1
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Ruiz-Ruano FJ, Camacho JPM. Irreproducible results and unsupported conclusions in Ahmad et al. [BMC genomics (2020) 21:656]. BMC Genomics 2023; 24:778. [PMID: 38105238 PMCID: PMC10726643 DOI: 10.1186/s12864-023-09883-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 12/07/2023] [Indexed: 12/19/2023] Open
Affiliation(s)
- Francisco J Ruiz-Ruano
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, SE-752 36, Sweden
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, 53113, Bonn, Germany
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2
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Vontzou N, Pei Y, Mueller JC, Reifová R, Ruiz-Ruano FJ, Schlebusch SA, Suh A. Songbird germline-restricted chromosome as a potential arena of genetic conflicts. Curr Opin Genet Dev 2023; 83:102113. [PMID: 37734346 DOI: 10.1016/j.gde.2023.102113] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/03/2023] [Accepted: 08/20/2023] [Indexed: 09/23/2023]
Abstract
Genetic conflicts can arise between components of the genome with different inheritance strategies. The germline-restricted chromosome (GRC) of songbirds shows unusual mitotic and meiotic transmission compared with the rest of the genome. It is excluded from somatic cells and maintained only in the germline. It is usually present in one copy in the male germline and eliminated during spermatogenesis, while in the female germline, it usually occurs in two copies and behaves as a regular chromosome. Here, we review what is known about the GRC's evolutionary history, genetic content, and expression and discuss how it may be involved in different types of genetic conflicts. Finally, we interrogate the potential role of the GRC in songbird germline development, highlighting several unsolved mysteries.
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Affiliation(s)
- Niki Vontzou
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, 53113 Bonn, Germany; School of Biological Sciences, University of East Anglia, Norwich, UK.
| | - Yifan Pei
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, 53113 Bonn, Germany; Institute of Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121 Bonn, Germany; Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Jakob C Mueller
- Department of Ornithology, Max Planck Institute for Biological Intelligence, 82319 Seewiesen, Germany
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Francisco J Ruiz-Ruano
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, 53113 Bonn, Germany; Institute of Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121 Bonn, Germany. https://twitter.com/@fjruizruano
| | - Stephen A Schlebusch
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Alexander Suh
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, 53113 Bonn, Germany; Institute of Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121 Bonn, Germany; Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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Schlebusch SA, Rídl J, Poignet M, Ruiz-Ruano FJ, Reif J, Pajer P, Pačes J, Albrecht T, Suh A, Reifová R. Rapid gene content turnover on the germline-restricted chromosome in songbirds. Nat Commun 2023; 14:4579. [PMID: 37516764 PMCID: PMC10387091 DOI: 10.1038/s41467-023-40308-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 07/20/2023] [Indexed: 07/31/2023] Open
Abstract
The germline-restricted chromosome (GRC) of songbirds represents a taxonomically widespread example of programmed DNA elimination. Despite its apparent indispensability, we still know very little about the GRC's genetic composition, function, and evolutionary significance. Here we assemble the GRC in two closely related species, the common and thrush nightingale. In total we identify 192 genes across the two GRCs, with many of them present in multiple copies. Interestingly, the GRC appears to be under little selective pressure, with the genetic content differing dramatically between the two species and many GRC genes appearing to be pseudogenized fragments. Only one gene, cpeb1, has a complete coding region in all examined individuals of the two species and shows no copy number variation. The acquisition of this gene by the GRC corresponds with the earliest estimates of the GRC origin, making it a good candidate for the functional indispensability of the GRC in songbirds.
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Affiliation(s)
- Stephen A Schlebusch
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.
| | - Jakub Rídl
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Manon Poignet
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Francisco J Ruiz-Ruano
- School of Biological Sciences, University of East Anglia, Norwich, UK
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
- Institute of Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121, Bonn, Germany
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, 53113, Bonn, Germany
| | - Jiří Reif
- Institute for Environmental Studies, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Zoology, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Petr Pajer
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01, Prague 6, San Antonio, Czech Republic
| | - Jan Pačes
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Tomáš Albrecht
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich, UK
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, 53113, Bonn, Germany
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.
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Mueller JC, Schlebusch SA, Pei Y, Poignet M, Vontzou N, Ruiz-Ruano FJ, Albrecht T, Reifová R, Forstmeier W, Suh A, Kempenaers B. Micro germline-restricted chromosome in blue tits: evidence for meiotic functions. Mol Biol Evol 2023; 40:7146701. [PMID: 37116210 PMCID: PMC10172847 DOI: 10.1093/molbev/msad096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 04/30/2023] Open
Abstract
The germline-restricted chromosome (GRC) is likely present in all songbird species, but differs widely in size and gene content. This extra chromosome has been described as either a microchromosome with only limited basic gene content or a macrochromosome with enriched gene functions related to female gonad and embryo development. Here, we assembled, annotated and characterized the first micro-GRC in the blue tit (Cyanistes caeruleus) using high-fidelity long-read sequencing data. Although some genes on the blue tit GRC show signals of pseudogenization, others potentially have important functions, either currently or in the past. We highlight the GRC gene paralog BMP15, which is among the highest expressed GRC genes both in blue tits and in zebra finches (Taeniopygia guttata), and is known to play a role in oocyte and follicular maturation in other vertebrates. The GRC genes of the blue tit are further enriched for functions related to the synaptonemal complex. We found a similar functional enrichment when analyzing published data on GRC genes from two nightingale species (Luscinia spp.). We hypothesize that these genes play a role in maintaining standard maternal inheritance or in recombining maternal and paternal GRCs during potential episodes of biparental inheritance.
