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Berdan EL, Aubier TG, Cozzolino S, Faria R, Feder JL, Giménez MD, Joron M, Searle JB, Mérot C. Structural Variants and Speciation: Multiple Processes at Play. Cold Spring Harb Perspect Biol 2024; 16:a041446. [PMID: 38052499 PMCID: PMC10910405 DOI: 10.1101/cshperspect.a041446] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Research on the genomic architecture of speciation has increasingly revealed the importance of structural variants (SVs) that affect the presence, abundance, position, and/or direction of a nucleotide sequence. SVs include large chromosomal rearrangements such as fusion/fissions and inversions and translocations, as well as smaller variants such as duplications, insertions, and deletions (CNVs). Although we have ample evidence that SVs play a key role in speciation, the underlying mechanisms differ depending on the type and length of the SV, as well as the ecological, demographic, and historical context. We review predictions and empirical evidence for classic processes such as underdominance due to meiotic aberrations and the coupling effect of recombination suppression before exploring how recent sequencing methodologies illuminate the prevalence and diversity of SVs. We discuss specific properties of SVs and their impact throughout the genome, highlighting that multiple processes are at play, and possibly interacting, in the relationship between SVs and speciation.
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Affiliation(s)
- Emma L Berdan
- Department of Marine Sciences, Gothenburg University, Gothenburg 40530, Sweden
- Bioinformatics Core, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Thomas G Aubier
- Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier Toulouse III, UMR 5174, CNRS/IRD, 31077 Toulouse, France
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Salvatore Cozzolino
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Napoli, Italia
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, 4485-661 Vairão, Portugal
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Mabel D Giménez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Genética Humana de Misiones (IGeHM), Parque de la Salud de la Provincia de Misiones "Dr. Ramón Madariaga," N3300KAZ Posadas, Misiones, Argentina
- Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, N3300LQH Posadas, Misiones, Argentina
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA
| | - Claire Mérot
- CNRS, UMR 6553 Ecobio, OSUR, Université de Rennes, 35000 Rennes, France
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Ansai S, Toyoda A, Yoshida K, Kitano J. Repositioning of centromere-associated repeats during karyotype evolution in Oryzias fishes. Mol Ecol 2023. [PMID: 38014620 DOI: 10.1111/mec.17222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 11/04/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023]
Abstract
The karyotype, which is the number and shape of chromosomes, is a fundamental characteristic of all eukaryotes. Karyotypic changes play an important role in many aspects of evolutionary processes, including speciation. In organisms with monocentric chromosomes, it was previously thought that chromosome number changes were mainly caused by centric fusions and fissions, whereas chromosome shape changes, that is, changes in arm numbers, were mainly due to pericentric inversions. However, recent genomic and cytogenetic studies have revealed examples of alternative cases, such as tandem fusions and centromere repositioning, found in the karyotypic changes within and between species. Here, we employed comparative genomic approaches to investigate whether centromere repositioning occurred during karyotype evolution in medaka fishes. In the medaka family (Adrianichthyidae), the three phylogenetic groups differed substantially in their karyotypes. The Oryzias latipes species group has larger numbers of chromosome arms than the other groups, with most chromosomes being metacentric. The O. javanicus species group has similar numbers of chromosomes to the O. latipes species group, but smaller arm numbers, with most chromosomes being acrocentric. The O. celebensis species group has fewer chromosomes than the other two groups and several large metacentric chromosomes that were likely formed by chromosomal fusions. By comparing the genome assemblies of O. latipes, O. javanicus, and O. celebensis, we found that repositioning of centromere-associated repeats might be more common than simple pericentric inversion. Our results demonstrated that centromere repositioning may play a more important role in karyotype evolution than previously appreciated.
