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Bernegossi AM, Galindo DJ, Peres PHF, Vozdova M, Cernohorska H, Kubickova S, Kadlcikova D, Rubes J, Duarte JMB. Comparative karyotype analysis of the red brocket deer (M. americana sensu lato and M. rufa) complex: evidence of drastic chromosomal evolution and implications on speciation process. J Appl Genet 2024; 65:601-614. [PMID: 38662189 DOI: 10.1007/s13353-024-00861-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/14/2024] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
Chromosomal rearrangements are often associated with playing a role in the speciation process. However, the underlying mechanism that favors the genetic isolation associated with chromosomal changes remains elusive. In this sense, the genus Mazama is recognized by its high level of karyotype diversity among species with similar morphology. A cryptic species complex has been identified within the genus, with the red brocket deer (Mazama americana and Mazama rufa) being the most impressive example. The chromosome variation was clustered in cytotypes with diploid numbers ranging from 42 to 53 and was correlated with geographical location. We conducted an analysis of chromosome evolution of the red brocket deer complex using comparative chromosome painting and Bacterial Artificial Chromosome (BAC) clones among different cytotypes. The aim was to deepen our understanding of the karyotypic relationships within the red brocket, thereby elucidating the significant chromosome variation among closely related species. This underscores the significance of chromosome changes as a key evolutionary process shaping their genomes. The results revealed the presence of three distinct cytogenetic lineages characterized by significant karyotypic divergence, suggesting the existence of efficient post-zygotic barriers. Tandem fusions constitute the main mechanism driving karyotype evolution, following a few centric fusions, inversion X-autosomal fusions. The BAC mapping has improved our comprehension of the karyotypic relationships within the red brocket deer complex, prompting questions regarding the role of these changes in the speciation process. We propose the red brocket as a model group to investigate how chromosomal changes contribute to isolation and explore the implications of these changes in taxonomy and conservation.
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Affiliation(s)
- Agda Maria Bernegossi
- Deer Research and Conservation Center (NUPECCE), School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, Sao Paulo, 14884-900, Brazil
| | - David Javier Galindo
- Deer Research and Conservation Center (NUPECCE), School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, Sao Paulo, 14884-900, Brazil.
- Laboratory of Animal Reproduction, Faculty of Veterinary Medicine, National University of San Marcos, San Borja, 15021, Lima, Peru.
| | - Pedro Henrique Faria Peres
- Deer Research and Conservation Center (NUPECCE), School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, Sao Paulo, 14884-900, Brazil
| | - Miluse Vozdova
- Central European Institute of Technology-Veterinary Research Institute, 621 00, Brno, Czech Republic
| | - Halina Cernohorska
- Central European Institute of Technology-Veterinary Research Institute, 621 00, Brno, Czech Republic
| | - Svatava Kubickova
- Central European Institute of Technology-Veterinary Research Institute, 621 00, Brno, Czech Republic
| | - Dita Kadlcikova
- Central European Institute of Technology-Veterinary Research Institute, 621 00, Brno, Czech Republic
| | - Jiri Rubes
- Central European Institute of Technology-Veterinary Research Institute, 621 00, Brno, Czech Republic
| | - José Maurício Barbanti Duarte
- Deer Research and Conservation Center (NUPECCE), School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, Sao Paulo, 14884-900, Brazil.
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Solovei I, Mirny L. Spandrels of the cell nucleus. Curr Opin Cell Biol 2024; 90:102421. [PMID: 39180905 DOI: 10.1016/j.ceb.2024.102421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 07/18/2024] [Accepted: 08/02/2024] [Indexed: 08/27/2024]
Abstract
S.J. Gould and R. Lewontin in their famous "Spandrels paper" (1979) argued that many anatomical elements arise in evolution not due to their "current utility" but rather due to other "reasons for origin", such as other developmental processes, physical constraints and mechanical forces. Here, in the same spirit, we argue that a variety of molecular processes, physical constraints, and mechanical forces, alone or together, generate structures that are detectable in the cell nucleus, yet these structures themselves may not carry any specific function, being a mere reflection of processes that produced them.
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Affiliation(s)
- Irina Solovei
- Biocenter, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany.
| | - Leonid Mirny
- Institute for Medical Engineering and Science, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
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3
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Deon GA, Dos Santos RZ, Sassi FDMC, Moreira-Filho O, Vicari MR, Porto-Foresti F, Utsunomia R, Cioffi MDB. The role of satellite DNAs in the chromosomal rearrangements and the evolution of the rare XY1Y2 sex system in Harttia (Siluriformes: Loricariidae). J Hered 2024; 115:541-551. [PMID: 38757192 DOI: 10.1093/jhered/esae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/15/2024] [Indexed: 05/18/2024] Open
Abstract
The underlying processes behind the formation, evolution, and long-term maintenance of multiple sex chromosomes have been largely neglected. Among vertebrates, fishes represent the group with the highest diversity of multiple sex chromosome systems and, with six instances, the Neotropical fish genus Harttia stands out by presenting the most remarkable diversity. However, although the origin mechanism of their sex chromosome systems is well discussed, little is known about the importance of some repetitive DNA classes in the differentiation of multiple systems. In this work, by employing a combination of cytogenetic and genomic procedures, we evaluated the satellite DNA composition of H. carvalhoi with a focus on their role in the evolution, structure, and differentiation process of the rare XY1Y2 multiple-sex chromosome system. The genome of H. carvalhoi contains a total of 28 satellite DNA families, with the A + T content ranging between 38.1% and 68.1% and the predominant presence of long satellites. The in situ hybridization experiments detected 15 satellite DNAs with positive hybridization signals mainly on centromeric and pericentromeric regions of almost all chromosomes or clustered on a few pairs. Five of them presented clusters on X, Y1, and/or Y2 sex chromosomes which were therefore selected for comparative hybridization in the other three congeneric species. We found several conserved satellites accumulated on sex chromosomes and also in regions that were involved in chromosomal rearrangements. Our results provide a new contribution of satellitome studies in multiple sex chromosome systems in fishes and represent the first satellitome study for a Siluriformes species.
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Affiliation(s)
- Geize Aparecida Deon
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Rodrigo Zeni Dos Santos
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, Bauru, São Paulo, Brazil
| | | | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Marcelo Ricardo Vicari
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Paraná, Brazil
| | - Fábio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, Bauru, São Paulo, Brazil
| | - Ricardo Utsunomia
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, Bauru, São Paulo, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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Jonika MM, Wilhoit KT, Chin M, Arekere A, Blackmon H. Drift drives the evolution of chromosome number II: The impact of range size on genome evolution in Carnivora. J Hered 2024; 115:524-531. [PMID: 38712909 PMCID: PMC11334210 DOI: 10.1093/jhered/esae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 01/03/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024] Open
Abstract
Chromosome number is a fundamental genomic trait that is often the first recorded characteristic of a genome. Across large clades, a common pattern emerges: many or even most lineages exhibit relative stasis, while a handful of lineages or species exhibit striking variation. Despite recent developments in comparative methods, most of this heterogeneity is still poorly understood. It is essential to understand why some lineages have rapid rates of chromosome number evolution, as it can impact a variety of other traits. Previous research suggests that biased female meiotic drive may shape rates of karyotype evolution in some mammals. However, Carnivora exhibits variation that this female meiotic drive model cannot explain. We hypothesize that variation in effective population size may underlie rate variation in Carnivora. To test this hypothesis, we estimated rates of fusions and fissions while accounting for range size, which we use as a proxy for effective population size. We reason fusions and fissions are deleterious or underdominant and that only in lineages with small range sizes will these changes be able to fix due to genetic drift. In this study, we find that the rates of fusions and fissions are elevated in taxa with small range sizes relative to those with large range sizes. Based on these findings, we conclude that 1) naturally occurring structural mutations that change chromosome number are underdominant or mildly deleterious, and 2) when population sizes are small, structural rearrangements may play an important role in speciation and reduction in gene flow among populations.
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Affiliation(s)
- Michelle M Jonika
- Department of Biology, Texas A&M University, College Station, TX, United States
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, United States
| | - Kayla T Wilhoit
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Maximos Chin
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Abhimanyu Arekere
- Department of Biology, Texas A&M University, College Station, TX, United States
- Department of Biomedical Engineering, University of Texas, Austin, TX, United States
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, TX, United States
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, United States
- Ecology and Evolutionary Biology Interdepartmental Program, Texas A&M University, College Station, TX, United States
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Gerton JL. A working model for the formation of Robertsonian chromosomes. J Cell Sci 2024; 137:jcs261912. [PMID: 38606789 PMCID: PMC11057876 DOI: 10.1242/jcs.261912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024] Open
Abstract
Robertsonian chromosomes form by fusion of two chromosomes that have centromeres located near their ends, known as acrocentric or telocentric chromosomes. This fusion creates a new metacentric chromosome and is a major mechanism of karyotype evolution and speciation. Robertsonian chromosomes are common in nature and were first described in grasshoppers by the zoologist W. R. B. Robertson more than 100 years ago. They have since been observed in many species, including catfish, sheep, butterflies, bats, bovids, rodents and humans, and are the most common chromosomal change in mammals. Robertsonian translocations are particularly rampant in the house mouse, Mus musculus domesticus, where they exhibit meiotic drive and create reproductive isolation. Recent progress has been made in understanding how Robertsonian chromosomes form in the human genome, highlighting some of the fundamental principles of how and why these types of fusion events occur so frequently. Consequences of these fusions include infertility and Down's syndrome. In this Hypothesis, I postulate that the conditions that allow these fusions to form are threefold: (1) sequence homology on non-homologous chromosomes, often in the form of repetitive DNA; (2) recombination initiation during meiosis; and (3) physical proximity of the homologous sequences in three-dimensional space. This Hypothesis highlights the latest progress in understanding human Robertsonian translocations within the context of the broader literature on Robertsonian chromosomes.
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Dumont BL, Gatti DM, Ballinger MA, Lin D, Phifer-Rixey M, Sheehan MJ, Suzuki TA, Wooldridge LK, Frempong HO, Lawal RA, Churchill GA, Lutz C, Rosenthal N, White JK, Nachman MW. Into the Wild: A novel wild-derived inbred strain resource expands the genomic and phenotypic diversity of laboratory mouse models. PLoS Genet 2024; 20:e1011228. [PMID: 38598567 PMCID: PMC11034653 DOI: 10.1371/journal.pgen.1011228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/22/2024] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
The laboratory mouse has served as the premier animal model system for both basic and preclinical investigations for over a century. However, laboratory mice capture only a subset of the genetic variation found in wild mouse populations, ultimately limiting the potential of classical inbred strains to uncover phenotype-associated variants and pathways. Wild mouse populations are reservoirs of genetic diversity that could facilitate the discovery of new functional and disease-associated alleles, but the scarcity of commercially available, well-characterized wild mouse strains limits their broader adoption in biomedical research. To overcome this barrier, we have recently developed, sequenced, and phenotyped a set of 11 inbred strains derived from wild-caught Mus musculus domesticus. Each of these "Nachman strains" immortalizes a unique wild haplotype sampled from one of five environmentally distinct locations across North and South America. Whole genome sequence analysis reveals that each strain carries between 4.73-6.54 million single nucleotide differences relative to the GRCm39 mouse reference, with 42.5% of variants in the Nachman strain genomes absent from current classical inbred mouse strain panels. We phenotyped the Nachman strains on a customized pipeline to assess the scope of disease-relevant neurobehavioral, biochemical, physiological, metabolic, and morphological trait variation. The Nachman strains exhibit significant inter-strain variation in >90% of 1119 surveyed traits and expand the range of phenotypic diversity captured in classical inbred strain panels. These novel wild-derived inbred mouse strain resources are set to empower new discoveries in both basic and preclinical research.
