1
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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 2024:10.1007/s13353-024-00861-4. [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] [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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2
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Wang S, Shen Y, Lin Z, Miao Y, Wang C, Zhang W, Zhang Y. New genes driven by segmental duplications share a testis-specific expression pattern in the chromosome-level genome assembly of tree sparrow. Integr Zool 2023. [PMID: 38014459 DOI: 10.1111/1749-4877.12789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Based on a chromosome-level genome assembly, a burst of new genes with different structures but a similar testis-specific expression pattern was detected in tree sparrow.
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Affiliation(s)
- Shengnan Wang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Lanzhou, China
| | - Yue Shen
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Lanzhou, China
| | - Zhaocun Lin
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Lanzhou, China
| | - Yuquan Miao
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Lanzhou, China
| | - Chengqi Wang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Lanzhou, China
| | - Wenya Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Lanzhou, China
| | - Yingmei Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Lanzhou, China
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3
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Bredemeyer KR, Hillier L, Harris AJ, Hughes GM, Foley NM, Lawless C, Carroll RA, Storer JM, Batzer MA, Rice ES, Davis BW, Raudsepp T, O'Brien SJ, Lyons LA, Warren WC, Murphy WJ. Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution. Nat Genet 2023; 55:1953-1963. [PMID: 37919451 PMCID: PMC10845050 DOI: 10.1038/s41588-023-01548-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/20/2023] [Indexed: 11/04/2023]
Abstract
The role of structurally dynamic genomic regions in speciation is poorly understood due to challenges inherent in diploid genome assembly. Here we reconstructed the evolutionary dynamics of structural variation in five cat species by phasing the genomes of three interspecies F1 hybrids to generate near-gapless single-haplotype assemblies. We discerned that cat genomes have a paucity of segmental duplications relative to great apes, explaining their remarkable karyotypic stability. X chromosomes were hotspots of structural variation, including enrichment with inversions in a large recombination desert with characteristics of a supergene. The X-linked macrosatellite DXZ4 evolves more rapidly than 99.5% of the genome clarifying its role in felid hybrid incompatibility. Resolved sensory gene repertoires revealed functional copy number changes associated with ecomorphological adaptations, sociality and domestication. This study highlights the value of gapless genomes to reveal structural mechanisms underpinning karyotypic evolution, reproductive isolation and ecological niche adaptation.
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Affiliation(s)
- Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - LaDeana Hillier
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Andrew J Harris
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Graham M Hughes
- School of Biology & Environmental Sciences, University College Dublin, Dublin, Ireland
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Colleen Lawless
- School of Biology & Environmental Sciences, University College Dublin, Dublin, Ireland
| | - Rachel A Carroll
- Department of Animal Sciences, University of Missouri, Columbia, MO, USA
| | | | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Edward S Rice
- Department of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Brian W Davis
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Terje Raudsepp
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Stephen J O'Brien
- Guy Harvey Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine & Surgery, University of Missouri, Columbia, MO, USA
| | - Wesley C Warren
- Department of Animal Sciences, University of Missouri, Columbia, MO, USA.
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA.
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4
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Santos da Silva K, Glugoski L, Vicari MR, de Souza ACP, Akama A, Pieczarka JC, Nagamachi CY. Mechanisms of Karyotypic Diversification in Ancistrus (Siluriformes, Loricariidae): Inferences from Repetitive Sequence Analysis. Int J Mol Sci 2023; 24:14159. [PMID: 37762461 PMCID: PMC10532334 DOI: 10.3390/ijms241814159] [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: 07/17/2023] [Revised: 08/14/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Ancistrus is a highly diverse neotropical fish genus that exhibits extensive chromosomal variability, encompassing karyotypic morphology, diploid chromosome number (2n = 34-54), and the evolution of various types of sex chromosome systems. Robertsonian rearrangements related to unstable chromosomal sites are here described. Here, the karyotypes of two Ancistrus species were comparatively analyzed using classical cytogenetic techniques, in addition to isolation, cloning, sequencing, molecular characterization, and fluorescence in situ hybridization of repetitive sequences (i.e., 18S and 5S rDNA; U1, U2, and U5 snDNA; and telomere sequences). The species analyzed here have different karyotypes: Ancistrus sp. 1 (2n = 38, XX/XY) and Ancistrus cirrhosus (2n = 34, no heteromorphic sex chromosomes). Comparative mapping showed different organizations for the analyzed repetitive sequences: 18S and U1 sequences occurred in a single site in all populations of the analyzed species, while 5S and U2 sequences could occur in single or multiple sites. A sequencing analysis confirmed the identities of the U1, U2, and U5 snDNA sequences. Additionally, a syntenic condition for U2-U5 snDNA was found in Ancistrus. In a comparative analysis, the sequences of rDNA and U snDNA showed inter- and intraspecific chromosomal diversification. The occurrence of Robertsonian rearrangements and other dispersal mechanisms of repetitive sequences are discussed.
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Affiliation(s)
- Kevin Santos da Silva
- Cytogenetics Laboratory, Center for Advanced Biodiversity Studies Science Institute Biological, Federal University of Pará, Belém 66075-110, Brazil; (K.S.d.S.); (J.C.P.)
| | - Larissa Glugoski
- Fish Cytogenetics Laboratory, Federal University of São Carlos, São Carlos 13565-905, Brazil;
- Laboratory of Chromosome Biology: Structure and Function Department of Structural Biology, Molecular and Genetic, University of Ponta Grossa State, Ponta Grossa 84010-330, Brazil;
| | - Marcelo Ricardo Vicari
- Laboratory of Chromosome Biology: Structure and Function Department of Structural Biology, Molecular and Genetic, University of Ponta Grossa State, Ponta Grossa 84010-330, Brazil;
| | | | - Alberto Akama
- Department of Zoology, Paraense Emilio Goeldi Museum, Belém 66040-170, Brazil;
| | - Julio Cesar Pieczarka
- Cytogenetics Laboratory, Center for Advanced Biodiversity Studies Science Institute Biological, Federal University of Pará, Belém 66075-110, Brazil; (K.S.d.S.); (J.C.P.)
| | - Cleusa Yoshiko Nagamachi
- Cytogenetics Laboratory, Center for Advanced Biodiversity Studies Science Institute Biological, Federal University of Pará, Belém 66075-110, Brazil; (K.S.d.S.); (J.C.P.)
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5
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Glugoski L, Nogaroto V, Deon GA, Azambuja M, Moreira-Filho O, Vicari MR. Enriched tandemly repeats in chromosomal fusion points of Rineloricaria latirostris (Boulenger, 1900) (Siluriformes: Loricariidae). Genome 2022; 65:479-489. [PMID: 35939838 DOI: 10.1139/gen-2022-0043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cytogenetic data showed the enrichment of repetitive DNAs in chromosomal rearrangement points between closely related species in armored catfishes. Still, few studies integrated cytogenetic and genomic data aiming to identify their prone-to-break DNA sites. Here, we aimed to obtain the repetitive fraction in Rineloricaria latirostris to recognize the microsatellite and homopolymers flanking the regions previously described as chromosomal fusion points. The results indicated that repetitive DNAs in R. latirostris are predominantly DNA transposons, and considering the microsatellite and homopolymers, A/T-rich expansions were the most abundant. The in situ localization demonstrated the A/T-rich repetitive sequences are scattered on the chromosomes, while A/G-rich microsatellites units were accumulated in some regions. The DNA transposon hAT, the 5S rDNA, and 45S rDNA (previously identified in Robertsonian fusion points in R. latirostris) are clusterized with some microsatellites, especially (CA)n, (GA)n, and poly-A, which also are enriched in regions of chromosomal fusions. Our findings demonstrated that repetitive sequences such as rDNAs, hAT transposon, and microsatellite units flank probable evolutionary breakpoint regions in R. latirostris. However, due to the sequence unit homologies in different chromosomal sites, these repeat DNAs only may have facilitated chromosome fusion events in R. latirostris rather than work as a double-strand breakpoint site.
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Affiliation(s)
- Larissa Glugoski
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Sao Carlos, São Paulo, Brazil;
| | - Viviane Nogaroto
- Universidade Estadual de Ponta Grossa, Departamento de Biologia Estrutural, Molecular e Genética, Ponta Grossa, Paraná, Brazil;
| | - Geize Aparecida Deon
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Sao Carlos, São Paulo, Brazil;
| | - Matheus Azambuja
- Universidade Federal do Paraná, Departamento de Genética, Curitiba, PR, Brazil;
| | - Orlando Moreira-Filho
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Sao Carlos, São Paulo, Brazil;
| | - Marcelo Ricardo Vicari
- Universidade Estadual de Ponta Grossa, Departamento de Biologia Estrutural, Molecular e Genética, Ponta Grossa, Paraná, Brazil.,Universidade Federal do Paraná, Departamento de Genética, Curitiba, PR, Brazil;
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6
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Deon GA, Glugoski L, Hatanaka T, Sassi FDMC, Nogaroto V, Bertollo LAC, Liehr T, Al-Rikabi A, Moreira Filho O, Cioffi MDB, Vicari MR. Evolutionary breakpoint regions and chromosomal remodeling in Harttia (Siluriformes: Loricariidae) species diversification. Genet Mol Biol 2022; 45:e20210170. [PMID: 35604463 PMCID: PMC9126045 DOI: 10.1590/1678-4685-gmb-2021-0170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 04/03/2022] [Indexed: 11/22/2022] Open
Abstract
The Neotropical armored catfish genus Harttia presents a wide
variation of chromosomal rearrangements among its representatives. Studies
indicate that translocation and Robertsonian rearrangements have triggered the
karyotype evolution in the genus, including differentiation of sex chromosome
systems. However, few studies used powerful tools, such as comparative whole
chromosome painting, to clarify this highly diversified scenario. Here, we
isolated probes from the X1 (a 5S rDNA carrier) and the X2
(a 45S rDNA carrier) chromosomes of Harttia punctata, which
displays an
X1X1X2X2/X1X2Y
multiple sex chromosome system. Those probes were applied in other
Harttia species to evidence homeologous chromosome blocks.
The resulting data reinforce that translocation events played a role in the
origin of the X1X2Y sex chromosome system in H.
punctata. The repositioning of homologous chromosomal blocks
carrying rDNA sites among ten Harttia species has also been
demonstrated. Anchored to phylogenetic data it was possible to evidence some
events of the karyotype diversification of the studied species and to prove an
independent origin for the two types of multiple sex chromosomes,
XX/XY1Y2 and
X1X1X2X2/X1X2Y,
that occur in Harttia species. The results point to
evolutionary breakpoint regions in the genomes within or adjacent to rDNA sites
that were widely reused in Harttia chromosome remodeling.