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Affiliation(s)
- Jakob C Mueller
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | | | - Yifan Pei
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | - Manon Poignet
- Department of Zoology, Charles University, Prague, Czech Republic
| | - Niki Vontzou
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
| | - Francisco J Ruiz-Ruano
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Tomáš Albrecht
- Department of Zoology, Charles University, Prague, Czech Republic
- Institute of Vertebrate Biology, Academy of Sciences, Czech Republic
| | - Radka Reifová
- Department of Zoology, Charles University, Prague, Czech Republic
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Science for Life Laboratory, Uppsala, Sweden
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
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Utsunomia R, Vaio M, Ruiz-Ruano FJ. Editorial: Cytogenomics: Structural Organization and Evolution of Genomes. Front Genet 2022; 13:938513. [PMID: 35754797 PMCID: PMC9224753 DOI: 10.3389/fgene.2022.938513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ricardo Utsunomia
- Department of Genetics, Institute of Biological Sciences and Health, Federal Rural University of Rio de Janeiro, Seropédica, Brazil.,Faculty of Sciences, São Paulo State University, Bauru, Brazil
| | - Magdalena Vaio
- Department of Plant Biology, Faculty of Agronomy, University of the Republic, Montevideo, Uruguay
| | - Francisco J Ruiz-Ruano
- Department of Organismal Biology-Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,School of Biological Sciences, Norwich Research Park University of East Anglia, Norwich, United Kingdom
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Borodin P, Chen A, Forstmeier W, Fouché S, Malinovskaya L, Pei Y, Reifová R, Ruiz-Ruano FJ, Schlebusch SA, Sotelo-Muñoz M, Torgasheva A, Vontzou N, Suh A. Mendelian nightmares: the germline-restricted chromosome of songbirds. Chromosome Res 2022; 30:255-272. [PMID: 35416568 PMCID: PMC9508068 DOI: 10.1007/s10577-022-09688-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/07/2022] [Accepted: 03/16/2022] [Indexed: 11/03/2022]
Abstract
Germline-restricted chromosomes (GRCs) are accessory chromosomes that occur only in germ cells. They are eliminated from somatic cells through programmed DNA elimination during embryo development. GRCs have been observed in several unrelated animal taxa and show peculiar modes of non-Mendelian inheritance and within-individual elimination. Recent cytogenetic and phylogenomic evidence suggests that a GRC is present across the species-rich songbirds, but absent in non-passerine birds, implying that over half of all 10,500 bird species have extensive germline/soma genome differences. Here, we review recent insights gained from genomic, transcriptomic, and cytogenetic approaches with regard to the genetic content, phylogenetic distribution, and inheritance of the songbird GRC. While many questions remain unsolved in terms of GRC inheritance, elimination, and function, we discuss plausible scenarios and future directions for understanding this widespread form of programmed DNA elimination.
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Affiliation(s)
- Pavel Borodin
- Siberian Department, Russian Academy of Sciences, Institute of Cytology and Genetics, Prospekt Akademika Lavrent'yeva 10, 630090, Novosibirsk, Russia
| | - Augustin Chen
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, Science for Life Laboratory, 752 36, Uppsala, Sweden
| | - Wolfgang Forstmeier
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Eberhard-Gwinner-Straße, 82319, Seewiesen, Germany.
| | - Simone Fouché
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, Science for Life Laboratory, 752 36, Uppsala, Sweden.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
| | - Lyubov Malinovskaya
- Siberian Department, Russian Academy of Sciences, Institute of Cytology and Genetics, Prospekt Akademika Lavrent'yeva 10, 630090, Novosibirsk, Russia
| | - Yifan Pei
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Eberhard-Gwinner-Straße, 82319, Seewiesen, Germany
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic.
| | - Francisco J Ruiz-Ruano
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, Science for Life Laboratory, 752 36, Uppsala, Sweden.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
| | - Stephen A Schlebusch
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Manuelita Sotelo-Muñoz
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Anna Torgasheva
- Siberian Department, Russian Academy of Sciences, Institute of Cytology and Genetics, Prospekt Akademika Lavrent'yeva 10, 630090, Novosibirsk, Russia.
| | - Niki Vontzou
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
| | - Alexander Suh
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, Science for Life Laboratory, 752 36, Uppsala, Sweden. .,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK.
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Camacho JPM, Cabrero J, López-León MD, Martín-Peciña M, Perfectti F, Garrido-Ramos MA, Ruiz-Ruano FJ. Author Correction: Satellitome comparison of two oedipodine grasshoppers highlights the contingent nature of satellite DNA evolution. BMC Biol 2022; 20:69. [PMID: 35317788 PMCID: PMC8941793 DOI: 10.1186/s12915-022-01260-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
| | - Josefa Cabrero
- Departamento de Genética, Universidad de Granada, 18071, Granada, Spain
| | | | | | - Francisco Perfectti
- Departamento de Genética, Universidad de Granada, 18071, Granada, Spain.,Research Unit Modeling Nature, Universidad de Granada, Granada, Spain
| | | | - Francisco J Ruiz-Ruano
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden. .,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK.
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Camacho JPM, Cabrero J, López-León MD, Martín-Peciña M, Perfectti F, Garrido-Ramos MA, Ruiz-Ruano FJ. Satellitome comparison of two oedipodine grasshoppers highlights the contingent nature of satellite DNA evolution. BMC Biol 2022; 20:36. [PMID: 35130900 PMCID: PMC8822648 DOI: 10.1186/s12915-021-01216-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/16/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The full catalog of satellite DNA (satDNA) within a same genome constitutes the satellitome. The Library Hypothesis predicts that satDNA in relative species reflects that in their common ancestor, but the evolutionary mechanisms and pathways of satDNA evolution have never been analyzed for full satellitomes. We compare here the satellitomes of two Oedipodine grasshoppers (Locusta migratoria and Oedaleus decorus) which shared their most recent common ancestor about 22.8 Ma ago. RESULTS We found that about one third of their satDNA families (near 60 in every species) showed sequence homology and were grouped into 12 orthologous superfamilies. The turnover rate of consensus sequences was extremely variable among the 20 orthologous family pairs analyzed in both species. The satDNAs shared by both species showed poor association with sequence signatures and motives frequently argued as functional, except for short inverted repeats allowing short dyad symmetries and non-B DNA conformations. Orthologous satDNAs frequently showed different FISH patterns at both intra- and interspecific levels. We defined indices of homogenization and degeneration and quantified the level of incomplete library sorting between species. CONCLUSIONS Our analyses revealed that satDNA degenerates through point mutation and homogenizes through partial turnovers caused by massive tandem duplications (the so-called satDNA amplification). Remarkably, satDNA amplification increases homogenization, at intragenomic level, and diversification between species, thus constituting the basis for concerted evolution. We suggest a model of satDNA evolution by means of recursive cycles of amplification and degeneration, leading to mostly contingent evolutionary pathways where concerted evolution emerges promptly after lineages split.