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Affiliation(s)
- Satoshi Ansai
- Laboratory of Genome Editing Breeding, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Kohta Yoshida
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
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3
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Bikchurina T, Pavlenko M, Kizilova E, Rubtsova D, Sheremetyeva I, Kartavtseva I, Torgasheva A, Borodin P. Chromosome Asynapsis Is the Main Cause of Male Sterility in the Interspecies Hybrids of East Asian Voles ( Alexandromys, Rodentia, Arvicolinae). Genes (Basel) 2023; 14:genes14051022. [PMID: 37239382 DOI: 10.3390/genes14051022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Closely related mammalian species often have differences in chromosome number and morphology, but there is still a debate about how these differences relate to reproductive isolation. To study the role of chromosome rearrangements in speciation, we used the gray voles in the Alexandromys genus as a model. These voles have a high level of chromosome polymorphism and substantial karyotypic divergence. We investigated testis histology and meiotic chromosome behavior in the captive-bred colonies of Alexandromys maximowiczii, Alexandromys mujanensis, two chromosome races of Alexandromys evoronensis, and their interracial and interspecies hybrids, to explore the relationship between karyotypic differences and male hybrid sterility. We found that the seminiferous tubules of the males of the parental species and the interracial hybrids, which were simple heterozygotes for one or more chromosome rearrangements, contained germ cells at all stages of spermatogenesis, indicating their potential fertility. Their meiotic cells displayed orderly chromosome synapsis and recombination. In contrast, all interspecies male hybrids, which were complex heterozygotes for a series of chromosome rearrangements, showed signs of complete sterility. Their spermatogenesis was mainly arrested at the zygotene- or pachytene-like stages due to the formation of complex multivalent chains, which caused extended chromosome asynapsis. The asynapsis led to the silencing of unsynapsed chromatin. We suggest that chromosome asynapsis is the main cause of meiotic arrest and male sterility in the interspecies hybrids of East Asian voles.
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Affiliation(s)
- Tatiana Bikchurina
- Department of Cytology and Genetics, Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Marina Pavlenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - Elena Kizilova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Daria Rubtsova
- Department of Cytology and Genetics, Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Irina Sheremetyeva
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - Irina Kartavtseva
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - Anna Torgasheva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Pavel Borodin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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Migration of repetitive DNAs during evolution of the permanent translocation heterozygosity in the oyster plant (Tradescantia section Rhoeo). Chromosoma 2022; 131:163-173. [PMID: 35896680 PMCID: PMC9470650 DOI: 10.1007/s00412-022-00776-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/28/2022] [Accepted: 07/14/2022] [Indexed: 11/30/2022]
Abstract
Due to translocation heterozygosity for all chromosomes in the cell complement, the oyster plant (Tradescantia spathacea) forms a complete meiotic ring. It also shows Rabl-arrangement at interphase, featured by polar centromere clustering. We demonstrate that the pericentromeric regions of the oyster plant are homogenized in concert by three subtelomeric sequences: 45S rDNA, (TTTAGGG)n motif, and TSrepI repeat. The Rabl-based clustering of pericentromeric regions may have been an excellent device to combine the subtelomere-pericentromere sequence migration (via inversions) with the pericentromere-pericentromere DNA movement (via whole arm translocations) that altogether led to the concerted homogenization of all the pericentromeric domains by the subtelomeric sequences. We also show that the repetitive sequence landscape of interstitial chromosome regions contains many loci consisting of Arabidopsis-type telomeric sequence or of TSrepI repeat, and it is extensively heterozygous. However, the sequence arrangement on some chromosomal arms suggest segmental inversions that are fully or partially homozygous, a fact that could be explained if the inversions started to create linkages already in a bivalent-forming ancestor. Remarkably, the subterminal TSrepI loci reside exclusively on the longer arms that could be due to sharing sequences between similarly-sized chromosomal arms in the interphase nucleus. Altogether, our study spotlights the supergene system of the oyster plant as an excellent model to link complex chromosome rearrangements, evolution of repetitive sequences, and nuclear architecture.
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Contributions to Trachelyopterus (Siluriformes: Auchenipteridae) species diagnosis by cytotaxonomic autapomorphies: from U2 snRNA chromosome polymorphism to rDNA and histone gene synteny. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00560-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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6
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Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. Unboxing mutations: Connecting mutation types with evolutionary consequences. Mol Ecol 2021; 30:2710-2723. [PMID: 33955064 DOI: 10.1111/mec.15936] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/30/2021] [Accepted: 04/20/2021] [Indexed: 01/09/2023]
Abstract
A key step in understanding the genetic basis of different evolutionary outcomes (e.g., adaptation) is to determine the roles played by different mutation types (e.g., SNPs, translocations and inversions). To do this we must simultaneously consider different mutation types in an evolutionary framework. Here, we propose a research framework that directly utilizes the most important characteristics of mutations, their population genetic effects, to determine their relative evolutionary significance in a given scenario. We review known population genetic effects of different mutation types and show how these may be connected to different evolutionary outcomes. We provide examples of how to implement this framework and pinpoint areas where more data, theory and synthesis are needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is a critical step towards understanding their evolutionary significance.