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Affiliation(s)
- Geize Aparecida Deon
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil.,Universidade Estadual de Ponta Grossa, Departamento de Biologia Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
| | - Larissa Glugoski
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil.,Universidade Estadual de Ponta Grossa, Departamento de Biologia Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
| | - Terumi Hatanaka
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
| | | | - Viviane Nogaroto
- Universidade Estadual de Ponta Grossa, Departamento de Biologia Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
| | | | - Thomas Liehr
- University Hospital Jena, Institute of Human Genetics, Jena, Germany
| | - Ahmed Al-Rikabi
- University Hospital Jena, Institute of Human Genetics, Jena, Germany.,Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
| | - Orlando Moreira Filho
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
| | - Marcelo de Bello Cioffi
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
| | - Marcelo Ricardo Vicari
- Universidade Estadual de Ponta Grossa, Departamento de Biologia Estrutural, Molecular e Genética, Ponta Grossa, PR, Brazil
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7
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Abstract
The study of chromosome evolution is undergoing a resurgence of interest owing to advances in DNA sequencing technology that facilitate the production of chromosome-scale whole-genome assemblies de novo. This review focuses on the history, methods, discoveries, and current challenges facing the field, with an emphasis on vertebrate genomes. A detailed examination of the literature on the biology of chromosome rearrangements is presented, specifically the relationship between chromosome rearrangements and phenotypic evolution, adaptation, and speciation. A critical review of the methods for identifying, characterizing, and visualizing chromosome rearrangements and computationally reconstructing ancestral karyotypes is presented. We conclude by looking to the future, identifying the enormous technical and scientific challenges presented by the accumulation of hundreds and eventually thousands of chromosome-scale assemblies.
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Affiliation(s)
- Joana Damas
- The Genome Center, University of California, Davis, California 95616, USA; , ,
| | - Marco Corbo
- The Genome Center, University of California, Davis, California 95616, USA; , ,
| | - Harris A Lewin
- The Genome Center, University of California, Davis, California 95616, USA; , , .,Department of Evolution and Ecology, College of Biological Sciences, University of California, Davis, California 95616, USA
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8
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Genome-wide unique insertion sequences among five Brucella species and demonstration of differential identification of Brucella by multiplex PCR assay. Sci Rep 2020; 10:6368. [PMID: 32286356 PMCID: PMC7156498 DOI: 10.1038/s41598-020-62472-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 03/02/2020] [Indexed: 11/17/2022] Open
Abstract
Brucellosis is a neglected zoonotic disease caused by alpha proteobacterial genus Brucella comprising of facultative intracellular pathogenic species that can infect both animals and humans. In this study, we aimed to identify genome-wide unique insertion sequence (IS) elements among Brucella abortus, B. melitensis, B. ovis, B. suis and B. canis for use in species differentiation by conducting an intensive in silico-based comparative genomic analysis. As a result, 25, 27, 37, 86 and 3 unique ISs were identified respectively and they had a striking pattern of distribution among them. To explain, a particular IS would be present in four species with 100% identity whereas completely absent in the fifth species. However, flanking regions of that IS element would be highly identical and conserved in all five species. Species-specific primers designed on these flanking conserved regions resulted in two different amplicons grouping the species into two: one that possesses IS and the other that lacks it. Seeking for species-specific amplicon size for particular species was sufficient to identify it irrespective of biovar. A multiplex PCR developed using these primers resulted in successful differentiation of the five species irrespective of biovars with significant specificity and sensitivity when examined on clinical samples.
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9
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Ostevik KL, Samuk K, Rieseberg LH. Ancestral Reconstruction of Karyotypes Reveals an Exceptional Rate of Nonrandom Chromosomal Evolution in Sunflower. Genetics 2020; 214:1031-1045. [PMID: 32033968 PMCID: PMC7153943 DOI: 10.1534/genetics.120.303026] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 02/03/2020] [Indexed: 12/20/2022] Open
Abstract
Mapping the chromosomal rearrangements between species can inform our understanding of genome evolution, reproductive isolation, and speciation. Here, we present a novel algorithm for identifying regions of synteny in pairs of genetic maps, which is implemented in the accompanying R package syntR. The syntR algorithm performs as well as previous ad hoc methods while being systematic, repeatable, and applicable to mapping chromosomal rearrangements in any group of species. In addition, we present a systematic survey of chromosomal rearrangements in the annual sunflowers, which is a group known for extreme karyotypic diversity. We build high-density genetic maps for two subspecies of the prairie sunflower, Helianthus petiolaris ssp. petiolaris and H. petiolaris ssp. fallax Using syntR, we identify blocks of synteny between these two subspecies and previously published high-density genetic maps. We reconstruct ancestral karyotypes for annual sunflowers using those synteny blocks and conservatively estimate that there have been 7.9 chromosomal rearrangements per million years, a high rate of chromosomal evolution. Although the rate of inversion is even higher than the rate of translocation in this group, we further find that every extant karyotype is distinguished by between one and three translocations involving only 8 of the 17 chromosomes. This nonrandom exchange suggests that specific chromosomes are prone to translocation and may thus contribute disproportionately to widespread hybrid sterility in sunflowers. These data deepen our understanding of chromosome evolution and confirm that Helianthus has an exceptional rate of chromosomal rearrangement that may facilitate similarly rapid diversification.
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Affiliation(s)
- Kate L Ostevik
- Department of Biology, Duke University, Durham, North Carolina 27701
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Kieran Samuk
- Department of Biology, Duke University, Durham, North Carolina 27701
| | - Loren H Rieseberg
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
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10
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Louzada S, Lopes M, Ferreira D, Adega F, Escudeiro A, Gama-Carvalho M, Chaves R. Decoding the Role of Satellite DNA in Genome Architecture and Plasticity-An Evolutionary and Clinical Affair. Genes (Basel) 2020; 11:E72. [PMID: 31936645 PMCID: PMC7017282 DOI: 10.3390/genes11010072] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 12/29/2019] [Accepted: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
Repetitive DNA is a major organizational component of eukaryotic genomes, being intrinsically related with their architecture and evolution. Tandemly repeated satellite DNAs (satDNAs) can be found clustered in specific heterochromatin-rich chromosomal regions, building vital structures like functional centromeres and also dispersed within euchromatin. Interestingly, despite their association to critical chromosomal structures, satDNAs are widely variable among species due to their high turnover rates. This dynamic behavior has been associated with genome plasticity and chromosome rearrangements, leading to the reshaping of genomes. Here we present the current knowledge regarding satDNAs in the light of new genomic technologies, and the challenges in the study of these sequences. Furthermore, we discuss how these sequences, together with other repeats, influence genome architecture, impacting its evolution and association with disease.
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Affiliation(s)
- Sandra Louzada
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Mariana Lopes
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Daniela Ferreira
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Filomena Adega
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Ana Escudeiro
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Margarida Gama-Carvalho
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Raquel Chaves
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
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11
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Fan H, Wu Q, Wei F, Yang F, Ng BL, Hu Y. Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution. Genome Biol 2019; 20:267. [PMID: 31810476 PMCID: PMC6898958 DOI: 10.1186/s13059-019-1889-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 11/15/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chromosome evolution is an important driver of speciation and species evolution. Previous studies have detected chromosome rearrangement events among different Carnivora species using chromosome painting strategies. However, few of these studies have focused on chromosome evolution at a nucleotide resolution due to the limited availability of chromosome-level Carnivora genomes. Although the de novo genome assembly of the giant panda is available, current short read-based assemblies are limited to moderately sized scaffolds, making the study of chromosome evolution difficult. RESULTS Here, we present a chromosome-level giant panda draft genome with a total size of 2.29 Gb. Based on the giant panda genome and published chromosome-level dog and cat genomes, we conduct six large-scale pairwise synteny alignments and identify evolutionary breakpoint regions. Interestingly, gene functional enrichment analysis shows that for all of the three Carnivora genomes, some genes located in evolutionary breakpoint regions are significantly enriched in pathways or terms related to sensory perception of smell. In addition, we find that the sweet receptor gene TAS1R2, which has been proven to be a pseudogene in the cat genome, is located in an evolutionary breakpoint region of the giant panda, suggesting that interchromosomal rearrangement may play a role in the cat TAS1R2 pseudogenization. CONCLUSIONS We show that the combined strategies employed in this study can be used to generate efficient chromosome-level genome assemblies. Moreover, our comparative genomics analyses provide novel insights into Carnivora chromosome evolution, linking chromosome evolution to functional gene evolution.
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Affiliation(s)
- Huizhong Fan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qi Wu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Fengtang Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Bee Ling Ng
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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12
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Oliveira da Silva W, Pieczarka JC, Rodrigues da Costa MJ, Ferguson-Smith MA, O'Brien PCM, Mendes-Oliveira AC, Rossi RV, Nagamachi CY. Chromosomal phylogeny and comparative chromosome painting among Neacomys species (Rodentia, Sigmodontinae) from eastern Amazonia. BMC Evol Biol 2019; 19:184. [PMID: 31601183 PMCID: PMC6785907 DOI: 10.1186/s12862-019-1515-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 09/16/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Neacomys genus is predominantly found in the Amazon region, and belongs to the most diverse tribe of the Sigmodontinae subfamily (Rodentia, Cricetidae, Oryzomyini). The systematics of this genus and questions about its diversity and range have been investigated by morphological, molecular (Cytb and COI sequences) and karyotype analysis (classic cytogenetics and chromosome painting), which have revealed candidate species and new distribution areas. Here we analyzed four species of Neacomys by chromosome painting with Hylaeamys megacephalus (HME) whole-chromosome probes, and compared the results with two previously studied Neacomys species and with other taxa from Oryzomyini and Akodontini tribes that have been hybridized with HME probes. Maximum Parsimony (MP) analyses were performed with the PAUP and T.N.T. software packages, using a non-additive (unordered) multi-state character matrix, based on chromosomal morphology, number and syntenic blocks. We also compared the chromosomal phylogeny obtained in this study with molecular topologies (Cytb and COI) that included eastern Amazonian species of Neacomys, to define the phylogenetic relationships of these taxa. RESULTS The comparative chromosome painting analysis of the seven karyotypes of the six species of Neacomys shows that their diversity is due to 17 fusion/fission events and one translocation, pericentric inversions in four syntenic blocks, and constitutive heterochromatin (CH) amplification/deletion of six syntenic autosomal blocks plus the X chromosome. The chromosomal phylogeny is consistent with the molecular relationships of species of Neacomys. We describe new karyotypes and expand the distribution area for species from eastern Amazonia and detect complex rearrangements by chromosome painting among the karyotypes. CONCLUSIONS Our phylogeny reflects the molecular relationships of the Akodontini and Oryzomyini taxa and supports the monophyly of Neacomys. This work presents new insights about the chromosomal evolution of this group, and we conclude that the karyotypic divergence is in accord with phylogenetic relationships.
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Affiliation(s)
- Willam Oliveira da Silva
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Julio Cesar Pieczarka
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Marlyson Jeremias Rodrigues da Costa
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Patricia Caroline Mary O'Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Rogério Vieira Rossi
- Instituto de Biociências, Universidade Federal do Mato Grosso (UFMT), Cuiabá, Mato Grosso, Brazil
| | - Cleusa Yoshiko Nagamachi
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, Instituto de Ciências Biológicas, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil.
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13
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Dai Z. Gene Repositioning Is Under Constraints After Evolutionary Conserved Gene Neighborhood Separate. Front Genet 2019; 10:1030. [PMID: 31632448 PMCID: PMC6785632 DOI: 10.3389/fgene.2019.01030] [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: 06/12/2019] [Accepted: 09/25/2019] [Indexed: 11/13/2022] Open
Abstract
Genes are not randomly distributed on eukaryotic chromosomes. Some neighboring genes show order conservation among species, while some neighboring genes separate during evolution even though their neighborhoods are conserved in some species. Here, I investigated whether after-separation gene repositioning is under natural selection for evolutionary conserved gene neighborhoods compared with nonconserved neighborhoods. After separation, genes with conserved neighborhoods show low-expression divergence between the after-separation species and the before-separation species. After genes separate from their conserved gene neighbors, their after-separation gene neighbors tend to show coexpression and coprotein complex with their before-separation gene neighbors. These results indicate evolutionary constraints on the selection of neighboring genes after evolutionary conserved gene neighborhoods separate.