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Affiliation(s)
| | - Josefa Cabrero
- Departamento de Genética, Universidad de Granada, 18071, Granada, Spain
| | | | | | - Francisco Perfectti
- Departamento de Genética, Universidad de Granada, 18071, Granada, Spain.,Research Unit Modeling Nature, Universidad de Granada, Granada, Spain
| | | | - Francisco J Ruiz-Ruano
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden. .,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK.
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9
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Pei Y, Forstmeier W, Ruiz-Ruano FJ, Mueller JC, Cabrero J, Camacho JPM, Alché JD, Franke A, Hoeppner M, Börno S, Gessara I, Hertel M, Teltscher K, Knief U, Suh A, Kempenaers B. Occasional paternal inheritance of the germline-restricted chromosome in songbirds. Proc Natl Acad Sci U S A 2022; 119:e2103960119. [PMID: 35058355 PMCID: PMC8794876 DOI: 10.1073/pnas.2103960119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 11/06/2021] [Indexed: 11/29/2022] Open
Abstract
Songbirds have one special accessory chromosome, the so-called germline-restricted chromosome (GRC), which is only present in germline cells and absent from all somatic tissues. Earlier work on the zebra finch (Taeniopygia guttata castanotis) showed that the GRC is inherited only through the female line-like the mitochondria-and is eliminated from the sperm during spermatogenesis. Here, we show that the GRC has the potential to be paternally inherited. Confocal microscopy using GRC-specific fluorescent in situ hybridization probes indicated that a considerable fraction of sperm heads (1 to 19%) in zebra finch ejaculates still contained the GRC. In line with these cytogenetic data, sequencing of ejaculates revealed that individual males from two families differed strongly and consistently in the number of GRCs in their ejaculates. Examining a captive-bred male hybrid of the two zebra finch subspecies (T. g. guttata and T. g. castanotis) revealed that the mitochondria originated from a castanotis mother, whereas the GRC came from a guttata father. Moreover, analyzing GRC haplotypes across nine castanotis matrilines, estimated to have diverged for up to 250,000 y, showed surprisingly little variability among GRCs. This suggests that a single GRC haplotype has spread relatively recently across all examined matrilines. A few diagnostic GRC mutations that arose since this inferred spreading suggest that the GRC has continued to jump across matriline boundaries. Our findings raise the possibility that certain GRC haplotypes could selfishly spread through the population via occasional paternal transmission, thereby outcompeting other GRC haplotypes that were limited to strict maternal inheritance, even if this was partly detrimental to organismal fitness.
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Affiliation(s)
- Yifan Pei
- Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology 82319 Seewiesen, Germany;
| | - Wolfgang Forstmeier
- Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology 82319 Seewiesen, Germany;
| | - Francisco J Ruiz-Ruano
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TU, United Kingdom;
- Department of Organismal Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University SE-752 36 Uppsala, Sweden
| | - Jakob C Mueller
- Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology 82319 Seewiesen, Germany
| | - Josefa Cabrero
- Department of Genetics, University of Granada E-18071 Granada, Spain
| | | | - Juan D Alché
- Department of Biochemistry, Cell and Molecular Biology of Plants, Estación Experimental del Zaidín, Spanish National Research Council E-18008 Granada, Spain
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel 24118 Kiel, Germany
| | - Marc Hoeppner
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel 24118 Kiel, Germany
| | - Stefan Börno
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics 14195 Berlin, Germany
| | - Ivana Gessara
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology 82319 Seewiesen, Germany
| | - Moritz Hertel
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology 82319 Seewiesen, Germany
| | - Kim Teltscher
- Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology 82319 Seewiesen, Germany
| | - Ulrich Knief
- Division of Evolutionary Biology, Faculty of Biology, Ludwig Maximilian University of Munich D-82152 Planegg-Martinsried, Germany
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TU, United Kingdom;
- Department of Organismal Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University SE-752 36 Uppsala, Sweden
| | - Bart Kempenaers
- Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology 82319 Seewiesen, Germany
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Affiliation(s)
| | - Francisco J. Ruiz-Ruano
- Department of Organismal Biology – Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- School of Biological Sciences, Norwich Research Park University of East Anglia, Norwich, UK
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11
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Milani D, Ruiz-Ruano FJ, Camacho JPM, Cabral-de-Mello DC. Out of patterns, the euchromatic B chromosome of the grasshopper Abracris flavolineata is not enriched in high-copy repeats. Heredity (Edinb) 2021; 127:475-483. [PMID: 34482369 PMCID: PMC8551250 DOI: 10.1038/s41437-021-00470-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 02/07/2023] Open
Abstract
In addition to the normal set of standard (A) chromosomes, some eukaryote species harbor supernumerary (B) chromosomes. In most cases, B chromosomes show differential condensation with respect to A chromosomes and display dark C-bands of heterochromatin, and some of them are highly enriched in repetitive DNA. Here we perform a comprehensive NGS (next-generation sequencing) analysis of the repeatome in the grasshopper Abracris flavolineata aimed at uncovering the molecular composition and origin of its B chromosome. Our results have revealed that this B chromosome shows a DNA repeat content highly similar to the DNA repeat content observed for euchromatic (non-C-banded) regions of A chromosomes. Moreover, this B chromosome shows little enrichment for high-copy repeats, with only a few elements showing overabundance in B-carrying individuals compared to the 0B individuals. Consequently, the few satellite DNAs (satDNAs) mapping on the B chromosome were mostly restricted to its centromeric and telomeric regions, and they displayed much smaller bands than those observed on the A chromosomes. Our data support the intraspecific origin of the B chromosome from the longest autosome by misdivision, isochromosome formation, and additional restructuring, with accumulation of specific repeats in one or both B chromosome arms, yielding a submetacentric B. Finally, the absence of B-specific satDNAs, which are frequent in other species, along with its euchromatic nature, suggest that this B chromosome arose recently and might still be starting a heterochromatinization process. On this basis, it could be a good model to investigate the initial steps of B chromosome evolution.