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Affiliation(s)
- Emma L Berdan
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | | | - Tanja Slotte
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Alexander Suh
- School of Biological Sciences - Organisms and the Environment, University of East Anglia, Norwich, UK.,Department of Organismal Biology - Systematic Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anja M Westram
- IST Austria, Klosterneuburg, Austria.,Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Inês Fragata
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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Termolino P, Falque M, Aiese Cigliano R, Cremona G, Paparo R, Ederveen A, Martin OC, Consiglio FM, Conicella C. Recombination suppression in heterozygotes for a pericentric inversion induces the interchromosomal effect on crossovers in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1163-1175. [PMID: 31436858 PMCID: PMC6973161 DOI: 10.1111/tpj.14505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 07/31/2019] [Accepted: 08/07/2019] [Indexed: 05/02/2023]
Abstract
During meiosis, recombination ensures allelic exchanges through crossovers (COs) between the homologous chromosomes. Advances in our understanding of the rules of COs have come from studies of mutations including structural chromosomal rearrangements that, when heterozygous, are known to impair COs in various organisms. In this work, we investigate the effect of a large heterozygous pericentric inversion on male and female recombination in Arabidopsis. The inversion was discovered in the Atmcc1 mutant background and was characterized through genetic and next-generation sequencing analysis. Reciprocal backcross populations, each consisting of over 400 individuals, obtained from the mutant and the wild type, both crossed with Landsberg erecta, were analyzed genome-wide by 143 single-nucleotide polymorphisms. The negative impact of inversion became evident in terms of CO loss in the rearranged chromosome in both male and female meiosis. No single-CO event was detected within the inversion, consistent with a post-meiotic selection operating against unbalanced gametes. Cytological analysis of chiasmata in F1 plants confirmed that COs were reduced in male meiosis in the chromosome with inversion. Crossover suppression on the rearranged chromosome is associated with a significant increase of COs in the other chromosomes, thereby maintaining unchanged the number of COs per cell. The CO pattern observed in our study is consistent with the interchromosomal (IC) effect as first described in Drosophila. In contrast to male meiosis, in female meiosis no IC effect is visible. This may be related to the greater strength of interference that constrains the CO number in excess of the minimum value imposed by CO assurance in Arabidopsis female meiosis.
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Affiliation(s)
- Pasquale Termolino
- Institute of Biosciences and Bioresources (IBBR)National Research Council of Italy (CNR)80055PorticiItaly
| | - Matthieu Falque
- Génétique Quantitative et Evolution‐Le MoulonInstitut National de la Recherche AgronomiqueUniversité Paris‐SudCNRSAgroParisTechUniversité Paris‐Saclay91190Gif‐sur‐YvetteFrance
| | | | - Gaetana Cremona
- Institute of Biosciences and Bioresources (IBBR)National Research Council of Italy (CNR)80055PorticiItaly
| | - Rosa Paparo
- Institute of Biosciences and Bioresources (IBBR)National Research Council of Italy (CNR)80055PorticiItaly
| | - Antoine Ederveen
- Department of Molecular Plant PhysiologyInstitute for Water and Wetland Research (IWWR)Radboud University Nijmegen9102 6500Nijmegenthe Netherlands
| | - Olivier C. Martin
- Génétique Quantitative et Evolution‐Le MoulonInstitut National de la Recherche AgronomiqueUniversité Paris‐SudCNRSAgroParisTechUniversité Paris‐Saclay91190Gif‐sur‐YvetteFrance
| | - Federica M. Consiglio
- Institute of Biosciences and Bioresources (IBBR)National Research Council of Italy (CNR)80055PorticiItaly
| | - Clara Conicella
- Institute of Biosciences and Bioresources (IBBR)National Research Council of Italy (CNR)80055PorticiItaly
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8
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Kapun M, Flatt T. The adaptive significance of chromosomal inversion polymorphisms inDrosophila melanogaster. Mol Ecol 2018; 28:1263-1282. [DOI: 10.1111/mec.14871] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/01/2018] [Accepted: 09/10/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Martin Kapun
- Department of BiologyUniversity of Fribourg Fribourg Switzerland
| | - Thomas Flatt
- Department of BiologyUniversity of Fribourg Fribourg Switzerland
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9
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Potter S, Bragg JG, Blom MPK, Deakin JE, Kirkpatrick M, Eldridge MDB, Moritz C. Chromosomal Speciation in the Genomics Era: Disentangling Phylogenetic Evolution of Rock-wallabies. Front Genet 2017; 8:10. [PMID: 28265284 PMCID: PMC5301020 DOI: 10.3389/fgene.2017.00010] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/18/2017] [Indexed: 12/24/2022] Open
Abstract
The association of chromosome rearrangements (CRs) with speciation is well established, and there is a long history of theory and evidence relating to "chromosomal speciation." Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about one episode of chromosomal speciation. Progressing from patterns of association between chromosome (and genic) change, to understanding processes of speciation requires both comparative studies across diverse systems and integration of genome-scale sequence comparisons with other lines of evidence. Here, we showcase a promising example of chromosomal speciation in a non-model organism, the endemic Australian marsupial genus Petrogale. We present initial phylogenetic results from exon-capture that resolve a history of divergence associated with extensive and repeated CRs. Yet it remains challenging to disentangle gene tree heterogeneity caused by recent divergence and gene flow in this and other such recent radiations. We outline a way forward for better integration of comparative genomic sequence data with evidence from molecular cytogenetics, and analyses of shifts in the recombination landscape and potential disruption of meiotic segregation and epigenetic programming. In all likelihood, CRs impact multiple cellular processes and these effects need to be considered together, along with effects of genic divergence. Understanding the effects of CRs together with genic divergence will require development of more integrative theory and inference methods. Together, new data and analysis tools will combine to shed light on long standing questions of how chromosome and genic divergence promote speciation.