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Affiliation(s)
- Zhiming Dai
- School of Data and Computer Science, Sun Yat-Sen University, Guangzhou, China.,Guangdong Province Key Laboratory of Big Data Analysis and Processing, Sun Yat-Sen University, Guangzhou, China
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14
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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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15
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de Oliveira EA, Bertollo LAC, Rab P, Ezaz T, Yano CF, Hatanaka T, Jegede OI, Tanomtong A, Liehr T, Sember A, Maruyama SR, Feldberg E, Viana PF, Cioffi MDB. Cytogenetics, genomics and biodiversity of the South American and African Arapaimidae fish family (Teleostei, Osteoglossiformes). PLoS One 2019; 14:e0214225. [PMID: 30908514 PMCID: PMC6433368 DOI: 10.1371/journal.pone.0214225] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/09/2019] [Indexed: 11/19/2022] Open
Abstract
Osteoglossiformes represents one of the most ancestral teleost lineages, currently widespread over almost all continents, except for Antarctica. However, data involving advanced molecular cytogenetics or comparative genomics are yet largely limited for this fish group. Therefore, the present investigations focus on the osteoglossiform family Arapaimidae, studying a unique fish model group with advanced molecular cytogenetic genomic tools. The aim is to better explore and clarify certain events and factors that had impact on evolutionary history of this fish group. For that, both South American and African representatives of Arapaimidae, namely Arapaima gigas and Heterotis niloticus, were examined. Both species differed markedly by diploid chromosome numbers, with 2n = 56 found in A. gigas and 2n = 40 exhibited by H. niloticus. Conventional cytogenetics along with fluorescence in situ hybridization revealed some general trends shared by most osteoglossiform species analyzed thus far, such as the presence of only one chromosome pair bearing 18S and 5S rDNA sites and karyotypes dominated by acrocentric chromosomes, resembling thus the patterns of hypothetical ancestral teleost karyotype. Furthermore, the genomes of A. gigas and H. niloticus display remarkable divergence in terms of repetitive DNA content and distribution, as revealed by comparative genomic hybridization (CGH). On the other hand, genomic diversity of single copy sequences studied through principal component analyses (PCA) based on SNP alleles genotyped by the DArT seq procedure demonstrated a very low genetic distance between the South American and African Arapaimidae species; this pattern contrasts sharply with the scenario found in other osteoglossiform species. Underlying evolutionary mechanisms potentially explaining the obtained data have been suggested and discussed.
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Affiliation(s)
- Ezequiel Aguiar de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, SP, Brazil
- Secretaria de Estado de Educação de Mato Grosso–SEDUC-MT, Cuiabá, MT, Brazil
| | - Luiz Antonio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, SP, Brazil
| | - Petr Rab
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Czech Republic
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Cassia Fernanda Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, SP, Brazil
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, SP, Brazil
| | | | - Alongklod Tanomtong
- Toxic Substances in Livestock and Aquatic Animals Research Group, KhonKaen University, Muang, KhonKaen, Thailand
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Czech Republic
| | - Sandra Regina Maruyama
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, SP, Brazil
| | - Eliana Feldberg
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Laboratório de Genética Animal, Petrópolis, CEP: Manaus, AM, Brazil
| | - Patrik Ferreira Viana
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Laboratório de Genética Animal, Petrópolis, CEP: Manaus, AM, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, SP, Brazil
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16
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Oliveira da Silva W, Rodrigues da Costa MJ, Pieczarka JC, Rissino J, Pereira JC, Ferguson-Smith MA, Nagamachi CY. Identification of two independent X-autosome translocations in closely related mammalian (Proechimys) species. Sci Rep 2019; 9:4047. [PMID: 30858413 PMCID: PMC6411977 DOI: 10.1038/s41598-019-40593-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 02/19/2019] [Indexed: 11/13/2022] Open
Abstract
Multiple sex chromosome systems have been described for several mammalian orders, with different species from the same genus sharing the same system (e.g., X1X2Y or XY1Y2). This is important because the translocated autosome may be influenced by the evolution of the recipient sex chromosome, and this may be related to speciation. It is often thought that the translocation of an autosome to a sex chromosome may share a common origin among phylogenetically related species. However, the neo-X chromosomes of Proechimys goeldii (2n = 24♀, 25♂/NFa = 42) and Proechimys gr. goeldii (2n = 16♀, 17♂/NFa = 14) have distinct sizes and morphologies that have made it difficult to determine whether they have the same or different origins. This study investigates the origins of the XY1Y2 sex chromosome determination system in P. goeldii (PGO) and P. gr. goeldii (PGG) and elucidates the chromosomal rearrangements in this low-diploid-number group of Proechimys species. Toward this end, we produced whole-chromosome probes for P. roberti (PRO; 2n = 30♂/NFa = 54) and P. goeldii (2n = 25♂/NFa = 42) and used them in comparative chromosomal mapping. Our analysis reveals that multiple translocations and inversions are responsible for the karyotype diversity of these species, with only three whole-chromosomes conserved between PRO and PGO and eight between PGO and PGG. Our data indicate that multiple sex chromosome systems have originated twice in Proechimys. As small populations are prone to the fixation of chromosomal rearrangements, we speculate that biological features of Rodentia contribute to this fixation. We also highlight the potential of these rodents as a model for studying sex chromosome evolution.
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Affiliation(s)
- Willam Oliveira da Silva
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, ICB, Universidade Federal do Pará, Belém, Pará, Brazil.,Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Julio Cesar Pieczarka
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, ICB, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Jorge Rissino
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, ICB, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Jorge C Pereira
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Cleusa Yoshiko Nagamachi
- Centro de Estudos Avançados da Biodiversidade, Laboratório de Citogenética, ICB, Universidade Federal do Pará, Belém, Pará, Brazil.
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17
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Barby FF, Bertollo LAC, de Oliveira EA, Yano CF, Hatanaka T, Ráb P, Sember A, Ezaz T, Artoni RF, Liehr T, Al-Rikabi ABH, Trifonov V, de Oliveira EHC, Molina WF, Jegede OI, Tanomtong A, de Bello Cioffi M. Emerging patterns of genome organization in Notopteridae species (Teleostei, Osteoglossiformes) as revealed by Zoo-FISH and Comparative Genomic Hybridization (CGH). Sci Rep 2019; 9:1112. [PMID: 30718776 PMCID: PMC6361938 DOI: 10.1038/s41598-019-38617-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 01/03/2019] [Indexed: 11/09/2022] Open
Abstract
Notopteridae (Teleostei, Osteoglossiformes) represents an old fish lineage with ten currently recognized species distributed in African and Southeastern Asian rivers. Their karyotype structures and diploid numbers remained conserved over long evolutionary periods, since African and Asian lineages diverged approximately 120 Mya. However, a significant genetic diversity was already identified for these species using molecular data. Thus, why the evolutionary relationships within Notopteridae are so diverse at the genomic level but so conserved in terms of their karyotypes? In an attempt to develop a more comprehensive picture of the karyotype and genome evolution in Notopteridae, we performed comparative genomic hybridization (CGH) and cross-species (Zoo-FISH) whole chromosome painting experiments to explore chromosome-scale intergenomic divergence among seven notopterid species, collected in different African and Southeast Asian river basins. CGH demonstrated an advanced stage of sequence divergence among the species and Zoo-FISH experiments showed diffuse and limited homology on inter-generic level, showing a temporal reduction of evolutionarily conserved syntenic regions. The sharing of a conserved chromosomal region revealed by Zoo-FISH in these species provides perspectives that several other homologous syntenic regions have remained conserved among their genomes despite long temporal isolation. In summary, Notopteridae is an interesting model for tracking the chromosome evolution as it is (i) ancestral vertebrate group with Gondwanan distribution and (ii) an example of animal group exhibiting karyotype stasis. The present study brings new insights into degree of genome divergence vs. conservation at chromosomal and sub-chromosomal level in representative sampling of this group.
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Affiliation(s)
- Felipe Faix Barby
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP, 13565-905, Brazil
| | - Luiz Antônio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP, 13565-905, Brazil
| | - Ezequiel Aguiar de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP, 13565-905, Brazil
| | - Cassia Fernanda Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP, 13565-905, Brazil
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP, 13565-905, Brazil
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia
| | - Roberto Ferreira Artoni
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
| | - Thomas Liehr
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
| | | | - Vladimir Trifonov
- Molecular and Cellular Biology, Russian Academy of Sciences, Novosibirsk, Russia
| | - Edivaldo H C de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Belém, Brazil
| | - Wagner Franco Molina
- Department of Cellular Biology and Genetics, Biosciences Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Oladele Ilesanmi Jegede
- Department of Fisheries and Aquaculture, Adamawa State University, P.M.B. 25, Mubi, Adamawa State, Nigeria
| | - Alongklod Tanomtong
- Toxic Substances in Livestock and Aquatic Animals Research Group, KhonKaen University, Muang, KhonKaen, 40002, Thailand
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP, 13565-905, Brazil.
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18
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Wang D, Wang L. GRSR: a tool for deriving genome rearrangement scenarios from multiple unichromosomal genome sequences. BMC Bioinformatics 2018; 19:291. [PMID: 30367596 PMCID: PMC6101096 DOI: 10.1186/s12859-018-2268-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Genome rearrangements describe changes in the genetic linkage relationship of large chromosomal regions, involving reversals, transpositions, block interchanges, deletions, insertions, fissions, fusions and translocations etc. Many algorithms for calculating rearrangement scenarios between two genomes have been proposed. Very often, the calculated rearrangement scenario is not unique for the same pair of permutations. Hence, how to decide which calculated rearrangement scenario is more biologically meaningful becomes an essential task. Up to now, several mechanisms for genome rearrangements have been studied. One important theory is that genome rearrangement may be mediated by repeats, especially for reversal events. Many reversal regions are found to be flanked by a pair of inverted repeats. As a result, whether there are repeats at the breakpoints of the calculated rearrangement events can shed a light on deciding whether the calculated rearrangement events is biologically meaningful. To our knowledge, there is no tool which can automatically identify rearrangement events and check whether there exist repeats at the breakpoints of each calculated rearrangement event. Results In this paper, we describe a new tool named GRSR which allows us to compare multiple unichromosomal genomes to identify “independent” (obvious) rearrangement events such as reversals, (inverted) block interchanges and (inverted) transpositions and automatically searches for repeats at the breakpoints of each rearrangement event. We apply our tool on the complete genomes of 28 Mycobacterium tuberculosis strains and 24 Shewanella strains respectively. In both Mycobacterium tuberculosis and Shewanella strains, our tool finds many reversal regions flanked by a pair of inverted repeats. In particular, the GRSR tool also finds an inverted transposition and an inverted block interchange in Shewanella, where the repeats at the ends of rearrangement regions remain unchanged after the rearrangement event. To our knowledge, this is the first time such a phenomenon for inverted transposition and inverted block interchange is reported in Shewanella. Conclusions From the calculated results, there are many examples supporting the theory that the existence of repeats at the breakpoints of a rearrangement event can make the sequences at the breakpoints remain unchanged before and after the rearrangement events, suggesting that the conservation of ends could possibly be a popular phenomenon in many types of genome rearrangement events.