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Affiliation(s)
- Beth L. Dumont
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
| | - Daniel M. Gatti
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Mallory A. Ballinger
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
| | - Dana Lin
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Megan Phifer-Rixey
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Michael J. Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York, United States of America
| | - Taichi A. Suzuki
- College of Health Solutions and Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, Arizona, United States of America
| | - Lydia K. Wooldridge
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Hilda Opoku Frempong
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
| | - Raman Akinyanju Lawal
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Gary A. Churchill
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
| | - Cathleen Lutz
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Nadia Rosenthal
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
- Graduate School of Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
- Graduate School of Biomedical Science and Engineering, The University of Maine, Orono, Maine, United States of America
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Jacqueline K. White
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Michael W. Nachman
- Department of Integrative Biology, Museum of Vertebrate Zoology, and Center for Computational Biology, University of California, Berkeley, Berkeley, California, United States of America
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7
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Yurchenko A, Pšenička T, Mora P, Ortega JAM, Baca AS, Rovatsos M. Cytogenetic Analysis of Satellitome of Madagascar Leaf-Tailed Geckos. Genes (Basel) 2024; 15:429. [PMID: 38674364 PMCID: PMC11049218 DOI: 10.3390/genes15040429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Satellite DNA (satDNA) consists of sequences of DNA that form tandem repetitions across the genome, and it is notorious for its diversity and fast evolutionary rate. Despite its importance, satDNA has been only sporadically studied in reptile lineages. Here, we sequenced genomic DNA and PCR-amplified microdissected W chromosomes on the Illumina platform in order to characterize the monomers of satDNA from the Henkel's leaf-tailed gecko U. henkeli and to compare their topology by in situ hybridization in the karyotypes of the closely related Günther's flat-tail gecko U. guentheri and gold dust day gecko P. laticauda. We identified seventeen different satDNAs; twelve of them seem to accumulate in centromeres, telomeres and/or the W chromosome. Notably, centromeric and telomeric regions seem to share similar types of satDNAs, and we found two that seem to accumulate at both edges of all chromosomes in all three species. We speculate that the long-term stability of all-acrocentric karyotypes in geckos might be explained from the presence of specific satDNAs at the centromeric regions that are strong meiotic drivers, a hypothesis that should be further tested.
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Affiliation(s)
- Alona Yurchenko
- Department of Ecology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic; (A.Y.); (T.P.)
| | - Tomáš Pšenička
- Department of Ecology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic; (A.Y.); (T.P.)
| | - Pablo Mora
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas s/n, E-23071 Jaen, Spain; (P.M.); (J.A.M.O.); (A.S.B.)
| | - Juan Alberto Marchal Ortega
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas s/n, E-23071 Jaen, Spain; (P.M.); (J.A.M.O.); (A.S.B.)
| | - Antonio Sánchez Baca
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas s/n, E-23071 Jaen, Spain; (P.M.); (J.A.M.O.); (A.S.B.)
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic; (A.Y.); (T.P.)
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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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9
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Jensen A, Swift F, de Vries D, Beck RMD, Kuderna LFK, Knauf S, Chuma IS, Keyyu JD, Kitchener AC, Farh K, Rogers J, Marques-Bonet T, Detwiler KM, Roos C, Guschanski K. Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation. Mol Biol Evol 2023; 40:msad247. [PMID: 37987553 PMCID: PMC10691879 DOI: 10.1093/molbev/msad247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/17/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023] Open
Abstract
Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation.
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Affiliation(s)
- Axel Jensen
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala SE-75236, Sweden
| | - Frances Swift
- School of Biological Sciences, Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Dorien de Vries
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Robin M D Beck
- School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK
| | - Lukas F K Kuderna
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald – Insel Riems 17493, Germany
| | | | - Julius D Keyyu
- Tanzania Wildlife Research Institute (TAWIRI), Arusha, Tanzania
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, Edinburgh EH8 9XP, UK
| | - Kyle Farh
- Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona 08003, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Barcelona 08010, Spain
| | - Kate M Detwiler
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL, USA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen 37077, Germany
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala SE-75236, Sweden
- School of Biological Sciences, Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
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10
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Sotola VA, Berg CS, Samuli M, Chen H, Mantel SJ, Beardsley PA, Yuan YW, Sweigart AL, Fishman L. Genomic mechanisms and consequences of diverse postzygotic barriers between monkeyflower species. Genetics 2023; 225:iyad156. [PMID: 37603838 DOI: 10.1093/genetics/iyad156] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 08/23/2023] Open
Abstract
The evolution of genomic incompatibilities causing postzygotic barriers to hybridization is a key step in species divergence. Incompatibilities take 2 general forms-structural divergence between chromosomes leading to severe hybrid sterility in F1 hybrids and epistatic interactions between genes causing reduced fitness of hybrid gametes or zygotes (Dobzhansky-Muller incompatibilities). Despite substantial recent progress in understanding the molecular mechanisms and evolutionary origins of both types of incompatibility, how each behaves across multiple generations of hybridization remains relatively unexplored. Here, we use genetic mapping in F2 and recombinant inbred line (RIL) hybrid populations between the phenotypically divergent but naturally hybridizing monkeyflowers Mimulus cardinalis and M. parishii to characterize the genetic basis of hybrid incompatibility and examine its changing effects over multiple generations of experimental hybridization. In F2s, we found severe hybrid pollen inviability (<50% reduction vs parental genotypes) and pseudolinkage caused by a reciprocal translocation between Chromosomes 6 and 7 in the parental species. RILs retained excess heterozygosity around the translocation breakpoints, which caused substantial pollen inviability when interstitial crossovers had not created compatible heterokaryotypic configurations. Strong transmission ratio distortion and interchromosomal linkage disequilibrium in both F2s and RILs identified a novel 2-locus genic incompatibility causing sex-independent gametophytic (haploid) lethality. The latter interaction eliminated 3 of the expected 9 F2 genotypic classes via F1 gamete loss without detectable effects on the pollen number or viability of F2 double heterozygotes. Along with the mapping of numerous milder incompatibilities, these key findings illuminate the complex genetics of plant hybrid breakdown and are an important step toward understanding the genomic consequences of natural hybridization in this model system.
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Affiliation(s)
- V Alex Sotola
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Colette S Berg
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Matthew Samuli
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Hongfei Chen
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Samuel J Mantel
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Paul A Beardsley
- Department of Biological Sciences, California State Polytechnic University, Pomona, CA 91768, USA
| | - Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Andrea L Sweigart
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
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11
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Lucek K, Giménez MD, Joron M, Rafajlović M, Searle JB, Walden N, Westram AM, Faria R. The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution. Cold Spring Harb Perspect Biol 2023; 15:a041447. [PMID: 37604585 PMCID: PMC10626258 DOI: 10.1101/cshperspect.a041447] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics. While an important role for CRs in speciation has been suggested, evidence primarily stems from theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon pairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at a macroevolutionary level has been supported by associations between species diversity and rates of evolution of CRs across phylogenies, these findings are limited to a restricted range of CRs and taxa. Now that more broadly applicable and precise CR detection approaches have become available, we address the challenges in filling some of the conceptual and empirical gaps between micro- and macroevolutionary studies on the role of CRs in speciation. We synthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life.
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Affiliation(s)
- Kay Lucek
- Biodiversity Genomics Laboratory, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - 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, 34293 Montpellier, France
| | - Marina Rafajlović
- Department of Marine Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden
- Centre for Marine Evolutionary Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA
| | - Nora Walden
- Centre for Organismal Studies, University of Heidelberg, 69117 Heidelberg, Germany
| | - Anja Marie Westram
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
- Faculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado;
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
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12
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Dumont BL, Gatti D, Ballinger MA, Lin D, Phifer-Rixey M, Sheehan MJ, Suzuki TA, Wooldridge LK, Frempong HO, Churchill G, Lutz C, Rosenthal N, White JK, Nachman MW. Into the Wild: A novel wild-derived inbred strain resource expands the genomic and phenotypic diversity of laboratory mouse models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558738. [PMID: 37790321 PMCID: PMC10542534 DOI: 10.1101/2023.09.21.558738] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The laboratory mouse has served as the premier animal model system for both basic and preclinical investigations for a century. However, laboratory mice capture a narrow subset of the genetic variation found in wild mouse populations. This consideration inherently restricts the scope of potential discovery in laboratory models and narrows the pool of potentially identified phenotype-associated variants and pathways. Wild mouse populations are reservoirs of predicted functional and disease-associated alleles, but the sparsity of commercially available, well-characterized wild mouse strains limits their broader adoption in biomedical research. To overcome this barrier, we have recently imported, sequenced, and phenotyped a set of 11 wild-derived inbred strains developed from wild-caught Mus musculus domesticus. Each of these "Nachman strains" immortalizes a unique wild haplotype sampled from five environmentally diverse locations across North and South America: Saratoga Springs, New York, USA; Gainesville, Florida, USA; Manaus, Brazil; Tucson, Arizona, USA; and Edmonton, Alberta, Canada. Whole genome sequence analysis reveals that each strain carries between 4.73-6.54 million single nucleotide differences relative to the mouse reference assembly, with 42.5% of variants in the Nachman strain genomes absent from classical inbred mouse strains. We phenotyped the Nachman strains on a customized pipeline to assess the scope of disease-relevant neurobehavioral, biochemical, physiological, metabolic, and morphological trait variation. The Nachman strains exhibit significant inter-strain variation in >90% of 1119 surveyed traits and expand the range of phenotypic diversity captured in classical inbred strain panels alone. Taken together, our work introduces a novel wild-derived inbred mouse strain resource that will enable new discoveries in basic and preclinical research. These strains are currently available through The Jackson Laboratory Repository under laboratory code NachJ.
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Affiliation(s)
- Beth L Dumont
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA, 02111, USA
- The University of Maine, Graduate School of Biomedical Science and Engineering, 5775 Stodder Hall, Room 46, Orono, ME, 04469, USA
| | - Daniel Gatti
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Mallory A Ballinger
- Department of Integrative Biology, Center for Computational Biology, and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Dana Lin
- Department of Integrative Biology, Center for Computational Biology, and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Michael J Sheehan
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Taichi A Suzuki
- College of Health Solutions and Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, AZ, USA 85281
| | | | - Hilda Opoku Frempong
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
- The University of Maine, Graduate School of Biomedical Science and Engineering, 5775 Stodder Hall, Room 46, Orono, ME, 04469, USA
| | - Gary Churchill
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA, 02111, USA
- The University of Maine, Graduate School of Biomedical Science and Engineering, 5775 Stodder Hall, Room 46, Orono, ME, 04469, USA
| | - Cathleen Lutz
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Nadia Rosenthal
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA, 02111, USA
- The University of Maine, Graduate School of Biomedical Science and Engineering, 5775 Stodder Hall, Room 46, Orono, ME, 04469, USA
| | | | - Michael W Nachman
- Department of Integrative Biology, Center for Computational Biology, and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA 94720, USA
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13
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Truong MA, Cané-Gasull P, Lens SMA. Modeling specific aneuploidies: from karyotype manipulations to biological insights. Chromosome Res 2023; 31:25. [PMID: 37640903 PMCID: PMC10462580 DOI: 10.1007/s10577-023-09735-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/11/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023]
Abstract
An abnormal chromosome number, or aneuploidy, underlies developmental disorders and is a common feature of cancer, with different cancer types exhibiting distinct patterns of chromosomal gains and losses. To understand how specific aneuploidies emerge in certain tissues and how they contribute to disease development, various methods have been developed to alter the karyotype of mammalian cells and mice. In this review, we provide an overview of both classic and novel strategies for inducing or selecting specific chromosomal gains and losses in human and murine cell systems. We highlight how these customized aneuploidy models helped expanding our knowledge of the consequences of specific aneuploidies to (cancer) cell physiology.