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Affiliation(s)
- Diogo Milani
- Departamento de Biologia Geral e Aplicada, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo, Brazil
| | - Francisco J Ruiz-Ruano
- Evolutionary Biology Centre, Department of Organismal Biology - Systematic Biology, Uppsala University, Uppsala, Sweden
- Norwich Research Park, School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Juan Pedro M Camacho
- Departamento de Genética, Facultad de Ciencias, UGR - Univ de Granada, Granada, Spain
| | - Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo, Brazil.
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12
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Ruiz-Ruano FJ, Navarro-Domínguez B, Camacho JPM, Garrido-Ramos MA. Transposable element landscapes illuminate past evolutionary events in the endangered fern Vandenboschia speciosa. Genome 2021; 65:95-103. [PMID: 34555288 DOI: 10.1139/gen-2021-0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Vandenboschia speciosa is an endangered tetraploid fern species with a large genome (10.5 Gb). Its geographical distribution is characterized by disjoined tertiary flora refuges, with relict populations that survived past climate crises. Here, we analyzed the transposable elements (TEs) and found that they comprise approximately 76% of the V. speciosa genome, thus being the most abundant type of DNA sequence in this gigantic genome. The V. speciosa genome is composed of 51% and 5.6% of Class I and Class II elements, respectively. LTR retrotransposons were the most abundant TEs in this species (at least 42% of the genome), followed by non-LTR retrotransposons, which constituted at least 8.7% of the genome of this species. We introduce an additional analysis to identify the nature of non-annotated elements (19% of the genome). A BLAST search of the non-annotated contigs against the V. speciosa TE database allowed for the identification of almost half of them, which were most likely diverged sequence variants of the annotated TEs. In general, the TE composition in V. speciosa resembles the TE composition in seed plants. In addition, repeat landscapes revealed three episodes of amplification for all TEs, most likely due to demographic changes associated with past climate crises.
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Affiliation(s)
- Francisco J Ruiz-Ruano
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain.,Department of Organismal Biology, Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Beatriz Navarro-Domínguez
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain.,Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Juan Pedro M Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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13
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Silva DMZDA, Ruiz-Ruano FJ, Utsunomia R, Martín-Peciña M, Castro JP, Freire PP, Carvalho RF, Hashimoto DT, Suh A, Oliveira C, Porto-Foresti F, Artoni RF, Foresti F, Camacho JPM. Long-term persistence of supernumerary B chromosomes in multiple species of Astyanax fish. BMC Biol 2021; 19:52. [PMID: 33740955 PMCID: PMC7976721 DOI: 10.1186/s12915-021-00991-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/24/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Eukaryote genomes frequently harbor supernumerary B chromosomes in addition to the "standard" A chromosome set. B chromosomes are thought to arise as byproducts of genome rearrangements and have mostly been considered intraspecific oddities. However, their evolutionary transcendence beyond species level has remained untested. RESULTS Here we reveal that the large metacentric B chromosomes reported in several fish species of the genus Astyanax arose in a common ancestor at least 4 million years ago. We generated transcriptomes of A. scabripinnis and A. paranae 0B and 1B individuals and used these assemblies as a reference for mapping all gDNA and RNA libraries to quantify coverage differences between B-lacking and B-carrying genomes. We show that the B chromosomes of A. scabripinnis and A. paranae share 19 protein-coding genes, of which 14 and 11 were also present in the B chromosomes of A. bockmanni and A. fasciatus, respectively. Our search for B-specific single-nucleotide polymorphisms (SNPs) identified the presence of B-derived transcripts in B-carrying ovaries, 80% of which belonged to nobox, a gene involved in oogenesis regulation. Importantly, the B chromosome nobox paralog is expressed > 30× more than the A chromosome paralog. This indicates that the normal regulation of this gene is altered in B-carrying females, which could potentially facilitate B inheritance at higher rates than Mendelian law prediction. CONCLUSIONS Taken together, our results demonstrate the long-term survival of B chromosomes despite their lack of regular pairing and segregation during meiosis and that they can endure episodes of population divergence leading to species formation.
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Affiliation(s)
- Duílio Mazzoni Zerbinato de Andrade Silva
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
| | - Francisco J Ruiz-Ruano
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden.
- Departamento de Genética, Universidad de Granada, 18071, Granada, Spain.
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK.
| | - Ricardo Utsunomia
- Departamento de Genética, Instituto de Ciências Biológicas e da Saúde, ICBS, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23897-000, Brazil
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, UNESP, Campus de Bauru, Bauru, SP, 17033-360, Brazil
| | | | - Jonathan Pena Castro
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, UFSCAR, São Carlos, SP, 13565-905, Brazil
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, UEPG, Ponta Grossa, PR, 84030-900, Brazil
| | - Paula Paccielli Freire
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
- Departamento de Imunologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, USP, São Paulo, SP, 05508-900, Brazil
| | - Robson Francisco Carvalho
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
| | - Diogo T Hashimoto
- Centro de Aquicultura, Universidade Estadual Paulista, UNESP, Campus Jaboticabal, Jaboticabal, SP, 14884-900, Brazil
| | - Alexander Suh
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Uppsala, Sweden
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, UK
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
| | - Fábio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, UNESP, Campus de Bauru, Bauru, SP, 17033-360, Brazil
| | - Roberto Ferreira Artoni
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, UFSCAR, São Carlos, SP, 13565-905, Brazil
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, UEPG, Ponta Grossa, PR, 84030-900, Brazil
| | - Fausto Foresti
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
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14
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dos Santos RZ, Calegari RM, Silva DMZDA, Ruiz-Ruano FJ, Melo S, Oliveira C, Foresti F, Uliano-Silva M, Porto-Foresti F, Utsunomia R. A Long-Term Conserved Satellite DNA That Remains Unexpanded in Several Genomes of Characiformes Fish Is Actively Transcribed. Genome Biol Evol 2021; 13:evab002. [PMID: 33502491 PMCID: PMC8210747 DOI: 10.1093/gbe/evab002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2021] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic genomes contain large amounts of repetitive DNA sequences, such as tandemly repeated satellite DNAs (satDNAs). These sequences are highly dynamic and tend to be genus- or species-specific due to their particular evolutionary pathways, although there are few unusual cases of conserved satDNAs over long periods of time. Here, we used multiple approaches to reveal that an satDNA named CharSat01-52 originated in the last common ancestor of Characoidei fish, a superfamily within the Characiformes order, ∼140-78 Ma, whereas its nucleotide composition has remained considerably conserved in several taxa. We show that 14 distantly related species within Characoidei share the presence of this satDNA, which is highly amplified and clustered in subtelomeric regions in a single species (Characidium gomesi), while remained organized as small clusters in all the other species. Defying predictions of the molecular drive of satellite evolution, CharSat01-52 shows similar values of intra- and interspecific divergence. Although we did not provide evidence for a specific functional role of CharSat01-52, its transcriptional activity was demonstrated in different species. In addition, we identified short tandem arrays of CharSat01-52 embedded within single-molecule real-time long reads of Astyanax paranae (536 bp-3.1 kb) and A. mexicanus (501 bp-3.9 kb). Such arrays consisted of head-to-tail repeats and could be found interspersed with other sequences, inverted sequences, or neighbored by other satellites. Our results provide a detailed characterization of an old and conserved satDNA, challenging general predictions of satDNA evolution.