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Affiliation(s)
- Dan Wang
- Department of Computer Science, City University of Hong Kong, 83 Tat Chee Ave., Hong Kong, People's Republic of China
| | - Lusheng Wang
- Department of Computer Science, City University of Hong Kong, 83 Tat Chee Ave., Hong Kong, People's Republic of China. .,University of Hong Kong Shenzhen Research Institute, Shenzhen Hi-Tech Industrial Park, Nanshan District, Shenzhen, People's Republic of China.
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19
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Pu L, Lin Y, Pevzner PA. Detection and analysis of ancient segmental duplications in mammalian genomes. Genome Res 2018; 28:901-909. [PMID: 29735604 PMCID: PMC5991524 DOI: 10.1101/gr.228718.117] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 04/26/2018] [Indexed: 01/07/2023]
Abstract
Although segmental duplications (SDs) represent hotbeds for genomic rearrangements and emergence of new genes, there are still no easy-to-use tools for identifying SDs. Moreover, while most previous studies focused on recently emerged SDs, detection of ancient SDs remains an open problem. We developed an SDquest algorithm for SD finding and applied it to analyzing SDs in human, gorilla, and mouse genomes. Our results demonstrate that previous studies missed many SDs in these genomes and show that SDs account for at least 6.05% of the human genome (version hg19), a 17% increase as compared to the previous estimate. Moreover, SDquest classified 6.42% of the latest GRCh38 version of the human genome as SDs, a large increase as compared to previous studies. We thus propose to re-evaluate evolution of SDs based on their accurate representation across multiple genomes. Toward this goal, we analyzed the complex mosaic structure of SDs and decomposed mosaic SDs into elementary SDs, a prerequisite for follow-up evolutionary analysis. We also introduced the concept of the breakpoint graph of mosaic SDs that revealed SD hotspots and suggested that some SDs may have originated from circular extrachromosomal DNA (ecDNA), not unlike ecDNA that contributes to accelerated evolution in cancer.
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Affiliation(s)
- Lianrong Pu
- Department of Computer Science and Technology, Shandong University, Jinan 250101, China.,Department of Computer Science and Engineering, University of California at San Diego, San Diego, California 92093, USA
| | - Yu Lin
- Department of Computer Science and Engineering, University of California at San Diego, San Diego, California 92093, USA.,Research School of Computer Science, Australian National University, Canberra, ACT 2601, Australia
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California at San Diego, San Diego, California 92093, USA
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20
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Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin AA, Karn RC, Laukaitis CM, Jingtao L, Martin F, Muffato M, Nachtweide S, Quail MA, Sisu C, Stanke M, Stefflova K, Van Oosterhout C, Veyrunes F, Ward B, Yang F, Yazdanifar G, Zadissa A, Adams DJ, Brazma A, Gerstein M, Paten B, Pham S, Keane TM, Odom DT, Flicek P. Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes. Genome Res 2018; 28:448-459. [PMID: 29563166 PMCID: PMC5880236 DOI: 10.1101/gr.234096.117] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 03/05/2018] [Indexed: 12/31/2022]
Abstract
Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four- and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli, which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.
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Affiliation(s)
- David Thybert
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
- Earlham Institute, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Maša Roller
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Fábio C P Navarro
- Yale University Medical School, Computational Biology and Bioinformatics Program, New Haven, Connecticut 06520, USA
| | - Ian Fiddes
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Christine Feig
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge CB2 0RE, United Kingdom
| | - David Martin-Galvez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Mikhail Kolmogorov
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92092, USA
| | - Václav Janoušek
- Department of Zoology, Faculty of Science, Charles University in Prague, 128 44 Prague, Czech Republic
| | - Wasiu Akanni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Bronwen Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Sarah Aldridge
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge CB2 0RE, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Varshith Chakrapani
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - William Chow
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Anthony Doran
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Matthew Dunn
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Leo Goodstadt
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, United Kingdom
| | - Kerstin Howe
- Yale University Medical School, Computational Biology and Bioinformatics Program, New Haven, Connecticut 06520, USA
| | - Matthew Howell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Ambre-Aurore Josselin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Robert C Karn
- Department of Medicine, College of Medicine, University of Arizona, Tuscon, Arizona 85724, USA
| | - Christina M Laukaitis
- Department of Medicine, College of Medicine, University of Arizona, Tuscon, Arizona 85724, USA
| | - Lilue Jingtao
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Fergal Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Stefanie Nachtweide
- Institute of Mathematics and Computer Science, University of Greifswald, Greifswald 17487, Germany
| | - Michael A Quail
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Cristina Sisu
- Yale University Medical School, Computational Biology and Bioinformatics Program, New Haven, Connecticut 06520, USA
| | - Mario Stanke
- Institute of Mathematics and Computer Science, University of Greifswald, Greifswald 17487, Germany
| | - Klara Stefflova
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge CB2 0RE, United Kingdom
| | - Cock Van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Frederic Veyrunes
- Institut des Sciences de l'Evolution de Montpellier, Université Montpellier/CNRS, 34095 Montpellier, France
| | - Ben Ward
- Earlham Institute, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Fengtang Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Golbahar Yazdanifar
- Department of Medicine, College of Medicine, University of Arizona, Tuscon, Arizona 85724, USA
| | - Amonida Zadissa
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Mark Gerstein
- Yale University Medical School, Computational Biology and Bioinformatics Program, New Haven, Connecticut 06520, USA
| | - Benedict Paten
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Son Pham
- Bioturing Inc, San Diego, California 92121, USA
| | - Thomas M Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Duncan T Odom
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge CB2 0RE, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
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21
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Pezer Ž, Chung AG, Karn RC, Laukaitis CM. Analysis of Copy Number Variation in the Abp Gene Regions of Two House Mouse Subspecies Suggests Divergence during the Gene Family Expansions. Genome Biol Evol 2018; 9:3858091. [PMID: 28575204 PMCID: PMC5513543 DOI: 10.1093/gbe/evx099] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2017] [Indexed: 12/26/2022] Open
Abstract
The Androgen-binding protein (Abp) gene region of the mouse genome contains 64 genes, some encoding pheromones that influence assortative mating between mice from different subspecies. Using CNVnator and quantitative PCR, we explored copy number variation in this gene family in natural populations of Mus musculus domesticus (Mmd) and Mus musculus musculus (Mmm), two subspecies of house mice that form a narrow hybrid zone in Central Europe. We found that copy number variation in the center of the Abp gene region is very common in wild Mmd, primarily representing the presence/absence of the final duplications described for the mouse genome. Clustering of Mmd individuals based on this variation did not reflect their geographical origin, suggesting no population divergence in the Abp gene cluster. However, copy number variation patterns differ substantially between Mmd and other mouse taxa. Large blocks of Abp genes are absent in Mmm, Mus musculus castaneus and an outgroup, Mus spretus, although with differences in variation and breakpoint locations. Our analysis calls into question the reliance on a reference genome for interpreting the detailed organization of genes in taxa more distant from the Mmd reference genome. The polymorphic nature of the gene family expansion in all four taxa suggests that the number of Abp genes, especially in the central gene region, is not critical to the survival and reproduction of the mouse. However, Abp haplotypes of variable length may serve as a source of raw genetic material for new signals influencing reproductive communication and thus speciation of mice.
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Affiliation(s)
- Željka Pezer
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Ruđer Bošković Institute, Zagreb, Croatia
| | - Amanda G Chung
- Department of Medicine, College of Medicine, University of Arizona
| | - Robert C Karn
- Department of Medicine, College of Medicine, University of Arizona
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22
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Karyotype relationships among selected deer species and cattle revealed by bovine FISH probes. PLoS One 2017; 12:e0187559. [PMID: 29112970 PMCID: PMC5675437 DOI: 10.1371/journal.pone.0187559] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/21/2017] [Indexed: 11/19/2022] Open
Abstract
The Cervidae family comprises more than fifty species divided into three subfamilies: Capreolinae, Cervinae and Hydropotinae. A characteristic attribute for the species included in this family is the great karyotype diversity, with the chromosomal numbers ranging from 2n = 6 observed in female Muntiacus muntjak vaginalis to 2n = 70 found in Mazama gouazoubira as a result of numerous Robertsonian and tandem fusions. This work reports chromosomal homologies between cattle (Bos taurus, 2n = 60) and nine cervid species using a combination of whole chromosome and region-specific paints and BAC clones derived from cattle. We show that despite the great diversity of karyotypes in the studied species, the number of conserved chromosomal segments detected by 29 cattle whole chromosome painting probes was 35 for all Cervidae samples. The detailed analysis of the X chromosomes revealed two different morphological types within Cervidae. The first one, present in the Capreolinae is a sub/metacentric X with the structure more similar to the bovine X. The second type found in Cervini and Muntiacini is an acrocentric X which shows rearrangements in the proximal part that have not yet been identified within Ruminantia. Moreover, we characterised four repetitive sequences organized in heterochromatic blocks on sex chromosomes of the reindeer (Rangifer tarandus). We show that these repeats gave no hybridization signals to the chromosomes of the closely related moose (Alces alces) and are therefore specific to the reindeer.
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23
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Wang D, Li S, Guo F, Ning K, Wang L. Core-genome scaffold comparison reveals the prevalence that inversion events are associated with pairs of inverted repeats. BMC Genomics 2017; 18:268. [PMID: 28356070 PMCID: PMC5372343 DOI: 10.1186/s12864-017-3655-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 03/22/2017] [Indexed: 01/01/2023] Open
Abstract
Background Genome rearrangement describes gross changes of chromosomal regions, plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. With more and more complete genomes accomplished, lots of genomic comparisons have been conducted in order to find genome rearrangements and the mechanisms which underlie the rearrangement events. In our opinion, genomic comparison of different individuals/strains within the same species (pan-genome) is more helpful to reveal the mechanisms for genome rearrangements since genomes of the same species are much closer to each other. Results We study the mechanism for inversion events via core-genome scaffold comparison of different strains within the same species. We focus on two kinds of bacteria, Pseudomonas aeruginosa and Escherichia coli, and investigate the inversion events among different strains of the same species. We find an interesting phenomenon that long (larger than 10,000 bp) inversion regions are flanked by a pair of Inverted Repeats (IRs). This mechanism can also explain why the breakpoint reuses for inversion events happen. We study the prevalence of the phenomenon and find that it is a major mechanism for inversions. The other observation is that for different rearrangement events such as transposition and inverted block interchange, the two ends of the swapped regions are also associated with repeats so that after the rearrangement operations the two ends of the swapped regions remain unchanged. To our knowledge, this is the first time such a phenomenon is reported for transposition event. Conclusions In both Pseudomonas aeruginosa and Escherichia coli strains, IRs were found at the two ends of long sequence inversions. The two ends of the inversion remained unchanged before and after the inversion event. The existence of IRs can explain the breakpoint reuse phenomenon. We also observed that other rearrangement operations such as transposition, inverted transposition, and inverted block interchange, had repeats (not necessarily inverted) at the ends of each segment, where the ends remained unchanged before and after the rearrangement operations. This suggests that the conservation of ends could possibly be a popular phenomenon in many types of chromosome rearrangement events. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3655-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dan Wang
- Department of Computer Science, City University of Hong Kong, 83 Tat Chee Ave., Hong Kong, SAR, People's Republic of China
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, 83 Tat Chee Ave., Hong Kong, SAR, People's Republic of China
| | - Fei Guo
- School of Computer Science and Technology, Tianjin University, Tianjin, People's Republic of China
| | - Kang Ning
- School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Lusheng Wang
- Department of Computer Science, City University of Hong Kong, 83 Tat Chee Ave., Hong Kong, SAR, People's Republic of China. .,University of Hong Kong Shenzhen Research Institute, Shenzhen Hi-Tech Industrial Park, Nanshan District, Shenzhen, People's Republic of China.