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Affiliation(s)
- My Anh Truong
- Oncode Institute and Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584, CG, Utrecht, The Netherlands
| | - Paula Cané-Gasull
- Oncode Institute and Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584, CG, Utrecht, The Netherlands
| | - Susanne M A Lens
- Oncode Institute and Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584, CG, Utrecht, The Netherlands.
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14
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Abstract
The p-arms of the five human acrocentric chromosomes bear nucleolar organizer regions (NORs) comprising ribosomal gene (rDNA) repeats that are organized in a homogeneous tandem array and transcribed in a telomere-to-centromere direction. Precursor ribosomal RNA transcripts are processed and assembled into ribosomal subunits, the nucleolus being the physical manifestation of this process. I review current understanding of nucleolar chromosome biology and describe current exploration into a role for the NOR chromosomal context. Full DNA sequences for acrocentric p-arms are now emerging, aided by the current revolution in long-read sequencing and genome assembly. Acrocentric p-arms vary from 10.1 to 16.7 Mb, accounting for ∼2.2% of the genome. Bordering rDNA arrays, distal junctions, and proximal junctions are shared among the p-arms, with distal junctions showing evidence of functionality. The remaining p-arm sequences comprise multiple satellite DNA classes and segmental duplications that facilitate recombination between heterologous chromosomes, which is likely also involved in Robertsonian translocations.
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Affiliation(s)
- Brian McStay
- Centre for Chromosome Biology, College of Science and Engineering, University of Galway, Galway, Ireland;
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15
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Zhou W, Furey NM, Soisook P, Thong VD, Lim BK, Rossiter SJ, Mao X. Diversification and introgression in four chromosomal taxa of the Pearson's horseshoe bat (Rhinolophus pearsoni) group. Mol Phylogenet Evol 2023; 183:107784. [PMID: 37040825 DOI: 10.1016/j.ympev.2023.107784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/11/2023] [Accepted: 04/07/2023] [Indexed: 04/13/2023]
Abstract
Chromosomal variation among closely related taxa is common in both plants and animals, and can reduce rates of introgression as well as promote reproductive isolation and speciation. In mammals, studies relating introgression to chromosomal variation have tended to focus on a few model systems and typically characterized levels of introgression using small numbers of loci. Here we took a genome-wide approach to examine how introgression rates vary among four closely related horseshoe bats (Rhinolophus pearsoni group) that possess different diploid chromosome numbers (2n = 42, 44, 46, and 60) resulting from Robertsonian (Rb) changes (fissions/fusions). Using a sequence capture we obtained orthologous loci for thousands of nuclear loci, as well as mitogenomes, and performed phylogenetic and population genetic analyses. We found that the taxon with 2n = 60 was the first to diverge in this group, and that the relationships among the three other taxa (2n = 42, 44 and 46) showed discordance across our different analyses. Our results revealed signatures of multiple ancient introgression events between the four taxa, with evidence of mitonuclar discordance in phylogenetic trees and reticulation events in their evolutionary history. Despite this, we found no evidence of recent and/or ongoing introgression between taxa. Overall, our results indicate that the effects of Rb changes on the reduction of introgression are complicated and that these may contribute to reproductive isolation and speciation in concert with other factors (e.g. phenotypic and genic divergence).
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Affiliation(s)
- Weiwei Zhou
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China
| | - Neil M Furey
- Fauna & Flora International (Cambodia), PO Box 1380, No. 19, Street 360, Boeng Keng Kong 1, Phnom Penh 12000, Cambodia
| | - Pipat Soisook
- Princess Maha Chakri Sirindhorn Natural History Museum, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Vu D Thong
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet Road, Cau Giay District, Hanoi, Viet Nam; Graduate University of Science and Technology, VAST, Viet Nam
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario M5S 2C6, Canada
| | - Stephen J Rossiter
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK.
| | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China.
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16
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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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17
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Yoshida K, Rödelsperger C, Röseler W, Riebesell M, Sun S, Kikuchi T, Sommer RJ. Chromosome fusions repatterned recombination rate and facilitated reproductive isolation during Pristionchus nematode speciation. Nat Ecol Evol 2023; 7:424-439. [PMID: 36717742 PMCID: PMC9998273 DOI: 10.1038/s41559-022-01980-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 12/29/2022] [Indexed: 02/01/2023]
Abstract
Large-scale genome-structural evolution is common in various organisms. Recent developments in speciation genomics revealed the importance of inversions, whereas the role of other genome-structural rearrangements, including chromosome fusions, have not been well characterized. We study genomic divergence and reproductive isolation of closely related nematodes: the androdioecious (hermaphroditic) model Pristionchus pacificus and its dioecious sister species Pristionchus exspectatus. A chromosome-level genome assembly of P. exspectatus using single-molecule and Hi-C sequencing revealed a chromosome-wide rearrangement relative to P. pacificus. Strikingly, genomic characterization and cytogenetic studies including outgroup species Pristionchus occultus indicated two independent fusions involving the same chromosome, ChrIR, between these related species. Genetic linkage analysis indicated that these fusions altered the chromosome-wide pattern of recombination, resulting in large low-recombination regions that probably facilitated the coevolution between some of the ~14.8% of genes across the entire genomes. Quantitative trait locus analyses for hybrid sterility in all three sexes revealed that major quantitative trait loci mapped to the fused chromosome ChrIR. While abnormal chromosome segregations of the fused chromosome partially explain hybrid female sterility, hybrid-specific recombination that breaks linkage of genes in the low-recombination region was associated with hybrid male sterility. Thus, recent chromosome fusions repatterned recombination rate and drove reproductive isolation during Pristionchus speciation.
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Affiliation(s)
- Kohta Yoshida
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany.
| | - Christian Rödelsperger
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany
| | - Waltraud Röseler
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany
| | - Metta Riebesell
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany
| | - Simo Sun
- Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Taisei Kikuchi
- Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology, Tübingen, Germany.
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18
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Chromosome territory reorganization through artificial chromosome fusion is compatible with cell fate determination and mouse development. Cell Discov 2023; 9:11. [PMID: 36693846 PMCID: PMC9873915 DOI: 10.1038/s41421-022-00511-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 12/18/2022] [Indexed: 01/26/2023] Open
Abstract
Chromosomes occupy discrete spaces in the interphase cell nucleus, called chromosome territory. The structural and functional relevance of chromosome territory remains elusive. We fused chromosome 15 and 17 in mouse haploid embryonic stem cells (haESCs), resulting in distinct changes of territories in the cognate chromosomes, but with little effect on gene expression, pluripotency and gamete functions of haESCs. The karyotype-engineered haESCs were successfully implemented in generating heterozygous (2n = 39) and homozygous (2n = 38) mouse models. Mice containing the fusion chromosome are fertile, and their representative tissues and organs display no phenotypic abnormalities, suggesting unscathed development. These results indicate that the mammalian chromosome architectures are highly resilient, and reorganization of chromosome territories can be readily tolerated during cell differentiation and mouse development.
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19
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Li Y, Wang S, Zhang Z, Luo J, Lin GL, Deng WD, Guo Z, Han FM, Wang LL, Li J, Wu SF, Liu HQ, He S, Murphy RW, Zhang ZJ, Cooper DN, Wu DD, Zhang YP. Large-Scale Chromosomal Changes Lead to Genome-Level Expression Alterations, Environmental Adaptation, and Speciation in the Gayal (Bos frontalis). Mol Biol Evol 2023; 40:6980758. [PMID: 36625089 PMCID: PMC9874039 DOI: 10.1093/molbev/msad006] [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: 08/09/2022] [Revised: 12/20/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Determining the functional consequences of karyotypic changes is invariably challenging because evolution tends to obscure many of its own footprints, such as accumulated mutations, recombination events, and demographic perturbations. Here, we describe the assembly of a chromosome-level reference genome of the gayal (Bos frontalis) thereby revealing the structure, at base-pair-level resolution, of a telo/acrocentric-to-telo/acrocentric Robertsonian translocation (2;28) (T/A-to-T/A rob[2;28]). The absence of any reduction in the recombination rate or genetic introgression within the fusion region of gayal served to challenge the long-standing view of a role for fusion-induced meiotic dysfunction in speciation. The disproportionate increase noted in the distant interactions across pro-chr2 and pro-chr28, and the change in open-chromatin accessibility following rob(2;28), may, however, have led to the various gene expression irregularities observed in the gayal. Indeed, we found that many muscle-related genes, located synthetically on pro-chr2 and pro-chr28, exhibited significant changes in expression. This, combined with genome-scale structural variants and expression alterations in genes involved in myofibril composition, may have driven the rapid sarcomere adaptation of gayal to its rugged mountain habitat. Our findings not only suggest that large-scale chromosomal changes can lead to alterations in genome-level expression, thereby promoting both adaptation and speciation, but also illuminate novel avenues for studying the relationship between karyotype evolution and speciation.
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Affiliation(s)
- Yan Li
- Corresponding authors: E-mails: ;
| | | | | | | | | | | | | | | | - Li-Li Wang
- Biomarker Technologies Corporation, Beijing, China
| | - Jie Li
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan and School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - He-Qun Liu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Sheng He
- Nujiang Livestock Technology Promotion Station, Nujiang, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada
| | - Zi-Jie Zhang
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan and School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, United Kingdom
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China,Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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20
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Pokrovac I, Pezer Ž. Recent advances and current challenges in population genomics of structural variation in animals and plants. Front Genet 2022; 13:1060898. [PMID: 36523759 PMCID: PMC9745067 DOI: 10.3389/fgene.2022.1060898] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/15/2022] [Indexed: 05/02/2024] Open
Abstract
The field of population genomics has seen a surge of studies on genomic structural variation over the past two decades. These studies witnessed that structural variation is taxonomically ubiquitous and represent a dominant form of genetic variation within species. Recent advances in technology, especially the development of long-read sequencing platforms, have enabled the discovery of structural variants (SVs) in previously inaccessible genomic regions which unlocked additional structural variation for population studies and revealed that more SVs contribute to evolution than previously perceived. An increasing number of studies suggest that SVs of all types and sizes may have a large effect on phenotype and consequently major impact on rapid adaptation, population divergence, and speciation. However, the functional effect of the vast majority of SVs is unknown and the field generally lacks evidence on the phenotypic consequences of most SVs that are suggested to have adaptive potential. Non-human genomes are heavily under-represented in population-scale studies of SVs. We argue that more research on other species is needed to objectively estimate the contribution of SVs to evolution. We discuss technical challenges associated with SV detection and outline the most recent advances towards more representative reference genomes, which opens a new era in population-scale studies of structural variation.
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Affiliation(s)
| | - Željka Pezer
- Laboratory for Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
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21
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Dysin AP, Shcherbakov YS, Nikolaeva OA, Terletskii VP, Tyshchenko VI, Dementieva NV. Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics. Genes (Basel) 2022; 13:genes13122221. [PMID: 36553488 PMCID: PMC9778375 DOI: 10.3390/genes13122221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/19/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance.