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Affiliation(s)
- Rodrigo Zeni dos Santos
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
| | - Rodrigo Milan Calegari
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
| | | | - Francisco J Ruiz-Ruano
- Department of Organismal Biology—Systematic Biology, Evolutionary Biology
Centre, Uppsala University, Uppsala, Sweden
| | - Silvana Melo
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de
Botucatu, Universidade Estadual Paulista, UNESP, Botucatu, Sao Paulo,
Brazil
| | - Claudio Oliveira
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de
Botucatu, Universidade Estadual Paulista, UNESP, Botucatu, Sao Paulo,
Brazil
| | - Fausto Foresti
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências de
Botucatu, Universidade Estadual Paulista, UNESP, Botucatu, Sao Paulo,
Brazil
| | | | - Fábio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
| | - Ricardo Utsunomia
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade
Estadual Paulista, UNESP, Campus de Bauru, Bauru, Sao Paulo, Brazil
- Departamento de Genética, Instituto de Ciências Biológicas e da Saúde, ICBS,
Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janerio,
Brazil
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15
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Ferretti ABSM, Milani D, Palacios-Gimenez OM, Ruiz-Ruano FJ, Cabral-de-Mello DC. High dynamism for neo-sex chromosomes: satellite DNAs reveal complex evolution in a grasshopper. Heredity (Edinb) 2020; 125:124-137. [PMID: 32499661 PMCID: PMC7426270 DOI: 10.1038/s41437-020-0327-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/24/2020] [Accepted: 05/25/2020] [Indexed: 12/18/2022] Open
Abstract
A common characteristic of sex chromosomes is the accumulation of repetitive DNA, which accounts for their diversification and degeneration. In grasshoppers, the X0 sex-determining system in males is considered ancestral. However, in some species, derived variants like neo-XY in males evolved several times independently by Robertsonian translocation. This is the case of Ronderosia bergii, in which further large pericentromeric inversion in the neo-Y also took place, making this species particularly interesting for investigating sex chromosome evolution. Here, we characterized the satellite DNAs (satDNAs) and transposable elements (TEs) of the species to investigate the quantitative differences in repeat composition between male and female genomes putatively associated with sex chromosomes. We found a total of 53 satDNA families and 56 families of TEs. The satDNAs were 13.5% more abundant in males than in females, while TEs were just 1.02% more abundant in females. These results imply differential amplification of satDNAs on neo-Y chromosome and a minor role of TEs in sex chromosome differentiation. We showed highly differentiated neo-XY sex chromosomes owing to major amplification of satDNAs in neo-Y. Furthermore, chromosomal mapping of satDNAs suggests high turnover of neo-sex chromosomes in R. bergii at the intrapopulation level, caused by multiple paracentric inversions, amplifications, and transpositions. Finally, the species is an example of the action of repetitive DNAs in the generation of variability for sex chromosomes after the suppression of recombination, and helps understand sex chromosome evolution at the intrapopulation level.
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Affiliation(s)
- Ana B S M Ferretti
- Departamento de Biologia Geral e Aplicada, UNESP-Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo, Brazil
| | - Diogo Milani
- Departamento de Biologia Geral e Aplicada, UNESP-Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo, Brazil
| | - Octavio M Palacios-Gimenez
- Department of Organismal Biology, Uppsala University, Evolutionary Biology Centre, Uppsala, Sweden
- Department of Ecology and Genetics, Uppsala University, Evolutionary Biology Centre, Uppsala, Sweden
| | - Francisco J Ruiz-Ruano
- Department of Organismal Biology, Uppsala University, Evolutionary Biology Centre, Uppsala, Sweden
- Department of Ecology and Genetics, Uppsala University, Evolutionary Biology Centre, Uppsala, Sweden
| | - Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, UNESP-Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo, Brazil.
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16
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Palacios-Gimenez OM, Milani D, Song H, Marti DA, López-León MD, Ruiz-Ruano FJ, Camacho JPM, Cabral-de-Mello DC. Eight Million Years of Satellite DNA Evolution in Grasshoppers of the Genus Schistocerca Illuminate the Ins and Outs of the Library Hypothesis. Genome Biol Evol 2020; 12:88-102. [PMID: 32211863 PMCID: PMC7093836 DOI: 10.1093/gbe/evaa018] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2020] [Indexed: 12/21/2022] Open
Abstract
Satellite DNA (satDNA) is an abundant class of tandemly repeated noncoding sequences, showing high rate of change in sequence, abundance, and physical location. However, the mechanisms promoting these changes are still controversial. The library model was put forward to explain the conservation of some satDNAs for long periods, predicting that related species share a common collection of satDNAs, which mostly experience quantitative changes. Here, we tested the library model by analyzing three satDNAs in ten species of Schistocerca grasshoppers. This group represents a valuable material because it diversified during the last 7.9 Myr across the American continent from the African desert locust (Schistocerca gregaria), and this thus illuminates the direction of evolutionary changes. By combining bioinformatic and cytogenetic, we tested whether these three satDNA families found in S. gregaria are also present in nine American species, and whether differential gains and/or losses have occurred in the lineages. We found that the three satDNAs are present in all species but display remarkable interspecies differences in their abundance and sequences while being highly consistent with genus phylogeny. The number of chromosomal loci where satDNA is present was also consistent with phylogeny for two satDNA families but not for the other. Our results suggest eminently chance events for satDNA evolution. Several evolutionary trends clearly imply either massive amplifications or contractions, thus closely fitting the library model prediction that changes are mostly quantitative. Finally, we found that satDNA amplifications or contractions may influence the evolution of monomer consensus sequences and by chance playing a major role in driftlike dynamics.