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24
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Potter S, Bragg JG, Blom MPK, Deakin JE, Kirkpatrick M, Eldridge MDB, Moritz C. Chromosomal Speciation in the Genomics Era: Disentangling Phylogenetic Evolution of Rock-wallabies. Front Genet 2017; 8:10. [PMID: 28265284 PMCID: PMC5301020 DOI: 10.3389/fgene.2017.00010] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/18/2017] [Indexed: 12/24/2022] Open
Abstract
The association of chromosome rearrangements (CRs) with speciation is well established, and there is a long history of theory and evidence relating to "chromosomal speciation." Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about one episode of chromosomal speciation. Progressing from patterns of association between chromosome (and genic) change, to understanding processes of speciation requires both comparative studies across diverse systems and integration of genome-scale sequence comparisons with other lines of evidence. Here, we showcase a promising example of chromosomal speciation in a non-model organism, the endemic Australian marsupial genus Petrogale. We present initial phylogenetic results from exon-capture that resolve a history of divergence associated with extensive and repeated CRs. Yet it remains challenging to disentangle gene tree heterogeneity caused by recent divergence and gene flow in this and other such recent radiations. We outline a way forward for better integration of comparative genomic sequence data with evidence from molecular cytogenetics, and analyses of shifts in the recombination landscape and potential disruption of meiotic segregation and epigenetic programming. In all likelihood, CRs impact multiple cellular processes and these effects need to be considered together, along with effects of genic divergence. Understanding the effects of CRs together with genic divergence will require development of more integrative theory and inference methods. Together, new data and analysis tools will combine to shed light on long standing questions of how chromosome and genic divergence promote speciation.
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Affiliation(s)
- Sally Potter
- Research School of Biology, Australian National University, ActonACT, Australia
- Australian Museum Research Institute, Australian Museum, SydneyNSW, Australia
| | - Jason G. Bragg
- National Herbarium of New South Wales, The Royal Botanic Gardens and Domain Trust, SydneyNSW, Australia
| | - Mozes P. K. Blom
- Department of Bioinformatics and Genetics, Swedish Museum of Natural HistoryStockholm, Sweden
| | - Janine E. Deakin
- Institute for Applied Ecology, University of Canberra, BruceACT, Australia
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, AustinTX, USA
| | - Mark D. B. Eldridge
- Australian Museum Research Institute, Australian Museum, SydneyNSW, Australia
| | - Craig Moritz
- Research School of Biology, Australian National University, ActonACT, Australia
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25
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Martinez PA, Jacobina UP, Fernandes RV, Brito C, Penone C, Amado TF, Fonseca CR, Bidau CJ. A comparative study on karyotypic diversification rate in mammals. Heredity (Edinb) 2016; 118:366-373. [PMID: 27804966 DOI: 10.1038/hdy.2016.110] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 09/19/2016] [Accepted: 09/27/2016] [Indexed: 01/23/2023] Open
Abstract
Chromosomal rearrangements have a relevant role in organismic evolution. However, little is known about the mechanisms that lead different phylogenetic clades to have different chromosomal rearrangement rates. Here, we investigate the causes behind the wide karyotypic diversity exhibited by mammals. In particular, we analyzed the role of metabolic, reproductive, biogeographic and genomic characteristics on the rates of macro- and microstructural karyotypic diversification (rKD) using comparative phylogenetic methods. We found evidence that reproductive characteristics such as larger litter size per year and longevity, by allowing a higher number of meioses in absolute time, favor a higher probability of chromosomal change. Furthermore, families with large geographic distributions but containing species with restricted geographic ranges showed a greater probability of fixation of macrostructural chromosomal changes in different geographic areas. Finally, rKD does not evolve by Brownian motion because the mutation rate depends on the concerted evolution of repetitive sequences. The decisive factors of rKD evolution will be natural selection, genetic drift and meiotic drive that will eventually allow or not the fixation of the rearrangements. Our results indicate that mammalian karyotypic diversity is influenced by historical and adaptive mechanisms where reproductive and genomic factors modulate the rate of chromosomal change.
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Affiliation(s)
- P A Martinez
- PIBi Lab-Laboratorio de Pesquisas Integrativas em Biodiversidade, Pós-Graduação em Ecologia e Conservação, Universidade Federal de Sergipe, São Cristovão, Brazil
| | | | - R V Fernandes
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - C Brito
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - C Penone
- Institute of Plant Science, University of Bern, Bern, Switzerland
| | - T F Amado
- BioMa-Biodiversity and Macroecology Lab, Department of Biology and Geology, Physics and Inorganic Chemistry, Rey Juan Carlos University, Mostoles, Spain
| | - C R Fonseca
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - C J Bidau
- Paraná y Los Claveles, Garupá, Argentina
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26
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Arjona-Medina JA, Trelles O. Refining borders of genome-rearrangements including repetitions. BMC Genomics 2016; 17:804. [PMID: 27801292 PMCID: PMC5088515 DOI: 10.1186/s12864-016-3069-4] [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] [Indexed: 11/22/2022] Open
Abstract
Background DNA rearrangement events have been widely studied in comparative genomic for many years. The importance of these events resides not only in the study about relatedness among different species, but also to determine the mechanisms behind evolution. Although there are many methods to identify genome-rearrangements (GR), the refinement of their borders has become a huge challenge. Until now no accepted method exists to achieve accurate fine-tuning: i.e. the notion of breakpoint (BP) is still an open issue, and despite repeated regions are vital to understand evolution they are not taken into account in most of the GR detection and refinement methods. Methods and results We propose a method to refine the borders of GR including repeated regions. Instead of removing these repetitions to facilitate computation, we take advantage of them using a consensus alignment sequence of the repeated region in between two blocks. Using the concept of identity vectors for Synteny Blocks (SB) and repetitions, a Finite State Machine is designed to detect transition points in the difference between such vectors. The method does not force the BP to be a region or a point but depends on the alignment transitions within the SBs and repetitions. Conclusion The accurate definition of the borders of SB and repeated genomic regions and consequently the detection of BP might help to understand the evolutionary model of species. In this manuscript we present a new proposal for such a refinement. Features of the SBs borders and BPs are different and fit with what is expected. SBs with more diversity in annotations and BPs short and richer in DNA replication and stress response, which are strongly linked with rearrangements. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3069-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- J A Arjona-Medina
- Advanced Computing Technologies Unit, RISC Software GmbH, Hagenberg, 4232, Upper Austria, Austria.
| | - O Trelles
- Department of Computer Architecture, University of Malaga, Campus de Teatinos, Malaga, 29071, Spain
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27
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Farré M, Narayan J, Slavov GT, Damas J, Auvil L, Li C, Jarvis ED, Burt DW, Griffin DK, Larkin DM. Novel Insights into Chromosome Evolution in Birds, Archosaurs, and Reptiles. Genome Biol Evol 2016; 8:2442-51. [PMID: 27401172 PMCID: PMC5010900 DOI: 10.1093/gbe/evw166] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Homologous synteny blocks (HSBs) and evolutionary breakpoint regions (EBRs) in mammalian chromosomes are enriched for distinct DNA features, contributing to distinct phenotypes. To reveal HSB and EBR roles in avian evolution, we performed a sequence-based comparison of 21 avian and 5 outgroup species using recently sequenced genomes across the avian family tree and a newly-developed algorithm. We identified EBRs and HSBs in ancestral bird, archosaurian (bird, crocodile, and dinosaur), and reptile chromosomes. Genes involved in the regulation of gene expression and biosynthetic processes were preferably located in HSBs, including for example, avian-specific HSBs enriched for genes involved in limb development. Within birds, some lineage-specific EBRs rearranged genes were related to distinct phenotypes, such as forebrain development in parrots. Our findings provide novel evolutionary insights into genome evolution in birds, particularly on how chromosome rearrangements likely contributed to the formation of novel phenotypes.
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Affiliation(s)
- Marta Farré
- Department of Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, University of London, NW1 0TU, UK
| | - Jitendra Narayan
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, SY23 3DA, UK
| | - Gancho T Slavov
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, SY23 3DA, UK
| | - Joana Damas
- Department of Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, University of London, NW1 0TU, UK
| | - Loretta Auvil
- Illinois Informatics Institute, University of Illinois, Urbana, IL 61801, USA
| | - Cai Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Erich D Jarvis
- Department of Neurobiology, Duke University Medical Center, Durham, NC, 27710, USA Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - David W Burt
- Department of Genomics and Genetics, the Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, University of London, NW1 0TU, UK
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28
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Sanders AD, Hills M, Porubský D, Guryev V, Falconer E, Lansdorp PM. Characterizing polymorphic inversions in human genomes by single-cell sequencing. Genome Res 2016; 26:1575-1587. [PMID: 27472961 PMCID: PMC5088599 DOI: 10.1101/gr.201160.115] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 06/13/2016] [Indexed: 12/23/2022]
Abstract
Identifying genomic features that differ between individuals and cells can help uncover the functional variants that drive phenotypes and disease susceptibilities. For this, single-cell studies are paramount, as it becomes increasingly clear that the contribution of rare but functional cellular subpopulations is important for disease prognosis, management, and progression. Until now, studying these associations has been challenged by our inability to map structural rearrangements accurately and comprehensively. To overcome this, we coupled single-cell sequencing of DNA template strands (Strand-seq) with custom analysis software to rapidly discover, map, and genotype genomic rearrangements at high resolution. This allowed us to explore the distribution and frequency of inversions in a heterogeneous cell population, identify several polymorphic domains in complex regions of the genome, and locate rare alleles in the reference assembly. We then mapped the entire genomic complement of inversions within two unrelated individuals to characterize their distinct inversion profiles and built a nonredundant global reference of structural rearrangements in the human genome. The work described here provides a powerful new framework to study structural variation and genomic heterogeneity in single-cell samples, whether from individuals for population studies or tissue types for biomarker discovery.
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Affiliation(s)
- Ashley D Sanders
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Mark Hills
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - David Porubský
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, NL-9713 AV Groningen, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, NL-9713 AV Groningen, The Netherlands
| | - Ester Falconer
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada
| | - Peter M Lansdorp
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3, Canada.,European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, NL-9713 AV Groningen, The Netherlands.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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29
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Adler PH, Yildirim A, Onder Z, Tasci GT, Duzlu O, Arslan MO, Ciloglu A, Sari B, Parmaksizoglu N, Inci A. Rearrangement hotspots in the sex chromosome of the Palearctic black fly Simulium bergi (Diptera, Simuliidae). COMPARATIVE CYTOGENETICS 2016; 10:295-310. [PMID: 27551350 PMCID: PMC4977804 DOI: 10.3897/compcytogen.v10i2.8855] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/01/2016] [Indexed: 06/06/2023]
Abstract
An extreme example of nonrandom rearrangements, especially inversion breaks, is described in the polytene chromosomes of the black fly Simulium bergi Rubtsov, 1956 from Armenia and Turkey. A total of 48 rearrangements was discovered, relative to the standard banding sequence for the subgenus Simulium Latreille, 1802. One rearrangement, an inversion (IIS-C) in the short arm of the second chromosome, was fixed. Six (12.5%) of the rearrangements were autosomal polymorphisms, and the remaining 41 (85.4%) were sex linked. More than 40 X- and Y-linked rearrangements, predominantly inversions, were clustered in the long arm of the second chromosome (IIL), representing about 15% of the total complement. The pattern conforms to a nonrandom model of chromosome breakage, perhaps associated with an underlying molecular mechanism.