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Affiliation(s)
- Artem P. Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
- Correspondence:
| | - Yuri S. Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Olga A. Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Valerii P. Terletskii
- All-Russian Research Veterinary Institute of Poultry Science-Branch of the Federal Scientific Center, All-Russian Research and Technological Poultry Institute (ARRVIPS), Lomonosov, 198412 St. Petersburg, Russia
| | - Valentina I. Tyshchenko
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Natalia V. Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
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22
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Zhang XM, Yan M, Yang Z, Xiang H, Tang W, Cai X, Wu Q, Liu X, Pei G, Li J. Creation of artificial karyotypes in mice reveals robustness of genome organization. Cell Res 2022; 32:1026-1029. [PMID: 36127403 PMCID: PMC9652337 DOI: 10.1038/s41422-022-00722-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 08/30/2022] [Indexed: 01/31/2023] Open
Affiliation(s)
- Xiaoyu Merlin Zhang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Meng Yan
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Zhenhua Yang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Hao Xiang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wei Tang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xindong Cai
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Qigui Wu
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xin Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Gang Pei
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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23
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Morgan AP, Hughes JJ, Didion JP, Jolley WJ, Campbell KJ, Threadgill DW, Bonhomme F, Searle JB, de Villena FPM. Population structure and inbreeding in wild house mice (Mus musculus) at different geographic scales. Heredity (Edinb) 2022; 129:183-194. [PMID: 35764696 PMCID: PMC9411160 DOI: 10.1038/s41437-022-00551-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 11/08/2022] Open
Abstract
House mice (Mus musculus) have spread globally as a result of their commensal relationship with humans. In the form of laboratory strains, both inbred and outbred, they are also among the most widely used model organisms in biomedical research. Although the general outlines of house mouse dispersal and population structure are well known, details have been obscured by either limited sample size or small numbers of markers. Here we examine ancestry, population structure, and inbreeding using SNP microarray genotypes in a cohort of 814 wild mice spanning five continents and all major subspecies of Mus, with a focus on M. m. domesticus. We find that the major axis of genetic variation in M. m. domesticus is a south-to-north gradient within Europe and the Mediterranean. The dominant ancestry component in North America, Australia, New Zealand, and various small offshore islands are of northern European origin. Next we show that inbreeding is surprisingly pervasive and highly variable, even between nearby populations. By inspecting the length distribution of homozygous segments in individual genomes, we find that inbreeding in commensal populations is mostly due to consanguinity. Our results offer new insight into the natural history of an important model organism for medicine and evolutionary biology.
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Affiliation(s)
- Andrew P Morgan
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
- Department of Medicine, Duke University Hospital, Durham, NC, USA.
| | - Jonathan J Hughes
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - John P Didion
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Independent Scientist, San Diego, CA, USA
| | | | | | - David W Threadgill
- Institute for Genome Sciences and Society, Texas A&M University, College Station, TX, USA
| | - Francois Bonhomme
- Institut des Sciences de l'Évolution Montpellier, Université de Montpellier, Montpellier, France
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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24
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Cappelletti E, Piras FM, Sola L, Santagostino M, Abdelgadir WA, Raimondi E, Lescai F, Nergadze SG, Giulotto E. Robertsonian fusion and centromere repositioning contributed to the formation of satellite-free centromeres during the evolution of zebras. Mol Biol Evol 2022; 39:6650076. [PMID: 35881460 PMCID: PMC9356731 DOI: 10.1093/molbev/msac162] [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] [Indexed: 11/13/2022] Open
Abstract
Centromeres are epigenetically specified by the histone H3 variant CENP-A and typically associated to highly repetitive satellite DNA. We previously discovered natural satellite-free neocentromeres in Equus caballus and E. asinus. Here, through ChIP-seq with an anti-CENP-A antibody, we found an extraordinarily high number of centromeres lacking satellite DNA in the zebras E. burchelli (15 of 22) and E. grevyi (13 of 23), demonstrating that the absence of satellite DNA at the majority of centromeres is compatible with genome stability and species survival and challenging the role of satellite DNA in centromere function. Nine satellite-free centromeres are shared between the two species in agreement with their recent separation. We assembled all centromeric regions and improved the reference genome of E. burchelli. Sequence analysis of the CENP-A binding domains revealed that they are LINE-1 and AT-rich with four of them showing DNA amplification. In the two zebras, satellite-free centromeres emerged from centromere repositioning or following Robertsonian fusion. In five chromosomes, the centromeric function arose near the fusion points, which are located within regions marked by traces of ancestral pericentromeric sequences. Therefore, besides centromere repositioning, Robertsonian fusions are an important source of satellite-free centromeres during evolution. Finally, in one case, a satellite-free centromere was seeded on an inversion breakpoint. At eleven chromosomes, whose primary constrictions seemed to be associated to satellite repeats by cytogenetic analysis, satellite-free neocentromeres were instead located near the ancestral inactivated satellite-based centromeres, therefore, the centromeric function has shifted away from a satellite repeat containing locus to a satellite-free new position.
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Affiliation(s)
- Eleonora Cappelletti
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Francesca M Piras
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Lorenzo Sola
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Marco Santagostino
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Wasma A Abdelgadir
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Elena Raimondi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Francesco Lescai
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Solomon G Nergadze
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Elena Giulotto
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
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25
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Mouse oocytes carrying metacentric Robertsonian chromosomes have fewer crossover sites and higher aneuploidy rates than oocytes carrying acrocentric chromosomes alone. Sci Rep 2022; 12:12028. [PMID: 35835815 PMCID: PMC9283534 DOI: 10.1038/s41598-022-16175-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 07/06/2022] [Indexed: 12/03/2022] Open
Abstract
Meiotic homologous recombination during fetal development dictates proper chromosome segregation in adult mammalian oocytes. Successful homologous synapsis and recombination during Meiotic Prophase I (MPI) depends on telomere-led chromosome movement along the nuclear envelope. In mice, all chromosomes are acrocentric, while other mammalian species carry a mixture of acrocentric and metacentric chromosomes. Such differences in telomeric structures may explain the exceptionally low aneuploidy rates in mice. Here, we tested whether the presence of metacentric chromosomes carrying Robertsonian translocations (RbT) affects the rate of homologous recombination or aneuploidy. We found a delay in MPI progression in RbT-carrier vs. wild-type (WT) fetal ovaries. Furthermore, resolution of distal telomere clusters, associated with synapsis initiation, was delayed and centromeric telomere clusters persisted until later MPI substages in RbT-carrier oocytes compared to WT oocytes. When chromosomes fully synapsed, higher percentages of RbT-carrier oocytes harbored at least one chromosome pair lacking MLH1 foci, which indicate crossover sites, compared to WT oocytes. Aneuploidy rates in ovulated eggs were also higher in RbT-carrier females than in WT females. In conclusion, the presence of metacentric chromosomes among acrocentric chromosomes in mouse oocytes delays MPI progression and reduces the efficiency of homologous crossover, resulting in a higher frequency of aneuploidy.
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26
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Dudka D, Lampson MA. Centromere drive: model systems and experimental progress. Chromosome Res 2022; 30:187-203. [PMID: 35731424 DOI: 10.1007/s10577-022-09696-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 11/28/2022]
Abstract
Centromeres connect chromosomes and spindle microtubules to ensure faithful chromosome segregation. Paradoxically, despite this conserved function, centromeric DNA evolves rapidly and centromeric proteins show signatures of positive selection. The centromere drive hypothesis proposes that centromeric DNA can act like a selfish genetic element and drive non-Mendelian segregation during asymmetric female meiosis. Resulting fitness costs lead to genetic conflict with the rest of the genome and impose a selective pressure for centromeric proteins to adapt by suppressing the costs. Here, we describe experimental model systems for centromere drive in yellow monkeyflowers and mice, summarize key findings demonstrating centromere drive, and explain molecular mechanisms. We further discuss efforts to test if centromeric proteins are involved in suppressing drive-associated fitness costs, highlight a model for centromere drive and suppression in mice, and put forth outstanding questions for future research.
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Affiliation(s)
- Damian Dudka
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Michael A Lampson
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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27
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Lucek K, Augustijnen H, Escudero M. A holocentric twist to chromosomal speciation? Trends Ecol Evol 2022; 37:655-662. [PMID: 35484024 DOI: 10.1016/j.tree.2022.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 10/18/2022]
Abstract
Chromosomal rearrangements trigger speciation by acting as barriers to gene flow. However, the underlying theory was developed with monocentric chromosomes in mind. Holocentric chromosomes, lacking a centromeric region, have repeatedly evolved and account for a significant fraction of extant biodiversity. Because chromosomal rearrangements may be more likely retained in holocentric species, holocentricity could provide a twist to chromosomal speciation. Here, we discuss how the abundance of chromosome-scale genomes, combined with novel analytical tools, offer the opportunity to assess the impacts of chromosomal rearrangements on rates of speciation by outlining a phylogenetic framework that aligns with the two major lines of chromosomal speciation theory. We further highlight how holocentric species could help to test for causal roles of chromosomal rearrangements in speciation.
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Affiliation(s)
- Kay Lucek
- Department of Environmental Sciences, University of Basel, Schönbeinstrasse 6, 4056 Basel, Switzerland.
| | - Hannah Augustijnen
- Department of Environmental Sciences, University of Basel, Schönbeinstrasse 6, 4056 Basel, Switzerland
| | - Marcial Escudero
- Department of Plant Biology and Ecology, University of Seville, Reina Mercedes, ES-41012 Seville, Spain
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28
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Searle JB, de Villena FPM. The evolutionary significance of meiotic drive. Heredity (Edinb) 2022; 129:44-47. [PMID: 35468941 DOI: 10.1038/s41437-022-00534-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/01/2022] [Accepted: 04/03/2022] [Indexed: 01/08/2023] Open
Affiliation(s)
- Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA.
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29
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Lypska A, Riabchenko N, Rodionova N, Burdo O. Radiation-induced effects on bone marrow of bank voles inhabiting the Chornobyl exclusion zone. Int J Radiat Biol 2022; 98:1366-1375. [PMID: 35230914 DOI: 10.1080/09553002.2022.2047823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
PURPOSE To investigate the effects of chronic exposure to low-dose radiation on bone marrow hematopoiesis of bank voles inhabiting the radioactively contaminated territory of the Chornobyl exclusion zone. MATERIALS AND METHODS Animals were collected within the highly radioactive area of the so-called Red Forest located close to the destroyed 4th reactor of the Chornobyl Nuclear Power Plant. Radioecological investigations included evaluation of radiocontamination of soil samples by 90Sr and 137Cs, levels of incorporated radionuclides in animals' bodies and organs, as well as the absorbed dose rates. The study of peripheral blood and bone marrow parameters combined with cytogenetic analysis of bone marrow micronucleated polychromatic erythrocytes and standard metaphase test was carried out. RESULTS The blood system of the exposed animals manifested significant changes in peripheral blood parameters (anaemia and leucocyte formula left shift), ineffective differentiation and maturation of bone marrow cells, particularly relevant to the erythroid and granulocyte pools. Increased yields of bone marrow micronucleated polychromatic erythrocytes and chromosomal aberrations, including dicentrics and Robertsonian fusion-like configurations, were revealed. CONCLUSIONS Observed disturbances in the bone marrow and peripheral blood suggest functional instability and inefficient compensatory and recovery reactions of the blood system of the bank voles from the contaminated areas of the Chornobyl exclusion zone. We assume that they are the consequences both of direct radiation exposure and hereditary pathological changes that have formed in a number of generations inhabiting radioactively contaminated areas.