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Affiliation(s)
- Octavio M Palacios-Gimenez
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Sweden
- Department of Organismal Biology, Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Diogo Milani
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Univ Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Hojun Song
- Department of Entomology, Texas A&M University
| | - Dardo A Marti
- Laboratorio de Genética Evolutiva, IBS, Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, CONICET, Posadas, Argentina
| | - Maria D López-León
- Departamento de Genética, Facultad de Ciencias, UGR - Univ de Granada, Spain
| | - Francisco J Ruiz-Ruano
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Sweden
- Department of Organismal Biology, Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | | | - Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências/IB, UNESP - Univ Estadual Paulista, Rio Claro, São Paulo, Brazil
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17
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Kinsella CM, Ruiz-Ruano FJ, Dion-Côté AM, Charles AJ, Gossmann TI, Cabrero J, Kappei D, Hemmings N, Simons MJP, Camacho JPM, Forstmeier W, Suh A. Programmed DNA elimination of germline development genes in songbirds. Nat Commun 2019; 10:5468. [PMID: 31784533 PMCID: PMC6884545 DOI: 10.1038/s41467-019-13427-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 11/08/2019] [Indexed: 02/08/2023] Open
Abstract
In some eukaryotes, germline and somatic genomes differ dramatically in their composition. Here we characterise a major germline–soma dissimilarity caused by a germline-restricted chromosome (GRC) in songbirds. We show that the zebra finch GRC contains >115 genes paralogous to single-copy genes on 18 autosomes and the Z chromosome, and is enriched in genes involved in female gonad development. Many genes are likely functional, evidenced by expression in testes and ovaries at the RNA and protein level. Using comparative genomics, we show that genes have been added to the GRC over millions of years of evolution, with embryonic development genes bicc1 and trim71 dating to the ancestor of songbirds and dozens of other genes added very recently. The somatic elimination of this evolutionarily dynamic chromosome in songbirds implies a unique mechanism to minimise genetic conflict between germline and soma, relevant to antagonistic pleiotropy, an evolutionary process underlying ageing and sexual traits. Songbirds have extensive germline–soma genome differences due to developmental elimination of a germline-specific chromosome (GRC). Here, the authors show that the GRC contains dozens of expressed developmental genes, some of which have been on the GRC since the ancestor of all songbirds.
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Affiliation(s)
- Cormac M Kinsella
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, SE-752 36, Uppsala, Sweden.,Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Francisco J Ruiz-Ruano
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, SE-752 36, Uppsala, Sweden. .,Department of Genetics, University of Granada, E-18071, Granada, Spain. .,Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, SE-752 36, Uppsala, Sweden.
| | - Anne-Marie Dion-Côté
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, SE-752 36, Uppsala, Sweden.,Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, 14853, USA.,Département de Biologie, Université de Moncton, Moncton, NB, E1A 3E9, Canada
| | - Alexander J Charles
- Department of Animal and Plant Sciences, University of Sheffield, S10 2TN, Sheffield, UK
| | - Toni I Gossmann
- Department of Animal and Plant Sciences, University of Sheffield, S10 2TN, Sheffield, UK.,Department of Animal Behaviour, Bielefeld University, D-33501, Bielefeld, Germany
| | - Josefa Cabrero
- Department of Genetics, University of Granada, E-18071, Granada, Spain
| | - Dennis Kappei
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117596, Singapore, Singapore
| | - Nicola Hemmings
- Department of Animal and Plant Sciences, University of Sheffield, S10 2TN, Sheffield, UK
| | - Mirre J P Simons
- Department of Animal and Plant Sciences, University of Sheffield, S10 2TN, Sheffield, UK
| | | | | | - Alexander Suh
- Department of Ecology and Genetics - Evolutionary Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, SE-752 36, Uppsala, Sweden. .,Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, SE-752 36, Uppsala, Sweden.
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18
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Castro JP, Hattori RS, Yoshinaga TT, Silva DMZDA, Ruiz-Ruano FJ, Foresti F, Santos MH, de Almeida MC, Moreira-Filho O, Artoni RF. Differential Expression of Genes Related to Sexual Determination Can Modify the Reproductive Cycle of Astyanax scabripinnis (Characiformes: Characidae) in B Chromosome Carrier Individuals. Genes (Basel) 2019; 10:E909. [PMID: 31717315 PMCID: PMC6896079 DOI: 10.3390/genes10110909] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/01/2019] [Accepted: 11/04/2019] [Indexed: 01/09/2023] Open
Abstract
The species complex Astyanax scabripinnis is one of the most studied with respect to origin, distribution, and frequency of B chromosomes, and is considered a model organism for evolutionary studies. Research using population inferences about the occurrence and frequency of the B chromosome shows seasonal variation between sexes, which is associated with the presence of this supernumerary element. We hypothesized that the B chromosome could influence the sex ratio of these animals. Based on this assumption, the present work aimed to investigate if differences exist among levels of gene expression with qRT-PCR of the amh (associated with testicular differentiation) and foxl2a (associated with ovarian differentiation) genes between B-carrier and non-B-carrier individuals. The results showed that for the amh gene, the difference in expression between animals with B chromosomes was not accentuated compared to that in animals without this chromosome. Expression of foxl2a in B-carrier females, however, was reduced by 73.56% compared to females that lacked the B chromosome. Males had no difference in expression of the amh and foxl2a genes between carriers and non-carriers of the B chromosome. Results indicate that the presence of B chromosomes is correlated with the differential expression of sex-associated genes. An analysis of these results integrated with data from other studies on the reproductive cycle in the same species reveals that this difference in expression may be expanding the reproductive cycle of the species.