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Affiliation(s)
- Peter H. Adler
- Department of Agricultural and Environmental Sciences, 130 McGinty Court, Clemson University, Clemson, SC 29634-0310 USA
| | - Alparslan Yildirim
- Department of Parasitology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - Zuhal Onder
- Department of Parasitology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - G. Taskin Tasci
- Department of Parasitology, Faculty of Veterinary Medicine, Kafkas University, Kars, Turkey
| | - Onder Duzlu
- Department of Parasitology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - M. Ozkan Arslan
- Department of Microbiology, Faculty of Medicine, Kafkas University, Kars, Turkey
| | - Arif Ciloglu
- Department of Parasitology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
| | - Baris Sari
- Department of Parasitology, Faculty of Veterinary Medicine, Kafkas University, Kars, Turkey
| | - Nilgun Parmaksizoglu
- Department of Parasitology, Faculty of Veterinary Medicine, Kafkas University, Kars, Turkey
| | - Abdullah Inci
- Department of Parasitology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Turkey
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30
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Sharakhov IV, Artemov GN, Sharakhova MV. Chromosome evolution in malaria mosquitoes inferred from physically mapped genome assemblies. J Bioinform Comput Biol 2016; 14:1630003. [PMID: 27021248 DOI: 10.1142/s0219720016300033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Polymorphic inversions in mosquitoes are distributed nonrandomly among chromosomes and are associated with ecological, behavioral, and physiological adaptations related to pathogen transmission. Despite their significance, the patterns and mechanism of genome rearrangements are not well understood. Recent sequencing and physical mapping of the genomes for 16 Anopheles mosquito species provided an opportunity to study chromosome evolution at the highest resolution. New studies revealed that fixed rearrangement accumulated [Formula: see text]3 times faster on the X chromosome than on autosomes. The highest densities of transposable elements (TEs) and satellites of different sizes have also been found on the X chromosome, suggesting a mechanism for the inversion generation. The high rate of X chromosome rearrangements is in sharp contrast with the paucity of polymorphic inversions on the X in the majority of anopheline species. This paper highlights the advances in understanding chromosome evolution in malaria vectors and discusses possible future directions in studying mechanisms and biological roles of genome rearrangements.
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Affiliation(s)
- Igor V Sharakhov
- 1 Department of Entomology, Virginia Tech, Blacksburg, Virginia 24061, USA.,2 Tomsk State University, Tomsk 634050, Russia
| | | | - Maria V Sharakhova
- 1 Department of Entomology, Virginia Tech, Blacksburg, Virginia 24061, USA.,2 Tomsk State University, Tomsk 634050, Russia
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31
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Leibowitz ML, Zhang CZ, Pellman D. Chromothripsis: A New Mechanism for Rapid Karyotype Evolution. Annu Rev Genet 2015; 49:183-211. [DOI: 10.1146/annurev-genet-120213-092228] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mitchell L. Leibowitz
- Department of Pediatric Oncology,
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115;
| | - Cheng-Zhong Zhang
- Department of Pediatric Oncology,
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215;
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115;
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
| | - David Pellman
- Department of Pediatric Oncology,
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115;
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
- Howard Hughes Medical Institute, Boston, Massachusetts 02115
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32
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Morgan AP, Welsh CE. Informatics resources for the Collaborative Cross and related mouse populations. Mamm Genome 2015; 26:521-39. [PMID: 26135136 DOI: 10.1007/s00335-015-9581-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/23/2015] [Indexed: 02/05/2023]
Affiliation(s)
- Andrew P Morgan
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Catherine E Welsh
- Department of Mathematics & Computer Science, Rhodes College, Memphis, TN, USA.
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33
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Farré M, Robinson TJ, Ruiz-Herrera A. An Integrative Breakage Model of genome architecture, reshuffling and evolution: The Integrative Breakage Model of genome evolution, a novel multidisciplinary hypothesis for the study of genome plasticity. Bioessays 2015; 37:479-88. [PMID: 25739389 DOI: 10.1002/bies.201400174] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 12/23/2022]
Abstract
Our understanding of genomic reorganization, the mechanics of genomic transmission to offspring during germ line formation, and how these structural changes contribute to the speciation process, and genetic disease is far from complete. Earlier attempts to understand the mechanism(s) and constraints that govern genome remodeling suffered from being too narrowly focused, and failed to provide a unified and encompassing view of how genomes are organized and regulated inside cells. Here, we propose a new multidisciplinary Integrative Breakage Model for the study of genome evolution. The analysis of the high-level structural organization of genomes (nucleome), together with the functional constrains that accompany genome reshuffling, provide insights into the origin and plasticity of genome organization that may assist with the detection and isolation of therapeutic targets for the treatment of complex human disorders.
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Affiliation(s)
- Marta Farré
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Campus UAB, Barcelona, Spain
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34
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Zurano JP, Ojeda DS, Bidau CJ, Molina WF, Ledesma MA, Martinez PA. A comparison of heterochromatic regions in three species of neotropical canids. ZOOL ANZ 2015. [DOI: 10.1016/j.jcz.2014.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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Lin Y, Nurk S, Pevzner PA. What is the difference between the breakpoint graph and the de Bruijn graph? BMC Genomics 2014; 15 Suppl 6:S6. [PMID: 25572416 PMCID: PMC4240671 DOI: 10.1186/1471-2164-15-s6-s6] [Citation(s) in RCA: 10] [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
The breakpoint graph and the de Bruijn graph are two key data structures in the studies of genome rearrangements and genome assembly. However, the classical breakpoint graphs are defined on two genomes (represented as sequences of synteny blocks), while the classical de Bruijn graphs are defined on a single genome (represented as DNA strings). Thus, the connection between these two graph models is not explicit. We generalize the notions of both the breakpoint graph and the de Bruijn graph, and make it transparent that the breakpoint graph and the de Bruijn graph are mathematically equivalent. The explicit description of the connection between these important data structures provides a bridge between two previously separated bioinformatics communities studying genome rearrangements and genome assembly.
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36
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A high resolution map of mammalian X chromosome fragile regions assessed by large-scale comparative genomics. Mamm Genome 2014; 25:618-35. [PMID: 25086724 DOI: 10.1007/s00335-014-9537-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 07/14/2014] [Indexed: 10/24/2022]
Abstract
Chromosomal evolution involves multiple changes at structural and numerical levels. These changes, which are related to the variation of the gene number and their location, can be tracked by the identification of syntenic blocks (SB). First reports proposed that ~180-280 SB might be shared by mouse and human species. More recently, further studies including additional genomes have identified up to ~1,400 SB during the evolution of eutherian species. A considerable number of studies regarding the X chromosome's structure and evolution have been undertaken because of its extraordinary biological impact on reproductive fitness and speciation. Some have identified evolutionary breakpoint regions and fragile sites at specific locations in the human X chromosome. However, mapping these regions to date has involved using low-to-moderate resolution techniques. Such scenario might be related to underestimating their total number and giving an inaccurate location. The present study included using a combination of bioinformatics methods for identifying, at base-pair level, chromosomal rearrangements occurring during X chromosome evolution in 13 mammalian species. A comparative technique using four different algorithms was used for optimizing the detection of hotspot regions in the human X chromosome. We identified a significant interspecific variation in SB size which was related to genetic information gain regarding the human X chromosome. We found that human hotspot regions were enriched by LINE-1 and Alu transposable elements, which may have led to intraspecific chromosome rearrangement events. New fragile regions located in the human X chromosome have also been postulated. We estimate that the high resolution map of X chromosome fragile sites presented here constitutes useful data concerning future studies on mammalian evolution and human disease.
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37
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Ebert G, Steininger A, Weißmann R, Boldt V, Lind-Thomsen A, Grune J, Badelt S, Heßler M, Peiser M, Hitzler M, Jensen LR, Müller I, Hu H, Arndt PF, Kuss AW, Tebel K, Ullmann R. Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7. BMC Genomics 2014; 15:537. [PMID: 24973960 PMCID: PMC4092221 DOI: 10.1186/1471-2164-15-537] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 06/17/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Segmental duplications (SDs) are not evenly distributed along chromosomes. The reasons for this biased susceptibility to SD insertion are poorly understood. Accumulation of SDs is associated with increased genomic instability, which can lead to structural variants and genomic disorders such as the Williams-Beuren syndrome. Despite these adverse effects, SDs have become fixed in the human genome. Focusing on chromosome 7, which is particularly rich in interstitial SDs, we have investigated the distribution of SDs in the context of evolution and the three dimensional organisation of the chromosome in order to gain insights into the mutual relationship of SDs and chromatin topology. RESULTS Intrachromosomal SDs preferentially accumulate in those segments of chromosome 7 that are homologous to marmoset chromosome 2. Although this formerly compact segment has been re-distributed to three different sites during primate evolution, we can show by means of public data on long distance chromatin interactions that these three intervals, and consequently the paralogous SDs mapping to them, have retained their spatial proximity in the nucleus. Focusing on SD clusters implicated in the aetiology of the Williams-Beuren syndrome locus we demonstrate by cross-species comparison that these SDs have inserted at the borders of a topological domain and that they flank regions with distinct DNA conformation. CONCLUSIONS Our study suggests a link of nuclear architecture and the propagation of SDs across chromosome 7, either by promoting regional SD insertion or by contributing to the establishment of higher order chromatin organisation themselves. The latter could compensate for the high risk of structural rearrangements and thus may have contributed to their evolutionary fixation in the human genome.