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Affiliation(s)
- Alla Lypska
- Department of Radiobiology and Radioecology, Institute for Nuclear Research of NAS of Ukraine, Kyiv, Ukraine
| | - Natalia Riabchenko
- Department of Radiobiology and Radioecology, Institute for Nuclear Research of NAS of Ukraine, Kyiv, Ukraine
| | - Natalia Rodionova
- Department of Radiobiology and Radioecology, Institute for Nuclear Research of NAS of Ukraine, Kyiv, Ukraine
| | - Olena Burdo
- Department of Radiobiology and Radioecology, Institute for Nuclear Research of NAS of Ukraine, Kyiv, Ukraine
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30
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Potter S, Bragg JG, Turakulov R, Eldridge MDB, Deakin J, Kirkpatrick M, Edwards RJ, Moritz C. Limited introgression between rock-wallabies with extensive chromosomal rearrangements. Mol Biol Evol 2021; 39:6448774. [PMID: 34865126 PMCID: PMC8788226 DOI: 10.1093/molbev/msab333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chromosome rearrangements can result in the rapid evolution of hybrid incompatibilities. Robertsonian fusions, particularly those with monobrachial homology, can drive reproductive isolation amongst recently diverged taxa. The recent radiation of rock-wallabies (genus Petrogale) is an important model to explore the role of Robertsonian fusions in speciation. Here, we pursue that goal using an extensive sampling of populations and genomes of Petrogale from north-eastern Australia. In contrast to previous assessments using mitochondrial DNA or nuclear microsatellite loci, genomic data are able to separate the most closely related species and to resolve their divergence histories. Both phylogenetic and population genetic analyses indicate introgression between two species that differ by a single Robertsonian fusion. Based on the available data, there is also evidence for introgression between two species which share complex chromosomal rearrangements. However, the remaining results show no consistent signature of introgression amongst species pairs and where evident, indicate generally low introgression overall. X-linked loci have elevated divergence compared with autosomal loci indicating a potential role for genic evolution to produce reproductive isolation in concert with chromosome change. Our results highlight the value of genome scale data in evaluating the role of Robertsonian fusions and structural variation in divergence, speciation, and patterns of molecular evolution.
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Affiliation(s)
- Sally Potter
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia.,Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Jason G Bragg
- National Herbarium of New South Wales, The Royal Botanical Gardens and Domain Trust, Sydney, NSW, Australia
| | - Rustamzhon Turakulov
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, Sydney, NSW, Australia
| | - Janine Deakin
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, TX, United States of America
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
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31
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How Important Are Structural Variants for Speciation? Genes (Basel) 2021; 12:genes12071084. [PMID: 34356100 PMCID: PMC8305853 DOI: 10.3390/genes12071084] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/04/2021] [Accepted: 07/14/2021] [Indexed: 12/11/2022] Open
Abstract
Understanding the genetic basis of reproductive isolation is a central issue in the study of speciation. Structural variants (SVs); that is, structural changes in DNA, including inversions, translocations, insertions, deletions, and duplications, are common in a broad range of organisms and have been hypothesized to play a central role in speciation. Recent advances in molecular and statistical methods have identified structural variants, especially inversions, underlying ecologically important traits; thus, suggesting these mutations contribute to adaptation. However, the contribution of structural variants to reproductive isolation between species—and the underlying mechanism by which structural variants most often contribute to speciation—remain unclear. Here, we review (i) different mechanisms by which structural variants can generate or maintain reproductive isolation; (ii) patterns expected with these different mechanisms; and (iii) relevant empirical examples of each. We also summarize the available sequencing and bioinformatic methods to detect structural variants. Lastly, we suggest empirical approaches and new research directions to help obtain a more complete assessment of the role of structural variants in speciation.
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32
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Katsube T, Wang B, Tanaka K, Ninomiya Y, Hirakawa H, Liu C, Maruyama K, Vares G, Liu Q, Kito S, Nakajima T, Fujimori A, Nenoi M. Synergistic Effects of Chronic Restraint-Induced Stress and Low-Dose 56Fe-particle Irradiation on Induction of Chromosomal Aberrations in Trp53-Heterozygous Mice. Radiat Res 2021; 196:100-112. [PMID: 33901294 DOI: 10.1667/rade-20-00218.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/26/2021] [Indexed: 11/03/2022]
Abstract
Astronauts can develop psychological stress (PS) during space flights due to the enclosed environment, microgravity, altered light-dark cycles, and risks of equipment failure or fatal mishaps. At the same time, they are exposed to cosmic rays including high atomic number and energy (HZE) particles such as iron-56 (Fe) ions. Psychological stress or radiation exposure can cause detrimental effects in humans. An earlier published pioneering study showed that chronic restraint-induced psychological stress (CRIPS) could attenuate Trp53 functions and increase carcinogenesis induced by low-linear energy transfer (LET) γ rays in Trp53-heterozygous (Trp53+/-) mice. To elucidate possible modification effects from CRIPS on high-LET HZE particle-induced health consequences, Trp53+/- mice were received both CRIPS and accelerated Fe ion irradiation. Six-week-old Trp53+/- C57BL/6N male mice were restrained 6 h per day for 28 consecutive days. On day 8, they received total-body Fe-particle irradiation (Fe-TBI, 0.1 or 2 Gy). Metaphase chromosome spreads prepared from splenocytes at the end of the 28-day restraint regimen were painted with the fluorescence in situ hybridization (FISH) probes for chromosomes 1 (green), 2 (red) and 3 (yellow). Induction of psychological stress in our experimental model was confirmed by increase in urinary corticosterone level on day 7 of restraint regimen. Regardless of Fe-TBI, CRIPS reduced splenocyte number per spleen at the end of the 28-day restraint regimen. At 2 Gy, Fe-TBI alone induced many aberrant chromosomes and no modifying effect was detected from CRIPS on induction of aberrant chromosomes. Notably, neither Fe-TBI at 0.1 Gy nor CRIPS alone induced any increase in the frequency of aberrant chromosomes, while simultaneous exposure resulted in a significant increase in the frequency of chromosomal exchanges. These findings clearly showed that CRIPS could enhance the frequency of chromosomal exchanges induced by Fe-TBI at a low dose of 0.1 Gy.
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Affiliation(s)
- Takanori Katsube
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba
| | - Bing Wang
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba
| | - Kaoru Tanaka
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba
| | - Yasuharu Ninomiya
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba
| | - Hirokazu Hirakawa
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba
| | - Cuihua Liu
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba
| | - Kouichi Maruyama
- Center for Advanced Radiation Emergency Medicine, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan
| | - Guillaume Vares
- Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Qiang Liu
- Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300192, PR China
| | - Seiji Kito
- Center for Animal Research and Education, Nagoya University, Nagoya 464-8601, Japan
| | - Tetsuo Nakajima
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba
| | - Akira Fujimori
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba
| | - Mitsuru Nenoi
- National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba
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33
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Thakur J, Packiaraj J, Henikoff S. Sequence, Chromatin and Evolution of Satellite DNA. Int J Mol Sci 2021; 22:ijms22094309. [PMID: 33919233 PMCID: PMC8122249 DOI: 10.3390/ijms22094309] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 12/15/2022] Open
Abstract
Satellite DNA consists of abundant tandem repeats that play important roles in cellular processes, including chromosome segregation, genome organization and chromosome end protection. Most satellite DNA repeat units are either of nucleosomal length or 5–10 bp long and occupy centromeric, pericentromeric or telomeric regions. Due to high repetitiveness, satellite DNA sequences have largely been absent from genome assemblies. Although few conserved satellite-specific sequence motifs have been identified, DNA curvature, dyad symmetries and inverted repeats are features of various satellite DNAs in several organisms. Satellite DNA sequences are either embedded in highly compact gene-poor heterochromatin or specialized chromatin that is distinct from euchromatin. Nevertheless, some satellite DNAs are transcribed into non-coding RNAs that may play important roles in satellite DNA function. Intriguingly, satellite DNAs are among the most rapidly evolving genomic elements, such that a large fraction is species-specific in most organisms. Here we describe the different classes of satellite DNA sequences, their satellite-specific chromatin features, and how these features may contribute to satellite DNA biology and evolution. We also discuss how the evolution of functional satellite DNA classes may contribute to speciation in plants and animals.
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Affiliation(s)
- Jitendra Thakur
- Department of Biology, Emory University, Atlanta, GA 30322, USA;
- Correspondence:
| | - Jenika Packiaraj
- Department of Biology, Emory University, Atlanta, GA 30322, USA;
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
- Fred Hutchinson Cancer Research Center, Howard Hughes Medical Institute, Seattle, WA 98109, USA
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Kazemi P, Taketo T. Two telomeric ends of acrocentric chromosome play distinct roles in homologous chromosome synapsis in the fetal mouse oocyte. Chromosoma 2021; 130:41-52. [PMID: 33492414 DOI: 10.1007/s00412-021-00752-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 12/16/2022]
Abstract
In mammalian oocytes, proper chromosome segregation at the first meiotic division is dictated by the presence and site of homologous chromosome recombination, which takes place in fetal life. Our current understanding of how homologous chromosomes find each other and initiate synapsis, which is prerequisite for homologous recombination, is limited. It is known that chromosome telomeres are anchored into the nuclear envelope (NE) at the early meiotic prophase I (MPI) and move along NE to facilitate homologous chromosome search and pairing. However, the mouse (Mus musculus) carries all acrocentric chromosomes with one telomeric end close to the centromere (subcentromeric telomere; C-telomere) and the other far away from the centromere (distal telomere; D-telomere), and how C- and D-telomeres participate in chromosome pairing and synapsis during the MPI progression is not well understood. Here, we found in the mouse oocyte that C- and D-telomeres transiently clustered in one area, but D-telomeres soon separated together from C-telomeres and then dispersed to preferentially initiate synapsis, while C-telomeres remained in clusters and synapsed at the last. In the Spo11 null oocyte, which is deficient in SPO11-dependent DSBs formation and homologous synapsis, the pattern of C- and D-telomere clustering and resolution was not affected, but synapsis was more frequently initiated at C-telomeres. These results suggest that SPO11 suppresses the early synapsis between C-telomeres in clusters.
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Affiliation(s)
- Parinaz Kazemi
- Department of Biology, McGill University, Montreal, QC, H3A 1B1, Canada
| | - Teruko Taketo
- Department of Biology, McGill University, Montreal, QC, H3A 1B1, Canada. .,Department of Surgery, McGill University, RI-MUHC, Montreal, QC, H4A 3J1, Canada. .,Department of Obstetrics/Gynecology, McGill University, RI-MUHC, Montreal, QC, H4A 3J1, Canada.
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Cherezov RO, Vorontsova JE, Simonova OB. TBP-Related Factor 2 as a Trigger for Robertsonian Translocations and Speciation. Int J Mol Sci 2020; 21:E8871. [PMID: 33238614 PMCID: PMC7700478 DOI: 10.3390/ijms21228871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 11/16/2022] Open
Abstract
Robertsonian (centric-fusion) translocation is the form of chromosomal translocation in which two long arms of acrocentric chromosomes are fused to form one metacentric. These translocations reduce the number of chromosomes while preserving existing genes and are considered to contribute to speciation. We asked whether hypomorphic mutations in genes that disrupt the formation of pericentromeric regions could lead to centric fusion. TBP-related factor 2 (Trf2) encodes an alternative general transcription factor. A decrease of TRF2 expression disrupts the structure of the pericentromeric regions and prevents their association into chromocenter. We revealed several centric fusions in two lines of Drosophila melanogaster with weak Trf2 alleles in genetic experiments. We performed an RNAi-mediated knock-down of Trf2 in Drosophila and S2 cells and demonstrated that Trf2 upregulates expression of D1-one of the major genes responsible for chromocenter formation and nuclear integrity in Drosophila. Our data, for the first time, indicate that Trf2 may be involved in transcription program responsible for structuring of pericentromeric regions and may contribute to new karyotypes formation in particular by promoting centric fusion. Insight into the molecular mechanisms of Trf2 function and its new targets in different tissues will contribute to our understanding of its phenomenon.
