alterations in epigenetic signatures for heterochromatinization. Furthermore, we detected novel house mouse Prdm9 allelic variants in the Rb system. Remarkably, mean recombination rates were positively correlated with a decrease in the number of ZnF domains in the Prdm9 gene. The suggestion that recombination can be modulated by both chromosomal reorganizations and genetic determinants that control the formation of double-stranded breaks during meiosis opens new avenues for understanding the role of recombination in chromosomal speciation.
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Affiliation(s)
- Laia Capilla
- Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Campus UAB 08193, Barcelona, Spain Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Campus UAB 08193, Barcelona, Spain
| | - Nuria Medarde
- Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Campus UAB 08193, Barcelona, Spain
| | | | - Maria Oliver-Bonet
- Unitat d'Investigació, Hospital Universitari Son Espases, Ctra Valldemossa 79, Palma 07010, Spain
| | - Jacint Ventura
- Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Campus UAB 08193, Barcelona, Spain
| | - Aurora Ruiz-Herrera
- Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Campus UAB 08193, Barcelona, Spain Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Campus UAB 08193, Barcelona, Spain
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50
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Rapid and inexpensive whole-genome genotyping-by-sequencing for crossover localization and fine-scale genetic mapping. G3-GENES GENOMES GENETICS 2015; 5:385-98. [PMID: 25585881 PMCID: PMC4349092 DOI: 10.1534/g3.114.016501] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The reshuffling of existing genetic variation during meiosis is important both during evolution and in breeding. The reassortment of genetic variants relies on the formation of crossovers (COs) between homologous chromosomes. The pattern of genome-wide CO distributions can be rapidly and precisely established by the short-read sequencing of individuals from F2 populations, which in turn are useful for quantitative trait locus (QTL) mapping. Although sequencing costs have decreased precipitously in recent years, the costs of library preparation for hundreds of individuals have remained high. To enable rapid and inexpensive CO detection and QTL mapping using low-coverage whole-genome sequencing of large mapping populations, we have developed a new method for library preparation along with Trained Individual GenomE Reconstruction, a probabilistic method for genotype and CO predictions for recombinant individuals. In an example case with hundreds of F2 individuals from two Arabidopsis thaliana accessions, we resolved most CO breakpoints to within 2 kb and reduced a major flowering time QTL to a 9-kb interval. In addition, an extended region of unusually low recombination revealed a 1.8-Mb inversion polymorphism on the long arm of chromosome 4. We observed no significant differences in the frequency and distribution of COs between F2 individuals with and without a functional copy of the DNA helicase gene RECQ4A. In summary, we present a new, cost-efficient method for large-scale, high-precision genotyping-by-sequencing.
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