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Affiliation(s)
- Grit Ebert
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- />Department of Biology, Chemistry and Pharmacy, Free University Berlin, 14195 Berlin, Germany
| | - Anne Steininger
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- />Department of Biology, Chemistry and Pharmacy, Free University Berlin, 14195 Berlin, Germany
| | - Robert Weißmann
- />Department of Human Genetics, University Medicine Greifswald, and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Fleischmannstraße 42-44, 17475 Greifswald, Germany
| | - Vivien Boldt
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- />Department of Biology, Chemistry and Pharmacy, Free University Berlin, 14195 Berlin, Germany
| | - Allan Lind-Thomsen
- />Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Jana Grune
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Stefan Badelt
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- />Institute for Theoretical Chemistry, University of Vienna, Waehringer Straße 17, A-1090 Vienna, Austria
| | - Melanie Heßler
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Matthias Peiser
- />Unit Experimental Research, Department of Product Safety, Federal Institute for Bundeswehr Institute of Radiobiology affiliated, the University of Ulm, Neuherbergstraße 11, 80937 Munich, Germany
| | - Manuel Hitzler
- />Unit Experimental Research, Department of Product Safety, Federal Institute for Bundeswehr Institute of Radiobiology affiliated, the University of Ulm, Neuherbergstraße 11, 80937 Munich, Germany
| | - Lars R Jensen
- />Department of Human Genetics, University Medicine Greifswald, and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Fleischmannstraße 42-44, 17475 Greifswald, Germany
| | - Ines Müller
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Hao Hu
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Peter F Arndt
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Andreas W Kuss
- />Department of Human Genetics, University Medicine Greifswald, and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Fleischmannstraße 42-44, 17475 Greifswald, Germany
| | - Katrin Tebel
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Reinhard Ullmann
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
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38
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Kawakami T, Smeds L, Backström N, Husby A, Qvarnström A, Mugal CF, Olason P, Ellegren H. A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution. Mol Ecol 2014; 23:4035-58. [PMID: 24863701 PMCID: PMC4149781 DOI: 10.1111/mec.12810] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Revised: 05/08/2014] [Accepted: 05/09/2014] [Indexed: 12/15/2022]
Abstract
Detailed linkage and recombination rate maps are necessary to use the full potential of genome sequencing and population genomic analyses. We used a custom collared flycatcher 50 K SNP array to develop a high-density linkage map with 37 262 markers assigned to 34 linkage groups in 33 autosomes and the Z chromosome. The best-order map contained 4215 markers, with a total distance of 3132 cm and a mean genetic distance between markers of 0.12 cm. Facilitated by the array being designed to include markers from most scaffolds, we obtained a second-generation assembly of the flycatcher genome that approaches full chromosome sequences (N50 super-scaffold size 20.2 Mb and with 1.042 Gb (of 1.116 Gb) anchored to and mostly ordered and oriented along chromosomes). We found that flycatcher and zebra finch chromosomes are entirely syntenic but that inversions at mean rates of 1.5–2.0 event (6.6–7.5 Mb) per My have changed the organization within chromosomes, rates high enough for inversions to potentially have been involved with many speciation events during avian evolution. The mean recombination rate was 3.1 cm/Mb and correlated closely with chromosome size, from 2 cm/Mb for chromosomes >100 Mb to >10 cm/Mb for chromosomes <10 Mb. This size dependence seemed entirely due to an obligate recombination event per chromosome; if 50 cm was subtracted from the genetic lengths of chromosomes, the rate per physical unit DNA was constant across chromosomes. Flycatcher recombination rate showed similar variation along chromosomes as chicken but lacked the large interior recombination deserts characteristic of zebra finch chromosomes.
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Affiliation(s)
- Takeshi Kawakami
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
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Dai Z, Xiong Y, Dai X. Neighboring genes show interchromosomal colocalization after their separation. Mol Biol Evol 2014; 31:1166-72. [PMID: 24505120 DOI: 10.1093/molbev/msu065] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The order of genes on eukaryotic chromosomes is nonrandom. Some neighboring genes show order conservation among species, while some neighboring genes separate during evolution. Here, we investigated whether neighboring genes show interactions after their separation. We found that neighboring gene pairs tend to show interchromosomal colocalization (i.e., nuclear colocalization) in the species in which they separate. These nuclear colocalized separated neighboring gene pairs 1) show neighborhood conservation in more species, 2) tend to be regulated by the same transcription factor, and 3) tend to be regulated by the same histone modification. These results suggest a mechanism by which neighboring genes could retain nuclear proximity after their separation.
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Affiliation(s)
- Zhiming Dai
- Department of Electronics and Communication Engineering, School of Information Science and Technology, Sun Yat-Sen University, Guangzhou, China
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40
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Andreyenkova NG, Kolesnikova TD, Makunin IV, Pokholkova GV, Boldyreva LV, Zykova TY, Zhimulev IF, Belyaeva ES. Late replication domains are evolutionary conserved in the Drosophila genome. PLoS One 2013; 8:e83319. [PMID: 24391753 PMCID: PMC3877026 DOI: 10.1371/journal.pone.0083319] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 11/01/2013] [Indexed: 12/20/2022] Open
Abstract
Drosophila chromosomes are organized into distinct domains differing in their predominant chromatin composition, replication timing and evolutionary conservation. We show on a genome-wide level that genes whose order has remained unaltered across 9 Drosophila species display late replication timing and frequently map to the regions of repressive chromatin. This observation is consistent with the existence of extensive domains of repressive chromatin that replicate extremely late and have conserved gene order in the Drosophila genome. We suggest that such repressive chromatin domains correspond to a handful of regions that complete replication at the very end of S phase. We further demonstrate that the order of genes in these regions is rarely altered in evolution. Substantial proportion of such regions significantly coincide with large synteny blocks. This indicates that there are evolutionary mechanisms maintaining the integrity of these late-replicating chromatin domains. The synteny blocks corresponding to the extremely late-replicating regions in the D. melanogaster genome consistently display two-fold lower gene density across different Drosophila species.
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Affiliation(s)
- Natalya G. Andreyenkova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Tatyana D. Kolesnikova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Igor V. Makunin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Research Computing Centre, The University of Queensland, Brisbane, St Lucia, QLD, Australia
| | - Galina V. Pokholkova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Lidiya V. Boldyreva
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Tatyana Yu. Zykova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Igor F. Zhimulev
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- * E-mail:
| | - Elena S. Belyaeva
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Xiaobo F, Pinthong K, Mkrtchyan H, Siripiyasing P, Kosyakova N, Supiwong W, Tanomtong A, Chaveerach A, Liehr T, de Bello Cioffi M, Weise A. First detailed reconstruction of the karyotype of Trachypithecus cristatus (Mammalia: Cercopithecidae). Mol Cytogenet 2013; 6:58. [PMID: 24341374 PMCID: PMC3914712 DOI: 10.1186/1755-8166-6-58] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 11/21/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The chromosomal homologies of human (Homo sapiens = HSA) and silvered leaf monkey (Trachypithecus cristatus = TCR) have been previously studied by classical chromosome staining and by fluorescence in situ hybridization (FISH) applying chromosome-specific DNA probes of all human chromosomes in the 1980s and 1990s, respectively. RESULTS However, as the resolution of these techniques is limited we used multicolor banding (MCB) at an ~250-band level, and other selected human DNA probes to establish a detailed chromosomal map of TCR. Therefore it was possible to precisely determine evolutionary conserved breakpoints, orientation of segments and distribution of specific regions in TCR compared to HSA. Overall, 69 evolutionary conserved breakpoints including chromosomal segments, which failed to be resolved in previous reports, were exactly identified and characterized. CONCLUSIONS This work also represents the first molecular cytogenetic one characterizing a multiple sex chromosome system with a male karyotype 44,XY1Y2. The obtained results are compared to other available data for old world monkeys and drawbacks in hominoid evolution are discussed.
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Affiliation(s)
- Fan Xiaobo
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, Jena D-07743, Germany
| | - Krit Pinthong
- Faculty of Science and Technology, Surindra Rajabhat University, 186 Moo 1, Surin, Maung District 32000, Thailand
| | - Hasmik Mkrtchyan
- Center of Medical Genetics and Primary Health Care, Abovyan Str 34/3, 001, Yerevan, Armenia
| | - Pornnarong Siripiyasing
- Faculty of Science and Technology, Rajabhat Maha Sarakham University, 80 Nakonsawan Rd, Maha Sarakham, Talad, Maung District 44000, Thailand
| | - Nadezda Kosyakova
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, Jena D-07743, Germany
| | - Weerayuth Supiwong
- Department of Biology, Faculty of Science, Khon Kaen University, 123 Moo 16 Mittapap Rd., Khon Kaen, Muang District 40002, Thailand
| | - Alongkoad Tanomtong
- Department of Biology, Faculty of Science, Khon Kaen University, 123 Moo 16 Mittapap Rd., Khon Kaen, Muang District 40002, Thailand
| | - Arunrat Chaveerach
- Department of Biology, Faculty of Science, Khon Kaen University, 123 Moo 16 Mittapap Rd., Khon Kaen, Muang District 40002, Thailand
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, Jena D-07743, Germany
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Anja Weise
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, Jena D-07743, Germany
- Institut für Humangenetik, Postfach, Jena D-07740, Germany
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Giannuzzi G, Pazienza M, Huddleston J, Antonacci F, Malig M, Vives L, Eichler EE, Ventura M. Hominoid fission of chromosome 14/15 and the role of segmental duplications. Genome Res 2013; 23:1763-73. [PMID: 24077392 PMCID: PMC3814877 DOI: 10.1101/gr.156240.113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ape chromosomes homologous to human chromosomes 14 and 15 were generated by a fission event of an ancestral submetacentric chromosome, where the two chromosomes were joined head-to-tail. The hominoid ancestral chromosome most closely resembles the macaque chromosome 7. In this work, we provide insights into the evolution of human chromosomes 14 and 15, performing a comparative study between macaque boundary region 14/15 and the orthologous human regions. We construct a 1.6-Mb contig of macaque BAC clones in the region orthologous to the ancestral hominoid fission site and use it to define the structural changes that occurred on human 14q pericentromeric and 15q subtelomeric regions. We characterize the novel euchromatin–heterochromatin transition region (∼20 Mb) acquired during the neocentromere establishment on chromosome 14, and find it was mainly derived through pericentromeric duplications from ancestral hominoid chromosomes homologous to human 2q14–qter and 10. Further, we show a relationship between evolutionary hotspots and low-copy repeat loci for chromosome 15, revealing a possible role of segmental duplications not only in mediating but also in “stitching” together rearrangement breakpoints.
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Affiliation(s)
- Giuliana Giannuzzi
- Dipartimento di Biologia, Università degli Studi di Bari "Aldo Moro," Bari 70125, Italy
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Watson CT, Garg P, Sharp AJ. Comment on "genomic hypomethylation in the human germline associates with selective structural mutability in the human genome". PLoS Genet 2013; 9:e1003332. [PMID: 23468658 PMCID: PMC3585013 DOI: 10.1371/journal.pgen.1003332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Corey T. Watson
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Paras Garg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Andrew J. Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- * E-mail:
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Xin H, Lee D, Hormozdiari F, Yedkar S, Mutlu O, Alkan C. Accelerating read mapping with FastHASH. BMC Genomics 2013; 14 Suppl 1:S13. [PMID: 23369189 PMCID: PMC3549798 DOI: 10.1186/1471-2164-14-s1-s13] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
With the introduction of next-generation sequencing (NGS) technologies, we are facing an exponential increase in the amount of genomic sequence data. The success of all medical and genetic applications of next-generation sequencing critically depends on the existence of computational techniques that can process and analyze the enormous amount of sequence data quickly and accurately. Unfortunately, the current read mapping algorithms have difficulties in coping with the massive amounts of data generated by NGS.We propose a new algorithm, FastHASH, which drastically improves the performance of the seed-and-extend type hash table based read mapping algorithms, while maintaining the high sensitivity and comprehensiveness of such methods. FastHASH is a generic algorithm compatible with all seed-and-extend class read mapping algorithms. It introduces two main techniques, namely Adjacency Filtering, and Cheap K-mer Selection.We implemented FastHASH and merged it into the codebase of the popular read mapping program, mrFAST. Depending on the edit distance cutoffs, we observed up to 19-fold speedup while still maintaining 100% sensitivity and high comprehensiveness.