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Affiliation(s)
| | | | - Olga B. Simonova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova str. 26, 119991 Moscow, Russia; (R.O.C.); (J.E.V.)
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Di-Nizo CB, Ferguson-Smith MA, Silva MJDJ. Extensive genomic reshuffling involved in the karyotype evolution of genus Cerradomys (Rodentia: Sigmodontinae: Oryzomyini). Genet Mol Biol 2020; 43:e20200149. [PMID: 33306775 PMCID: PMC7783725 DOI: 10.1590/1678-4685-gmb-2020-0149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 09/07/2020] [Indexed: 11/22/2022] Open
Abstract
Rodents of the genus Cerradomys belong to the tribe Oryzomyini
and present high chromosome variability with diploid numbers ranging from 2n=46
to 60. Classical cytogenetics and fluorescence in situ
hybridization (FISH) with telomeric and whole chromosome-specific probes of
another Oryzomyini, Oligoryzomys moojeni (OMO), were used to
assess the karyotype evolution of the genus. Results were integrated into a
molecular phylogeny to infer the hypothetical direction of chromosome changes.
The telomeric FISH showed signals in telomeres in species that diverged early in
the phylogeny, plus interstitial telomeric signals (ITS) in some species from
the most derived clades (C. langguthi,C. vivoi, C. goytaca, and C.
subflavus). Chromosome painting revealed homology from 23 segments
of C. maracajuensis and C. marinhus to 32 of
C. vivoi. Extensive chromosome reorganization was
responsible for karyotypic differences in closely related species. Major drivers
for genomic reshuffling were in tandem and centric fusion,
fission, paracentric and pericentric inversions or centromere repositioning.
Chromosome evolution was associated with an increase and decrease in diploid
number in different lineages and ITS indicate remnants of ancient telomeres.
Cytogenetics results corroborates that C. goytaca is not a
junior synonym of C. subflavus since the karyotypic differences
found may lead to reproductive isolation.
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Affiliation(s)
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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Gil-Fernández A, Saunders PA, Martín-Ruiz M, Ribagorda M, López-Jiménez P, Jeffries DL, Parra MT, Viera A, Rufas JS, Perrin N, Veyrunes F, Page J. Meiosis reveals the early steps in the evolution of a neo-XY sex chromosome pair in the African pygmy mouse Mus minutoides. PLoS Genet 2020; 16:e1008959. [PMID: 33180767 PMCID: PMC7685469 DOI: 10.1371/journal.pgen.1008959] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/24/2020] [Accepted: 10/06/2020] [Indexed: 01/30/2023] Open
Abstract
Sex chromosomes of eutherian mammals are highly different in size and gene content, and share only a small region of homology (pseudoautosomal region, PAR). They are thought to have evolved through an addition-attrition cycle involving the addition of autosomal segments to sex chromosomes and their subsequent differentiation. The events that drive this process are difficult to investigate because sex chromosomes in almost all mammals are at a very advanced stage of differentiation. Here, we have taken advantage of a recent translocation of an autosome to both sex chromosomes in the African pygmy mouse Mus minutoides, which has restored a large segment of homology (neo-PAR). By studying meiotic sex chromosome behavior and identifying fully sex-linked genetic markers in the neo-PAR, we demonstrate that this region shows unequivocal signs of early sex-differentiation. First, synapsis and resolution of DNA damage intermediates are delayed in the neo-PAR during meiosis. Second, recombination is suppressed or largely reduced in a large portion of the neo-PAR. However, the inactivation process that characterizes sex chromosomes during meiosis does not extend to this region. Finally, the sex chromosomes show a dual mechanism of association at metaphase-I that involves the formation of a chiasma in the neo-PAR and the preservation of an ancestral achiasmate mode of association in the non-homologous segments. We show that the study of meiosis is crucial to apprehend the onset of sex chromosome differentiation, as it introduces structural and functional constrains to sex chromosome evolution. Synapsis and DNA repair dynamics are the first processes affected in the incipient differentiation of X and Y chromosomes, and they may be involved in accelerating their evolution. This provides one of the very first reports of early steps in neo-sex chromosome differentiation in mammals, and for the first time a cellular framework for the addition-attrition model of sex chromosome evolution. Sex chromosomes seem to evolve and differentiate at different rates in different taxa. The reasons for this variability are still debated. It is well established that recombination suppression around the sex-determining region triggers differentiation, and several studies have investigated this process from a genetic point of view. However, the cellular context in which recombination arrest occurs has received little attention so far. In this report, we show that meiosis, the cellular division in which pairing and recombination between chromosomes takes place, can affect the incipient differentiation of X and Y chromosomes. Combining cytogenetic and genomic approaches, we found that in the African pygmy mouse Mus minutoides, which has recently undergone sex chromosome-autosome fusions, synapsis and DNA repair dynamics are disturbed along the newly added region of the sex chromosomes. We argue that these alterations are a by-product of the fusion itself, and cause recombination suppression across a large region of the neo-sex chromosome pair. Therefore, we propose that the meiotic context in which sex or neo-sex chromosomes arise is crucial to understand the very early stages of their differentiation, as it could promote or hinder recombination suppression, and therefore impact the rate at which these chromosomes differentiate.
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Affiliation(s)
- Ana Gil-Fernández
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Paul A. Saunders
- Institut des Sciences de l'Evolution, ISEM UMR 5554 (CNRS/Université Montpellier/IRD/EPHE), Montpellier, France
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Marta Martín-Ruiz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marta Ribagorda
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pablo López-Jiménez
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Daniel L. Jeffries
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - María Teresa Parra
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Alberto Viera
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Julio S. Rufas
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Frederic Veyrunes
- Institut des Sciences de l'Evolution, ISEM UMR 5554 (CNRS/Université Montpellier/IRD/EPHE), Montpellier, France
| | - Jesús Page
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
- * E-mail:
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de Vos JM, Augustijnen H, Bätscher L, Lucek K. Speciation through chromosomal fusion and fission in Lepidoptera. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190539. [PMID: 32654638 DOI: 10.1098/rstb.2019.0539] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Changes in chromosome numbers may strongly affect reproductive barriers, because individuals heterozygous for distinct karyotypes are typically expected to be at least partially sterile or to show reduced recombination. Therefore, several classic speciation models are based on chromosomal changes. One import mechanism generating variation in chromosome numbers is fusion and fission of existing chromosomes, which is particularly likely in species with holocentric chromosomes, i.e. chromosomes that lack a single centromere. Holocentric chromosomes evolved repeatedly across the tree of life, including in Lepidoptera. Although changes in chromosome numbers are hypothesized to be an important driver of the spectacular diversification of Lepidoptera, comparative studies across the order are lacking. We performed the first comprehensive literature survey of karyotypes for Lepidoptera species since the 1970s and tested if, and how, chromosomal variation might affect speciation. Even though a meta-analysis of karyological differences between closely related taxa did not reveal an effect on the degree of reproductive isolation, phylogenetic diversification rate analyses across the 16 best-covered genera indicated a strong, positive association of rates of chromosome number evolution and speciation. These findings suggest a macroevolutionary impact of varying chromosome numbers in Lepidoptera and likely apply to other taxonomic groups, especially to those with holocentric chromosomes. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
- Jurriaan M de Vos
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Hannah Augustijnen
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Livio Bätscher
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Kay Lucek
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
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Meiotic Chromosome Contacts as a Plausible Prelude for Robertsonian Translocations. Genes (Basel) 2020; 11:genes11040386. [PMID: 32252399 PMCID: PMC7230836 DOI: 10.3390/genes11040386] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/28/2020] [Accepted: 03/31/2020] [Indexed: 12/12/2022] Open
Abstract
Robertsonian translocations are common chromosomal alterations. Chromosome variability affects human health and natural evolution. Despite the significance of such mutations, no mechanisms explaining the emergence of such translocations have yet been demonstrated. Several models have explored possible changes in interphase nuclei. Evidence for non-homologous chromosomes end joining in meiosis is scarce, and is often limited to uncovering mechanisms in damaged cells only. This study presents a primarily qualitative analysis of contacts of non-homologous chromosomes by short arms, during meiotic prophase I in the mole vole, Ellobius alaicus, a species with a variable karyotype, due to Robertsonian translocations. Immunocytochemical staining of spermatocytes demonstrated the presence of four contact types for non-homologous chromosomes in meiotic prophase I: (1) proximity, (2) touching, (3) anchoring/tethering, and (4) fusion. Our results suggest distinct mechanisms for chromosomal interactions in meiosis. Thus, we propose to change the translocation mechanism model from ‘contact first’ to ‘contact first in meiosis’.
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40
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Xia Y, Yuan X, Luo W, Yuan S, Zeng X. The Origin and Evolution of Chromosomal Reciprocal Translocation in Quasipaa boulengeri (Anura, Dicroglossidae). Front Genet 2020; 10:1364. [PMID: 32038718 PMCID: PMC6985567 DOI: 10.3389/fgene.2019.01364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/12/2019] [Indexed: 11/28/2022] Open
Abstract
Chromosomal rearrangements have long fascinated evolutionary biologists for being widely implicated in causing genetic differentiation. Suppressed recombination has been demonstrated in various species with inversion; however, there is controversy over whether such recombination suppression would facilitate divergence in reciprocal translocation with reduced fitness. In this study, we used the spiny frog, Quasipaa boulengeri, whose western Sichuan Basin populations exhibit translocation polymorphisms, to test whether the genetic markers on translocated (rearranged) or normal chromosomes have driven this genetic differentiation. We also investigated its overall genetic structure and the possibility of chromosomal fixation. Whole-chromosome painting and genetic structure clustering suggested a single origin of the translocation polymorphisms, and high-throughput sequencing of rearranged chromosomes isolated many markers with known localizations on chromosomes. Using these markers, distinct patterns of gene flow were found between rearranged and normal chromosomes. Genetic differentiation was only found in the translocated chromosomes, not in normal chromosomes or the mitochondrial genome. Hybrid unfitness cannot explain the genetic differentiation, as then the differentiation would be observed throughout the whole genome. Our results suggest that suppressed recombination drives genetic differentiation into a balanced chromosomal polymorphism. Mapping to a reference genome, we found that the region of genetic differentiation covered a wide range of translocated chromosomes, not only in the vicinity of chromosomal breakpoints. Our results imply that the suppressed recombination region could be extended by accumulation of repetitive sequences or capture of alleles that are adapted to the local environment, following the spread and/or fixation of chromosomal rearrangement.