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Affiliation(s)
- Jonathan Pena Castro
- Departamento de Genética e Evolução, Programa de Pós-Graduação em Biologia Evolutiva e Genética Molecular, Universidade Federal de São Carlos, Rodovia Washington Luis, Km 235, Monjolinho, São Carlos, SP 13565-905, Brazil; (O.M.-F.); (R.F.A.)
| | - Ricardo Shohei Hattori
- Estação Experimental de Salmonicultura de Campos do Jordão, UPD-CJ (APTA/SAA), Campos do Jordão, São Paulo, SP 12460-000, Brazil;
| | - Túlio Teruo Yoshinaga
- Faculdade de Medicina Veterinária e Zootecnia da Universidade de São Paulo, Departamento de Cirurgia, Universidade de São Paulo, Butantã, Rua Professor Orlando Marque Paiva, São Paulo, SP 05508-270, Brazil;
| | - Duílio Mazzoni Zerbinato de Andrade Silva
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP 18618-970, Brazil; (D.M.Z.d.A.S.); (F.F.)
| | - Francisco J. Ruiz-Ruano
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden;
| | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP 18618-970, Brazil; (D.M.Z.d.A.S.); (F.F.)
| | - Mateus Henrique Santos
- Departamento de Biologia Estrutural, Molecular e Genética, Programa de Pós-Graduação em Biologia Evolutiva, Universidade Estadual de Ponta Grossa, Avenida Carlos Cavalcanti, 4748, Ponta Grossa, PR 84030-900, Brazil; (M.H.S.); (M.C.d.A.)
| | - Mara Cristina de Almeida
- Departamento de Biologia Estrutural, Molecular e Genética, Programa de Pós-Graduação em Biologia Evolutiva, Universidade Estadual de Ponta Grossa, Avenida Carlos Cavalcanti, 4748, Ponta Grossa, PR 84030-900, Brazil; (M.H.S.); (M.C.d.A.)
| | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Programa de Pós-Graduação em Biologia Evolutiva e Genética Molecular, Universidade Federal de São Carlos, Rodovia Washington Luis, Km 235, Monjolinho, São Carlos, SP 13565-905, Brazil; (O.M.-F.); (R.F.A.)
| | - Roberto Ferreira Artoni
- Departamento de Genética e Evolução, Programa de Pós-Graduação em Biologia Evolutiva e Genética Molecular, Universidade Federal de São Carlos, Rodovia Washington Luis, Km 235, Monjolinho, São Carlos, SP 13565-905, Brazil; (O.M.-F.); (R.F.A.)
- Departamento de Biologia Estrutural, Molecular e Genética, Programa de Pós-Graduação em Biologia Evolutiva, Universidade Estadual de Ponta Grossa, Avenida Carlos Cavalcanti, 4748, Ponta Grossa, PR 84030-900, Brazil; (M.H.S.); (M.C.d.A.)
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19
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Serrano-Freitas ÉA, Silva DMZA, Ruiz-Ruano FJ, Utsunomia R, Araya-Jaime C, Oliveira C, Camacho JPM, Foresti F. Satellite DNA content of B chromosomes in the characid fish Characidium gomesi supports their origin from sex chromosomes. Mol Genet Genomics 2019; 295:195-207. [PMID: 31624915 DOI: 10.1007/s00438-019-01615-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 10/01/2019] [Indexed: 12/28/2022]
Abstract
The origin of supernumerary (B) chromosomes is clearly conditioned by their ancestry from the standard (A) chromosomes. Sequence similarity between A and B chromosomes is thus crucial to determine B chromosome origin. For this purpose, we compare here the DNA sequences from A and B chromosomes in the characid fish Characidium gomesi using two main approaches. First, we found 59 satellite DNA (satDNA) families constituting the satellitome of this species and performed FISH analysis for 18 of them. This showed the presence of six satDNAs on the B chromosome: one shared with sex chromosomes and autosomes, two shared with sex chromosomes, one shared with autosomes and two being B-specific. This indicated that B chromosomes most likely arose from the sex chromosomes. Our second approach consisted of the analysis of five repetitive DNA families: 18S and 5S ribosomal DNA (rDNA), the H3 histone gene, U2 snDNA and the most abundant satDNA (CgoSat01-184) on DNA obtained from microdissected B chromosomes and from B-lacking genomes. PCR and sequence analysis of these repetitive sequences was successful for three of them (5S rDNA, H3 histone gene and CgoSat01-184), and sequence comparison revealed that DNA sequences obtained from the B chromosomes displayed higher identity with C. gomesi genomic DNA than with those obtained from other Characidium species. Taken together, our results support the intraspecific origin of B chromosomes in C. gomesi and point to sex chromosomes as B chromosome ancestors, which raises interesting prospects for future joint research on the genetic content of sex and B chromosomes in this species.
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Affiliation(s)
- Érica A Serrano-Freitas
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil.,Centro de Ciências Biológicas e da Saúde, Fundação Educacional de Penápolis, Funepe, Penápolis, SP, 16303-180, Brazil
| | - Duílio M Z A Silva
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil.