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Affiliation(s)
- Hongyi Xin
- Depts. of Computer Science and Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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Marotta M, Chen X, Inoshita A, Stephens R, Budd GT, Crowe JP, Lyons J, Kondratova A, Tubbs R, Tanaka H. A common copy-number breakpoint of ERBB2 amplification in breast cancer colocalizes with a complex block of segmental duplications. Breast Cancer Res 2012. [PMID: 23181561 PMCID: PMC4053137 DOI: 10.1186/bcr3362] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Introduction Segmental duplications (low-copy repeats) are the recently duplicated genomic segments in the human genome that display nearly identical (> 90%) sequences and account for about 5% of euchromatic regions. In germline, duplicated segments mediate nonallelic homologous recombination and thus cause both non-disease-causing copy-number variants and genomic disorders. To what extent duplicated segments play a role in somatic DNA rearrangements in cancer remains elusive. Duplicated segments often cluster and form genomic blocks enriched with both direct and inverted repeats (complex genomic regions). Such complex regions could be fragile and play a mechanistic role in the amplification of the ERBB2 gene in breast tumors, because repeated sequences are known to initiate gene amplification in model systems. Methods We conducted polymerase chain reaction (PCR)-based assays for primary breast tumors and analyzed publically available array-comparative genomic hybridization data to map a common copy-number breakpoint in ERBB2-amplified primary breast tumors. We further used molecular, bioinformatics, and population-genetics approaches to define duplication contents, structural variants, and haplotypes within the common breakpoint. Results We found a large (> 300-kb) block of duplicated segments that was colocalized with a common-copy number breakpoint for ERBB2 amplification. The breakpoint that potentially initiated ERBB2 amplification localized in a region 1.5 megabases (Mb) on the telomeric side of ERBB2. The region is very complex, with extensive duplications of KRTAP genes, structural variants, and, as a result, a paucity of single-nucleotide polymorphism (SNP) markers. Duplicated segments are varied in size and degree of sequence homology, indicating that duplications have occurred recurrently during genome evolution. Conclusions Amplification of the ERBB2 gene in breast tumors is potentially initiated by a complex region that has unusual genomic features and thus requires rigorous, labor-intensive investigation. The haplotypes we provide could be useful to identify the potential association between the complex region and ERBB2 amplification.
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Wavelet analysis of DNA walks on the human and chimpanzee MAGE/CSAG-palindromes. GENOMICS PROTEOMICS & BIOINFORMATICS 2012; 10:230-6. [PMID: 23084779 PMCID: PMC5054716 DOI: 10.1016/j.gpb.2012.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 02/18/2012] [Accepted: 03/02/2012] [Indexed: 11/22/2022]
Abstract
The palindrome is one class of symmetrical duplications with reverse complementary characters, which is widely distributed in many organisms. Graphical representation of DNA sequence provides a simple way of viewing and comparing various genomic structures. Through 3-D DNA walk analysis, the similarity and differences in nucleotide composition, as well as the evolutionary relationship between human and chimpanzee MAGE/CSAG-palindromes, can be clearly revealed. Further wavelet analysis indicated that duplicated segments have irregular patterns compared to their surrounding sequences. However, sequence similarity analysis suggests that there is possible common ancestor between human and chimpanzee MAGE/CSAG-palindromes. Based on the specific distribution and orientation of the repeated sequences, a simple possible evolutionary model of the palindromes is suggested, which may help us to better understand the evolutionary course of the genes and the symmetrical sequences.
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Li J, Harris RA, Cheung SW, Coarfa C, Jeong M, Goodell MA, White LD, Patel A, Kang SH, Shaw C, Chinault AC, Gambin T, Gambin A, Lupski JR, Milosavljevic A. Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome. PLoS Genet 2012; 8:e1002692. [PMID: 22615578 PMCID: PMC3355074 DOI: 10.1371/journal.pgen.1002692] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 03/21/2012] [Indexed: 12/27/2022] Open
Abstract
The hotspots of structural polymorphisms and structural mutability in the human genome remain to be explained mechanistically. We examine associations of structural mutability with germline DNA methylation and with non-allelic homologous recombination (NAHR) mediated by low-copy repeats (LCRs). Combined evidence from four human sperm methylome maps, human genome evolution, structural polymorphisms in the human population, and previous genomic and disease studies consistently points to a strong association of germline hypomethylation and genomic instability. Specifically, methylation deserts, the ∼1% fraction of the human genome with the lowest methylation in the germline, show a tenfold enrichment for structural rearrangements that occurred in the human genome since the branching of chimpanzee and are highly enriched for fast-evolving loci that regulate tissue-specific gene expression. Analysis of copy number variants (CNVs) from 400 human samples identified using a custom-designed array comparative genomic hybridization (aCGH) chip, combined with publicly available structural variation data, indicates that association of structural mutability with germline hypomethylation is comparable in magnitude to the association of structural mutability with LCR–mediated NAHR. Moreover, rare CNVs occurring in the genomes of individuals diagnosed with schizophrenia, bipolar disorder, and developmental delay and de novo CNVs occurring in those diagnosed with autism are significantly more concentrated within hypomethylated regions. These findings suggest a new connection between the epigenome, selective mutability, evolution, and human disease. The human genome contains many loci with high incidence of structural mutations, including insertions and deletions of chromosomal segments. This excessive mutability has accelerated evolution and contributed to human disease but has yet to be explained. Segments of DNA repeated in low-copy numbers (LCRs) have been previously implicated in promoting structural mutability in specific disease-associated loci. Lack of methylation (hypomethylation) of genomic DNA has been previously associated with high structural mutability in gibbons and in human cancer cells, but the association with structural mutability in the human germline has not been explored prior to this study. Our analyses confirm the role of LCRs in promoting structural mutability on the genome scale but also reveal a surprisingly strong association of genomic instability with hypomethylation. Specifically, evolutionary analyses reveal that methylation deserts, the ∼1% fraction of the human genome with the lowest methylation in human sperm, harbor a tenfold higher number of structural mutations than genome-wide average. Moreover, the structural mutations in individuals diagnosed with schizophrenia, bipolar disorder, developmental delay, and autism are significantly more concentrated within hypomethylated regions. Our findings suggest a new connection between methylation of genomic DNA, selective structural mutability, evolution, and human disease.
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Affiliation(s)
- Jian Li
- Bioinformatics Research Laboratory, Epigenome Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
| | - R. Alan Harris
- Bioinformatics Research Laboratory, Epigenome Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Cristian Coarfa
- Bioinformatics Research Laboratory, Epigenome Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Mira Jeong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Margaret A. Goodell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lisa D. White
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sung-Hae Kang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - A. Craig Chinault
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - Anna Gambin
- Institute of Informatics, Warsaw University, Warsaw, Poland
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children's Hospital, Houston, Texas, United States of America
| | - Aleksandar Milosavljevic
- Bioinformatics Research Laboratory, Epigenome Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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Yegorov S, Good S. Using paleogenomics to study the evolution of gene families: origin and duplication history of the relaxin family hormones and their receptors. PLoS One 2012; 7:e32923. [PMID: 22470432 PMCID: PMC3310001 DOI: 10.1371/journal.pone.0032923] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 02/05/2012] [Indexed: 11/28/2022] Open
Abstract
Recent progress in the analysis of whole genome sequencing data has resulted in the emergence of paleogenomics, a field devoted to the reconstruction of ancestral genomes. Ancestral karyotype reconstructions have been used primarily to illustrate the dynamic nature of genome evolution. In this paper, we demonstrate how they can also be used to study individual gene families by examining the evolutionary history of relaxin hormones (RLN/INSL) and relaxin family peptide receptors (RXFP). Relaxin family hormones are members of the insulin superfamily, and are implicated in the regulation of a variety of primarily reproductive and neuroendocrine processes. Their receptors are G-protein coupled receptors (GPCR's) and include members of two distinct evolutionary groups, an unusual characteristic. Although several studies have tried to elucidate the origins of the relaxin peptide family, the evolutionary origin of their receptors and the mechanisms driving the diversification of the RLN/INSL-RXFP signaling systems in non-placental vertebrates has remained elusive. Here we show that the numerous vertebrate RLN/INSL and RXFP genes are products of an ancestral receptor-ligand system that originally consisted of three genes, two of which apparently trace their origins to invertebrates. Subsequently, diversification of the system was driven primarily by whole genome duplications (WGD, 2R and 3R) followed by almost complete retention of the ligand duplicates in most vertebrates but massive loss of receptor genes in tetrapods. Interestingly, the majority of 3R duplicates retained in teleosts are potentially involved in neuroendocrine regulation. Furthermore, we infer that the ancestral AncRxfp3/4 receptor may have been syntenically linked to the AncRln-like ligand in the pre-2R genome, and show that syntenic linkages among ligands and receptors have changed dynamically in different lineages. This study ultimately shows the broad utility, with some caveats, of incorporating paleogenomics data into understanding the evolution of gene families.
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Affiliation(s)
- Sergey Yegorov
- Department of Biology, University of Winnipeg, Winnipeg, Manitoba, Canada
| | - Sara Good
- Department of Biology, University of Winnipeg, Winnipeg, Manitoba, Canada
- * E-mail:
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49
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Ma X, Rogacheva MV, Nishant KT, Zanders S, Bustamante CD, Alani E. Mutation hot spots in yeast caused by long-range clustering of homopolymeric sequences. Cell Rep 2012; 1:36-42. [PMID: 22832106 DOI: 10.1016/j.celrep.2011.10.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 09/29/2011] [Accepted: 10/21/2011] [Indexed: 11/18/2022] Open
Abstract
Evolutionary theory assumes that mutations occur randomly in the genome; however, studies performed in a variety of organisms indicate the existence of context-dependent mutation biases. Sources of mutagenesis variation across large genomic contexts (e.g., hundreds of bases) have not been identified. Here, we use high-coverage whole-genome sequencing of a conditional mismatch repair mutant line of diploid yeast to identify mutations that accumulated after 160 generations of growth. The vast majority of the mutations accumulated as insertion/deletions (in/dels) in homopolymeric [poly(dA:dT)] and repetitive DNA tracts. Surprisingly, the likelihood of an in/del mutation in a given poly(dA:dT) tract is increased by the presence of nearby poly(dA:dT) tracts in up to a 1,000 bp region centered on the given tract. Our work suggests that specific mutation hot spots can contribute disproportionately to the genetic variation that is introduced into populations and provides long-range genomic sequence context that contributes to mutagenesis.
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Affiliation(s)
- Xin Ma
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA
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50
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Abstract
Structural variation (SV) encompasses diverse types of genomic variants including deletions, duplications, inversions, transpositions, translocations, and complex rearrangements, and is now recognized to be an abundant class of genetic variation in mammals. Different individuals, or strains, of a given species can differ by thousands of variants. However, despite a large number of studies over the past decade and impressive progress on many fronts, there remain significant gaps in our knowledge, particularly in species other than human. Arguably the most relevant among these are genetically tractable models such as mouse, rat, and dog. The emergence of efficient and affordable DNA sequencing technologies presents an opportunity to make rapid progress toward understanding the nature, origin, and function of SV in these, and other, domesticated species. Here, we summarize the current state of knowledge of SV in mammals, with a focus on the similarities and differences between domesticated species and human. We then present methods to identify SV breakpoints from next-generation sequence (NGS) data by paired-end mapping, split-read mapping, and local assembly, and discuss challenges that arise when interpreting these data in lineages with complex breeding histories and incomplete reference genomes. We further describe technical modifications that allow for identification of variants involving repetitive DNA elements such as transposons and segmental duplications. Finally, we explore a few of the key biological insights that can be gained by applying NGS methods to model organisms.
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Affiliation(s)
- Ira M Hall
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.
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