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Affiliation(s)
- Sally Potter
- Research School of Biology, Australian National University, ActonACT, Australia
- Australian Museum Research Institute, Australian Museum, SydneyNSW, Australia
| | - Jason G. Bragg
- National Herbarium of New South Wales, The Royal Botanic Gardens and Domain Trust, SydneyNSW, Australia
| | - Mozes P. K. Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural HistoryStockholm, Sweden
| | - Janine E. Deakin
- Institute for Applied Ecology, University of Canberra, BruceACT, Australia
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, AustinTX, USA
| | - Mark D. B. Eldridge
- Australian Museum Research Institute, Australian Museum, SydneyNSW, Australia
| | - Craig Moritz
- Research School of Biology, Australian National University, ActonACT, Australia
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del Priore L, Pigozzi MI. Heterologous Synapsis and Crossover Suppression in Heterozygotes for a Pericentric Inversion in the Zebra Finch. Cytogenet Genome Res 2015; 147:154-60. [DOI: 10.1159/000442656] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2015] [Indexed: 11/19/2022] Open
Abstract
In the zebra finch, 2 alternative morphs regarding centromere position were described for chromosome 6. This polymorphism was interpreted to be the result of a pericentric inversion, but other causes of the centromere repositioning were not ruled out. We used immunofluorescence localization to examine the distribution of MLH1 foci on synaptonemal complexes to test the prediction that pericentric inversions cause synaptic irregularities and/or crossover suppression in heterozygotes. We found complete suppression of crossing over in the region involved in the rearrangement in male and female heterozygotes. In contrast, the same region showed high levels of crossing over in homozygotes for the acrocentric form of this chromosome. No inversion loops or synaptic irregularities were detected along bivalent 6 in heterozygotes suggesting that heterologous pairing is achieved during zygotene or early pachytene. Altogether these findings strongly indicate that the polymorphic chromosome 6 originated by a pericentric inversion. Since inversions are common rearrangements in karyotypic evolution in birds, it seems likely that early heterologous pairing could help to fix these rearrangements, preventing crossing overs in heterozygotes and their deleterious effects on fertility.
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Walker LI, Soto MA, Spotorno ÁE. Similarities and differences among the chromosomes of the wild guinea pig Cavia tschudii and the domestic guinea pig Cavia porcellus (Rodentia, Caviidae). COMPARATIVE CYTOGENETICS 2014; 8:153-67. [PMID: 25147626 PMCID: PMC4137285 DOI: 10.3897/compcytogen.v8i2.7509] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 06/10/2014] [Indexed: 06/02/2023]
Abstract
Cavia tschudii Fitzinger, 1867 is a wild guinea pig species living in South America that according to the analysis of mitochondrial genes is the closest wild form of the domestic guinea pig. To investigate the genetic divergence between the wild and domestic species of guinea pigs from a cytogenetic perspective, we characterized and compared the C, G and AgNOR banded karyotypes of molecularly identified Cavia tschudii and Cavia porcellus Linnaeus, 1758 specimens for the first time. Both species showed 64 chromosomes of similar morphology, although C. tschudii had four medium size submetacentric pairs that were not observed in the C. porcellus karyotype. Differences in the C bands size and the mean number of AgNOR bands between the karyotypes of the two species were detected. Most of the two species chromosomes showed total G band correspondence, suggesting that they probably represent large syntenic blocks conserved over time. Partial G band correspondence detected among the four submetacentric chromosomes present only in the C. tschudii karyotype and their subtelocentric homologues in C. porcellus may be explained by the occurrence of four pericentric inversions that probably emerged and were fixed in the C. tschudii populations under domestication. The role of the chromosomal and genomic differences in the divergence of these two Cavia species is discussed.