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Affiliation(s)
- Yun Xia
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiuyun Yuan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,College of Computer Science, Sichuan University, Chengdu, China
| | - Wei Luo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Siqi Yuan
- College of Bioengineering, Sichuan University of Science & Engineering, Zigong, China
| | - Xiaomao Zeng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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41
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Romanenko SA, Lyapunova EA, Saidov AS, O'Brien PCM, Serdyukova NA, Ferguson-Smith MA, Graphodatsky AS, Bakloushinskaya I. Chromosome Translocations as a Driver of Diversification in Mole Voles Ellobius (Rodentia, Mammalia). Int J Mol Sci 2019; 20:E4466. [PMID: 31510061 PMCID: PMC6769443 DOI: 10.3390/ijms20184466] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/04/2019] [Accepted: 09/09/2019] [Indexed: 12/23/2022] Open
Abstract
The involvement of chromosome changes in the initial steps of speciation is controversial. Here we examine diversification trends within the mole voles Ellobius, a group of subterranean rodents. The first description of their chromosome variability was published almost 40 years ago. Studying the G-band structure of chromosomes in numerous individuals revealed subsequent homologous, step-by-step, Robertsonian translocations, which changed diploid numbers from 54 to 30. Here we used a molecular cytogenetic strategy which demonstrates that chromosomal translocations are not always homologous; consequently, karyotypes with the same diploid number can carry different combinations of metacentrics. We further showed that at least three chromosomal forms with 2n = 34 and distinct metacentrics inhabit the Pamir-Alay mountains. Each of these forms independently hybridized with E. tancrei, 2n = 54, forming separate hybrid zones. The chromosomal variations correlate slightly with geographic barriers. Additionally, we confirmed that the emergence of partial or monobrachial homology appeared to be a strong barrier for hybridization in nature, in contradistinction to experiments which we reported earlier. We discuss the possibility of whole arm reciprocal translocations for mole voles. Our findings suggest that chromosomal translocations lead to diversification and speciation.
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Affiliation(s)
- Svetlana A Romanenko
- Institute of Molecular and Cellular Biology, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia.
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia.
| | - Elena A Lyapunova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia.
| | - Abdusattor S Saidov
- Institute of Zoology and Parasitology, Academy of Sciences of Tajikistan, Dushanbe 734025, Tajikistan.
| | - Patricia C M O'Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Natalia A Serdyukova
- Institute of Molecular and Cellular Biology, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia.
| | - Malcolm A Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia.
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia.
| | - Irina Bakloushinskaya
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia.
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42
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Deakin JE, Potter S, O'Neill R, Ruiz-Herrera A, Cioffi MB, Eldridge MDB, Fukui K, Marshall Graves JA, Griffin D, Grutzner F, Kratochvíl L, Miura I, Rovatsos M, Srikulnath K, Wapstra E, Ezaz T. Chromosomics: Bridging the Gap between Genomes and Chromosomes. Genes (Basel) 2019; 10:genes10080627. [PMID: 31434289 PMCID: PMC6723020 DOI: 10.3390/genes10080627] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/10/2019] [Accepted: 08/13/2019] [Indexed: 02/07/2023] Open
Abstract
The recent advances in DNA sequencing technology are enabling a rapid increase in the number of genomes being sequenced. However, many fundamental questions in genome biology remain unanswered, because sequence data alone is unable to provide insight into how the genome is organised into chromosomes, the position and interaction of those chromosomes in the cell, and how chromosomes and their interactions with each other change in response to environmental stimuli or over time. The intimate relationship between DNA sequence and chromosome structure and function highlights the need to integrate genomic and cytogenetic data to more comprehensively understand the role genome architecture plays in genome plasticity. We propose adoption of the term 'chromosomics' as an approach encompassing genome sequencing, cytogenetics and cell biology, and present examples of where chromosomics has already led to novel discoveries, such as the sex-determining gene in eutherian mammals. More importantly, we look to the future and the questions that could be answered as we enter into the chromosomics revolution, such as the role of chromosome rearrangements in speciation and the role more rapidly evolving regions of the genome, like centromeres, play in genome plasticity. However, for chromosomics to reach its full potential, we need to address several challenges, particularly the training of a new generation of cytogeneticists, and the commitment to a closer union among the research areas of genomics, cytogenetics, cell biology and bioinformatics. Overcoming these challenges will lead to ground-breaking discoveries in understanding genome evolution and function.
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Affiliation(s)
- Janine E Deakin
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia.
| | - Sally Potter
- Research School of Biology, Australian National University, Acton, ACT 2601, Australia
- Australian Museum Research Institute, Australian Museum, 1 William St Sydney, NSW 2010, Australia
| | - Rachel O'Neill
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Marcelo B Cioffi
- Laboratório de Citogenética de Peixes, Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP 13565-905, Brazil
| | - Mark D B Eldridge
- Australian Museum Research Institute, Australian Museum, 1 William St Sydney, NSW 2010, Australia
| | - Kichi Fukui
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita 565-0871, Osaka, Japan
| | - Jennifer A Marshall Graves
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia
- School of Life Sciences, LaTrobe University, Melbourne, VIC 3168, Australia
| | - Darren Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Frank Grutzner
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 128 44 Prague 2, Czech Republic
| | - Ikuo Miura
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Michail Rovatsos
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics & Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Erik Wapstra
- School of Natural Sciences, University of Tasmania, Hobart 7000, Australia
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia.
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43
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Bakloushinskaya I, Lyapunova EA, Saidov AS, Romanenko SA, O’Brien PC, Serdyukova NA, Ferguson-Smith MA, Matveevsky S, Bogdanov AS. Rapid chromosomal evolution in enigmatic mammal with XX in both sexes, the Alay mole vole Ellobiusalaicus Vorontsov et al., 1969 (Mammalia, Rodentia). COMPARATIVE CYTOGENETICS 2019; 13:147-177. [PMID: 31275526 PMCID: PMC6597615 DOI: 10.3897/compcytogen.v13i2.34224] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/28/2019] [Indexed: 06/01/2023]
Abstract
Evolutionary history and taxonomic position for cryptic species may be clarified by using molecular and cytogenetic methods. The subterranean rodent, the Alay mole vole Ellobiusalaicus Vorontsov et al., 1969 is one of three sibling species constituting the subgenus Ellobius Fischer, 1814, all of which lost the Y chromosome and obtained isomorphic XX sex chromosomes in both males and females. E.alaicus is evaluated by IUCN as a data deficient species because their distribution, biology, and genetics are almost unknown. We revealed specific karyotypic variability (2n = 52-48) in E.alaicus due to different Robertsonian translocations (Rbs). Two variants of hybrids (2n = 53, different Rbs) with E.tancrei Blasius, 1884 were found at the Northern slopes of the Alay Ridge and in the Naryn district, Kyrgyzstan. We described the sudden change in chromosome numbers from 2n = 50 to 48 and specific karyotype structure for mole voles, which inhabit the entrance to the Alay Valley (Tajikistan), and revealed their affiliation as E.alaicus by cytochrome b and fragments of nuclear XIST and Rspo1 genes sequencing. To date, it is possible to expand the range of E.alaicus from the Alay Valley (South Kyrgyzstan) up to the Ferghana Ridge and the Naryn Basin, Tien Shan at the north-east and to the Pamir-Alay Mountains (Tajikistan) at the west. The closeness of E.tancrei and E.alaicus is supported, whereas specific chromosome and molecular changes, as well as geographic distribution, verified the species status for E.alaicus. The case of Ellobius species accented an unevenness in rates of chromosome and nucleotide changes along with morphological similarity, which is emblematic for cryptic species.
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Affiliation(s)
- Irina Bakloushinskaya
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, RussiaKoltzov Institute of Developmental Biology, Russian Academy of SciencesMoscowRussia
| | - Elena A. Lyapunova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, RussiaKoltzov Institute of Developmental Biology, Russian Academy of SciencesMoscowRussia
| | - Abdusattor S. Saidov
- Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe, TajikistanPavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of TajikistanDushanbeTajikistan
| | - Svetlana A. Romanenko
- Institute of Molecular and Cellular Biology, Siberian Branch RAS, Novosibirsk, RussiaInstitute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of SciencesNovosibirskRussia
- Novosibirsk State University, Novosibirsk, RussiaNovosibirsk State UniversityNovosibirskRussia
| | - Patricia C.M. O’Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UKUniversity of CambridgeCambridgeUnited Kingdom
| | - Natalia A. Serdyukova
- Institute of Molecular and Cellular Biology, Siberian Branch RAS, Novosibirsk, RussiaInstitute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of SciencesNovosibirskRussia
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UKUniversity of CambridgeCambridgeUnited Kingdom
| | - Sergey Matveevsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, RussiaVavilov Institute of General Genetics, Russian Academy of SciencesMoscowRussia
| | - Alexey S. Bogdanov
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, RussiaKoltzov Institute of Developmental Biology, Russian Academy of SciencesMoscowRussia
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Bikchurina TI, Tomgorova EK, Torgasheva AA, Bagirov VA, Volkova NA, Borodin PM. Chromosome synapsis, recombination and epigenetic modification in rams heterozygous for metacentric chromosome 3 of the domestic sheep Ovis aries and acrocentric homologs of the argali Ovis ammon. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Hybridization of domestic animal breeds with their wild relatives is a promising method for increasing the genetic diversity of farm animals. Resource populations derived from the hybridization of various breeds of domestic sheep with mouflon and argali are an important source of breeding material. The karyotypes of argali and domestic sheep differ for a Robertsonian translocation, which occurred in the common ancestor of mouflon and domestic sheep (Ovis aries) due to the centric fusion of chromosomes 5 and 11 of the argali (O. ammon) into chromosome 3 of sheep. It is known that heterozygosity for translocation can lead to synapsis, recombination and chromosome segregation abnormalities in meiosis. Meiosis in the heterozygotes for translocation that distinguishes the karyotypes of sheep and argali has not yet been studied. We examined synapsis, recombination, and epigenetic modification of chromosomes involved in this rearrangement in heterozygous rams using immunolocalization of key proteins of meiosis. In the majority of cells, we observed complete synapsis between the sheep metacentric chromosome and two argali acrocentric chromosomes with the formation of a trivalent. In a small proportion of cells at the early pachytene stage we observed delayed synapsis in pericentromeric regions of the trivalent. Unpaired sites were subjected to epigenetic modification, namely histone H2A.X phosphorylation. However, by the end of the pachytene, these abnormalities had been completely eliminated. Asynapsis was replaced by a nonhomologous synapsis between the centromeric regions of the acrocentric chromosomes. By the end of the pachytene, the γH2A.X signal had been preserved only at the XY bivalent and was absent from the trivalent. The translocation trivalent did not differ from the normal bivalents of metacentric chromosomes for the number and distribution of recombination sites as well as for the degree of centromeric and crossover interference. Thus, we found that heterozygosity for the domestic sheep chromosome 3 and argali chromosomes 5 and 11 does not cause significant alterations in key processes of prophase I meiosis and, therefore, should not lead to a decrease in fertility of the offspring from interspecific sheep hybridization.