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Affiliation(s)
- Laura I. Walker
- Laboratorio de Citogenética Evolutiva, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile. Casilla 70061, Santiago 7, Chile
| | - Miguel A. Soto
- Laboratorio de Citogenética Evolutiva, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile. Casilla 70061, Santiago 7, Chile
| | - Ángel E. Spotorno
- Laboratorio de Citogenética Evolutiva, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile. Casilla 70061, Santiago 7, Chile
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Kapun M, van Schalkwyk H, McAllister B, Flatt T, Schlötterer C. Inference of chromosomal inversion dynamics from Pool-Seq data in natural and laboratory populations of Drosophila melanogaster. Mol Ecol 2013; 23:1813-27. [PMID: 24372777 PMCID: PMC4359753 DOI: 10.1111/mec.12594] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 10/23/2013] [Accepted: 11/06/2013] [Indexed: 12/21/2022]
Abstract
Sequencing of pools of individuals (Pool-Seq) represents a reliable and cost-effective approach
for estimating genome-wide SNP and transposable element insertion frequencies. However, Pool-Seq
does not provide direct information on haplotypes so that, for example, obtaining inversion
frequencies has not been possible until now. Here, we have developed a new set of diagnostic marker
SNPs for seven cosmopolitan inversions in Drosophila melanogaster that can be used
to infer inversion frequencies from Pool-Seq data. We applied our novel marker set to Pool-Seq data
from an experimental evolution study and from North American and Australian latitudinal clines. In
the experimental evolution data, we find evidence that positive selection has driven the frequencies
of In(3R)C and
In(3R)Mo to increase over time. In the clinal
data, we confirm the existence of frequency clines for In(2L)t,
In(3L)P and In(3R)Payne in both North America and Australia and
detect a previously unknown latitudinal cline for In(3R)Mo in North America. The
inversion markers developed here provide a versatile and robust tool for characterizing inversion
frequencies and their dynamics in Pool-Seq data from diverse D. melanogaster
populations.
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Affiliation(s)
- Martin Kapun
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, Vienna, A-1210, Austria; Vienna graduate school of Population Genetics, Iowa City, IA, 52242, USA
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13
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Hultén MA. On the origin of crossover interference: A chromosome oscillatory movement (COM) model. Mol Cytogenet 2011; 4:10. [PMID: 21477316 PMCID: PMC3103480 DOI: 10.1186/1755-8166-4-10] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 04/08/2011] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND It is now nearly a century since it was first discovered that crossovers between homologous parental chromosomes, originating at the Prophase stage of Meiosis I, are not randomly placed. In fact, the number and distribution of crossovers are strictly regulated with crossovers/chiasmata formed in optimal positions along the length of individual chromosomes, facilitating regular chromosome segregation at the first meiotic division. In spite of much research addressing this question, the underlying mechanism(s) for the phenomenon called crossover/chiasma interference is/are still unknown; and this constitutes an outstanding biological enigma. RESULTS The Chromosome Oscillatory Movement (COM) model for crossover/chiasma interference implies that, during Prophase of Meiosis I, oscillatory movements of the telomeres (attached to the nuclear membrane) and the kinetochores (within the centromeres) create waves along the length of chromosome pairs (bivalents) so that crossing-over and chiasma formation is facilitated by the proximity of parental homologs induced at the nodal regions of the waves thus created. This model adequately explains the salient features of crossover/chiasma interference, where (1) there is normally at least one crossover/chiasma per bivalent, (2) the number is correlated to bivalent length, (3) the positions are dependent on the number per bivalent, (4) interference distances are on average longer over the centromere than along chromosome arms, and (5) there are significant changes in carriers of structural chromosome rearrangements. CONCLUSIONS The crossover/chiasma frequency distribution in humans and mice with normal karyotypes as well as in carriers of structural chromosome rearrangements are those expected on the COM model. Further studies are underway to analyze mechanical/mathematical aspects of this model for the origin of crossover/chiasma interference, using string replicas of the homologous chromosomes at the Prophase stage of Meiosis I. The parameters to vary in this type of experiment will include: (1) the mitotic karyotype, i.e. ranked length and centromere index of the chromosomes involved, (2) the specific bivalent/multivalent length and flexibility, dependent on the way this structure is positioned within the nucleus and the size of the respective meiocyte nuclei, (3) the frequency characteristics of the oscillatory movements at respectively the telomeres and the kinetochores.
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Affiliation(s)
- Maj A Hultén
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, CMM L8:02, Karolinska Institutet, Karolinska University Hospital, Solna, S-17 1 76 Stockholm, Sweden.
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