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Affiliation(s)
- T. I. Bikchurina
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University; Federal Scientific Center for Animal Husbandry – VIZH named after academician L.K. Ernst
| | - E. K. Tomgorova
- Federal Scientific Center for Animal Husbandry – VIZH named after academician L.K. Ernst
| | - A. A. Torgasheva
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University; Federal Scientific Center for Animal Husbandry – VIZH named after academician L.K. Ernst
| | - V. A. Bagirov
- Federal Scientific Center for Animal Husbandry – VIZH named after academician L.K. Ernst
| | - N. A. Volkova
- Federal Scientific Center for Animal Husbandry – VIZH named after academician L.K. Ernst
| | - P. M. Borodin
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University; Federal Scientific Center for Animal Husbandry – VIZH named after academician L.K. Ernst
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Sävilammi T, Primmer CR, Varadharajan S, Guyomard R, Guiguen Y, Sandve SR, Vøllestad LA, Papakostas S, Lien S. The Chromosome-Level Genome Assembly of European Grayling Reveals Aspects of a Unique Genome Evolution Process Within Salmonids. G3 (BETHESDA, MD.) 2019; 9:1283-1294. [PMID: 30833292 PMCID: PMC6505133 DOI: 10.1534/g3.118.200919] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/04/2019] [Indexed: 12/13/2022]
Abstract
Salmonids represent an intriguing taxonomical group for investigating genome evolution in vertebrates due to their relatively recent last common whole genome duplication event, which occurred between 80 and 100 million years ago. Here, we report on the chromosome-level genome assembly of European grayling (Thymallus thymallus), which represents one of the earliest diverged salmonid subfamilies. To achieve this, we first generated relatively long genomic scaffolds by using a previously published draft genome assembly along with long-read sequencing data and a linkage map. We then merged those scaffolds by applying synteny evidence from the Atlantic salmon (Salmo salar) genome. Comparisons of the European grayling genome assembly to the genomes of Atlantic salmon and Northern pike (Esox lucius), the latter used as a nonduplicated outgroup, detailed aspects of the characteristic chromosome evolution process that has taken place in European grayling. While Atlantic salmon and other salmonid genomes are portrayed by the typical occurrence of numerous chromosomal fusions, European grayling chromosomes were confirmed to be fusion-free and were characterized by a relatively large proportion of paracentric and pericentric inversions. We further reported on transposable elements specific to either the European grayling or Atlantic salmon genome, on the male-specific sdY gene in the European grayling chromosome 11A, and on regions under residual tetrasomy in the homeologous European grayling chromosome pairs 9A-9B and 25A-25B. The same chromosome pairs have been observed under residual tetrasomy in Atlantic salmon and in other salmonids, suggesting that this feature has been conserved since the subfamily split.
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Affiliation(s)
- Tiina Sävilammi
- Department of Biology, University of Turku, 20014 Turku, Finland
| | - Craig R Primmer
- Organismal & Evolutionary Biology Research Program, Faculty of Biological & Environmental Sciences
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | | | - René Guyomard
- INRA, UMR1313 GABI Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78352, Jouy-en-Josas Cedex, France
| | - Yann Guiguen
- INRA, UR1037 Fish Physiology and Genomics, F-35000, Rennes, France
| | - Simen R Sandve
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1430 Ås, Norway
| | | | | | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, 1430 Ås, Norway
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Ribagorda M, Berríos S, Solano E, Ayarza E, Martín-Ruiz M, Gil-Fernández A, Parra MT, Viera A, Rufas JS, Capanna E, Castiglia R, Fernández-Donoso R, Page J. Meiotic behavior of a complex hexavalent in heterozygous mice for Robertsonian translocations: insights for synapsis dynamics. Chromosoma 2019; 128:149-163. [PMID: 30826871 DOI: 10.1007/s00412-019-00695-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/27/2019] [Accepted: 02/18/2019] [Indexed: 12/11/2022]
Abstract
Natural populations of the house mouse Mus musculus domesticus show great diversity in chromosomal number due to the presence of chromosomal rearrangements, mainly Robertsonian translocations. Breeding between two populations with different chromosomal configurations generates subfertile or sterile hybrid individuals due to impaired meiotic development. In this study, we have analyzed prophase-I spermatocytes of hybrids formed by crossing mice from Vulcano and Lipari island populations. Both populations have a 2n = 26 karyotype but different combinations of Robertsonian translocations. We studied the progress of synapsis, recombination, and meiotic silencing of unsynapsed chromosomes during prophase-I through the immunolocalization of the proteins SYCP3, SYCP1, γH2AX, RAD51, and MLH1. In these hybrids, a hexavalent is formed that, depending on the degree of synapsis between chromosomes, can adopt an open chain, a ring, or a closed configuration. The frequency of these configurations varies throughout meiosis, with the maximum degree of synapsis occurring at mid pachytene. In addition, we observed the appearance of heterologous synapsis between telocentric and metacentric chromosomes; however, this synapsis seems to be transient and unstable and unsynapsed regions are frequently observed in mid-late pachytene. Interestingly, we found that chiasmata are frequently located at the boundaries of unsynapsed chromosomal regions in the hexavalent during late pachytene. These results provide new clues about synapsis dynamics during meiosis. We propose that mechanical forces generated along chromosomes may induce premature desynapsis, which, in turn, might be counteracted by the location of chiasmata. Despite these and additional meiotic features, such as the accumulation of γH2AX on unsynapsed chromosome regions, we observed a large number of cells that progressed to late stages of prophase-I, indicating that synapsis defects may not trigger a meiotic crisis in these hybrids.
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Affiliation(s)
- Marta Ribagorda
- 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
| | - Emanuela Solano
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Università degli Studi di Roma La Sapienza, Rome, Italy
| | - Eliana Ayarza
- Departamento de Tecnología Médica, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Marta Martín-Ruiz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ana Gil-Fernández
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - María Teresa Parra
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Alberto Viera
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Julio S Rufas
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ernesto Capanna
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Università degli Studi di Roma La Sapienza, Rome, Italy
| | - Riccardo Castiglia
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Università degli Studi di Roma La Sapienza, Rome, Italy
| | - Raúl Fernández-Donoso
- Programa de Genética Humana, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Jesús Page
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain.
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Nucleolar Expression and Chromosomal Associations in Robertsonian Spermatocytes of Mus musculus domesticus. Genes (Basel) 2019; 10:genes10020120. [PMID: 30736350 PMCID: PMC6410149 DOI: 10.3390/genes10020120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/01/2019] [Accepted: 02/05/2019] [Indexed: 02/08/2023] Open
Abstract
We studied and compared the nucleolar expression or nucleoli from specific bivalents in spermatocytes of the standard Mus musculus domesticus 2n=40, of Robertsonian (Rb) homozygotes 2n = 24 and heterozygotes 2n = 32. We analyzed 200 nuclear microspreads of each specific nucleolar chromosome and spermatocyte karyotype, using FISH to identify specific nucleolar bivalents, immunofluorescence for both fibrillarin of the nucleolus and the synaptonemal complex of the bivalents, and DAPI for heterochromatin. There was nucleolar expression in all the chromosomal conditions studied. By specific nucleolar bivalent, the quantitative relative nucleolar expression was higher in the bivalent 12 than in its derivatives, lower in the bivalent 15 than in its derivatives and higher in the bivalent 16 than its Rb derivatives. In the interactions between non-homologous chromosomal domains, the nucleolar bivalents were preferentially associated through pericentromeric heterochromatin with other bivalents of similar morphology and sometimes with other nucleolar bivalents. We suggest that the nucleolar expression in Rb nucleolar chromosomes is modified as a consequence of different localization of ribosomal genes (NOR) in the Rb chromosomes, its proximity to heterochromatin and its associations with chromosomes of the same morphology.
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48
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Blackmon H, Justison J, Mayrose I, Goldberg EE. Meiotic drive shapes rates of karyotype evolution in mammals. Evolution 2019; 73:511-523. [PMID: 30690715 PMCID: PMC6590138 DOI: 10.1111/evo.13682] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 01/07/2019] [Indexed: 02/06/2023]
Abstract
Chromosome number is perhaps the most basic characteristic of a genome, yet generalizations that can explain the evolution of this trait across large clades have remained elusive. Using karyotype data from over 1000 mammals, we developed and applied a phylogenetic model of chromosome evolution that links chromosome number changes with karyotype morphology. Using our model, we infer that rates of chromosome number evolution are significantly lower in species with karyotypes that consist of either all bibrachial or all monobrachial chromosomes than in species with a mix of both types of morphologies. We suggest that species with homogeneous karyotypes may represent cases where meiotic drive acts to stabilize the karyotype, favoring the chromosome morphologies already present in the genome. In contrast, rapid bouts of chromosome number evolution in taxa with mixed karyotypes may indicate that a switch in the polarity of female meiotic drive favors changes in chromosome number. We do not find any evidence that karyotype morphology affects rates of speciation or extinction. Furthermore, we document that switches in meiotic drive polarity are likely common and have occurred in most major clades of mammals, and that rapid remodeling of karyotypes may be more common than once thought.
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Affiliation(s)
- Heath Blackmon
- Department of Biology, Texas A&M University, College Station, Texas 77843
| | - Joshua Justison
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota 55108
| | - Itay Mayrose
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Emma E Goldberg
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota 55108
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Barra V, Fachinetti D. The dark side of centromeres: types, causes and consequences of structural abnormalities implicating centromeric DNA. Nat Commun 2018; 9:4340. [PMID: 30337534 PMCID: PMC6194107 DOI: 10.1038/s41467-018-06545-y] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 09/06/2018] [Indexed: 12/18/2022] Open
Abstract
Centromeres are the chromosomal domains required to ensure faithful transmission of the genome during cell division. They have a central role in preventing aneuploidy, by orchestrating the assembly of several components required for chromosome separation. However, centromeres also adopt a complex structure that makes them susceptible to being sites of chromosome rearrangements. Therefore, preservation of centromere integrity is a difficult, but important task for the cell. In this review, we discuss how centromeres could potentially be a source of genome instability and how centromere aberrations and rearrangements are linked with human diseases such as cancer.
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Affiliation(s)
- V Barra
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, F-75005, Paris, France
| | - D Fachinetti
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, F-75005, Paris, France.
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50
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Martínez-Vargas J, Muñoz-Muñoz F, López-Fuster MJ, Cubo J, Ventura J. Multimethod Approach to the Early Postnatal Growth of the Mandible in Mice from a Zone of Robertsonian Polymorphism. Anat Rec (Hoboken) 2018; 301:1360-1381. [PMID: 29669189 DOI: 10.1002/ar.23835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 11/30/2017] [Accepted: 12/27/2017] [Indexed: 11/11/2022]
Abstract
The western European house mouse (Mus musculus domesticus) shows high karyotypic diversity owing to Robertsonian translocations. Morphometric studies conducted with adult mice suggest that karyotype evolution due to these chromosomal reorganizations entails variation in the form and the patterns of morphological covariation of the mandible. However, information is much scarcer regarding the effect of these rearrangements on the growth pattern of the mouse mandible over early postnatal ontogeny. Here we compare mandible growth from the second to the eighth week of postnatal life between two ontogenetic series of mice from wild populations, with the standard karyotype and with Robertsonian translocations respectively, reared under the same conditions. A multi-method approach is used, including bone histology analyses of mandible surfaces and cross-sections, as well as geometric morphometric analyses of mandible form. The mandibles of both standard and Robertsonian mice display growth acceleration around weaning, anteroposterior direction of bone maturation, a predominance of bone deposition fields over ontogeny, and relatively greater expansion of the posterior mandible region correlated with the ontogenetic increase in mandible size. Nevertheless, differences exist between the two mouse groups regarding the timing of histological maturation of the mandible, the localization of certain bone remodeling fields, the temporospatial patterns of morphological variation, and the organization into two main modules. The dissimilarities in the process of mandible growth between the two groups of mice become more evident around sexual maturity, and could arise from alterations that Robertsonian translocations may exert on genes involved in the bone remodeling mechanism. Anat Rec, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Jessica Martínez-Vargas
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Cerdanyola del Vallès), Spain
| | - Francesc Muñoz-Muñoz
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Cerdanyola del Vallès), Spain
| | - María José López-Fuster
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, and Institut de Recerca de la Biodiversitat (IRBio), Facultat de Biologia, Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Jorge Cubo
- Sorbonne Université, CNRS-INSU, Institut des Sciences de la Terre Paris, ISTeP UMR 7193, F-75005 Paris, France
| | - Jacint Ventura
- Departament de Biologia Animal, de Biologia Vegetal i d'Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, E-08193 Bellaterra (Cerdanyola del Vallès), Spain
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