| | - Francisco J Ruiz-Ruano
- Departamento de Genética, Universidad de Granada, 18071, Granada, Spain.,Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, 75236, Uppsala, Sweden
| | - Ricardo Utsunomia
- Departamento de Genética, Instituto de Ciências Biológicas e da Saúde, ICBS, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ, 23897-000, Brazil
| | - Cristian Araya-Jaime
- Instituto de Investigación Multidisciplinar en Ciencia y Tecnología, Universidad de La Serena, 1720256, La Serena, Chile.,Laboratorio de Genética y Citogenética Vegetal, Departamento de Biología, Universidad de La Serena, 1720256, La Serena, Chile
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
| | | | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESP, Distrito de Rubião Junior, Botucatu, SP, 18618-970, Brazil
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Nobile AB, Freitas-Souza D, Ruiz-Ruano FJ, Nobile MLMO, Costa GO, de Lima FP, Camacho JPM, Foresti F, Oliveira C. DNA metabarcoding of Neotropical ichthyoplankton: Enabling high accuracy with lower cost. MBMG 2019. [DOI: 10.3897/mbmg.3.35060] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Knowledge of ichthyoplankton dynamics is extremely important for conservation management as it can provide information about preferential spawning sites, reproductive period, migratory routes and recruitment success, which can be used to guide management and conservation efforts. However, identification of the eggs and larvae of Neotropical freshwater fish is a difficult task. DNA barcodes have emerged as an alternative and highly accurate approach for species identification, but DNA barcoding can be time-consuming and costly. To solve this problem, we aimed to develop a simple protocol based on DNA metabarcoding, to investigate whether it is possible to detect and quantify all species present in a pool of organisms. To do this, 230 larvae were cut in half, one half was sequenced by the Sanger technique and the other half was used to compose six arrays with a pool of larvae that were sequenced using a next-generation technique (NGS). The results of the Sanger sequencing allowed the identification of almost all larvae at species level, and the results from NGS showed high accuracy in species detection, ranging from 83% to 100%, with an average of 95% in all samples. No false positives were detected. The frequency of organisms in the two methods was positively correlated (Pearson), with low variation among species. In conclusion, this protocol represents a considerable advance in ichthyoplankton studies, allowing a rapid, cost-effective, quali-quantitative approach that improves the accuracy of identification.
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21
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Utsunomia R, Silva DMZDA, Ruiz-Ruano FJ, Goes CAG, Melo S, Ramos LP, Oliveira C, Porto-Foresti F, Foresti F, Hashimoto DT. Satellitome landscape analysis of Megaleporinus macrocephalus (Teleostei, Anostomidae) reveals intense accumulation of satellite sequences on the heteromorphic sex chromosome. Sci Rep 2019; 9:5856. [PMID: 30971780 PMCID: PMC6458115 DOI: 10.1038/s41598-019-42383-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 03/26/2019] [Indexed: 11/09/2022] Open
Abstract
The accumulation of repetitive DNA sequences on the sex-limited W or Y chromosomes is a well-known process that is likely triggered by the suppression of recombination between the sex chromosomes, which leads to major differences in their sizes and genetic content. Here, we report an analysis conducted on the satellitome of Megaleporinus macrocephalus that focuses specifically on the satDNAs that have been shown to have higher abundances in females and are putatively located on the W chromosome in this species. We characterized 164 satellite families in M. macrocephalus, which is, by far, the most satellite-rich species discovered to date. Subsequently, we mapped 30 satellites, 22 of which were located on the W chromosome, and 14 were shown to exist only on the W chromosome. Finally, we report two simple, quick and reliable methods that can be used for sex identification in M. macrocephalus individuals using fin clips or scales, which could be applicable to future studies conducted in the field of aquaculture.
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Affiliation(s)
- Ricardo Utsunomia
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Distrito de Rubião Junior, s/n, 18618-970, Botucatu, SP, Brazil. .,Departamento de Genética, Universidad de Granada, 18071, Granada, Spain.
| | | | | | - Caio Augusto Gomes Goes
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista - UNESP, Campus de Bauru, 17033-360, Bauru, SP, Brazil
| | - Silvana Melo
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Distrito de Rubião Junior, s/n, 18618-970, Botucatu, SP, Brazil
| | - Lucas Peres Ramos
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Distrito de Rubião Junior, s/n, 18618-970, Botucatu, SP, Brazil
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Distrito de Rubião Junior, s/n, 18618-970, Botucatu, SP, Brazil
| | - Fábio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista - UNESP, Campus de Bauru, 17033-360, Bauru, SP, Brazil
| | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista - UNESP, Distrito de Rubião Junior, s/n, 18618-970, Botucatu, SP, Brazil
| | - Diogo Teruo Hashimoto
- CAUNESP, Universidade Estadual Paulista - UNESP, Campus Jaboticabal, 14884-900, Jaboticabal, SP, Brazil
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Ruiz-Ruano FJ, Navarro-Domínguez B, Camacho JPM, Garrido-Ramos MA. Characterization of the satellitome in lower vascular plants: the case of the endangered fern Vandenboschia speciosa. Ann Bot 2019; 123:587-599. [PMID: 30357311 PMCID: PMC6417484 DOI: 10.1093/aob/mcy192] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 10/04/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND AND AIMS Vandenboschia speciosa is a highly vulnerable fern species, with a large genome (10.5 Gb). Haploid gametophytes and diploid sporophytes are perennial, can reproduce vegetatively, and certain populations are composed only of independent gametophytes. These features make this fern a good model: (1) for high-throughput analysis of satellite DNA (satDNA) to investigate possible evolutionary trends in satDNA sequence features; (2) to determine the relative contribution of satDNA and other repetitive DNAs to its large genome; and (3) to analyse whether the reproduction mode or phase alternation between long-lasting haploid and diploid stages influences satDNA abundance or divergence. METHODS We analysed the repetitive fraction of the genome of this species in three different populations (one comprised only of independent gametophytes) using Illumina sequencing and bioinformatic analysis with RepeatExplorer and satMiner. KEY RESULTS The satellitome of V. speciosa is composed of 11 satDNA families, most of them showing a short repeat length and being A + T rich. Some satDNAs had complex repeats composed of sub-repeats, showing high similarity to shorter satDNAs. Three families had particular structural features and highly conserved motifs. SatDNA only amounts to approx. 0.4 % of its genome. Likewise, microsatellites do not represent more than 2 %, but transposable elements (TEs) represent approx. 50 % of the sporophytic genomes. We found high resemblance in satDNA abundance and divergence between both gametophyte and sporophyte samples from the same population and between populations. CONCLUSIONS (1) Longer (and older) satellites in V. speciosa have a higher A + T content and evolve from shorter ones and, in some cases, microsatellites were a source of new satDNAs; (2) the satellitome does not explain the huge genome size in this species while TEs are the major repetitive component of the V. speciosa genome and mostly contribute to its large genome; and (3) reproduction mode or phase alternation between gametophytes and sporophytes does not entail accumulation or divergence of satellites.
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Affiliation(s)
- F J Ruiz-Ruano
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - B Navarro-Domínguez
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - J P M Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - M A Garrido-Ramos
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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23
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Aleix-Mata G, Ruiz-Ruano FJ, PÉrez JM, Sarasa M, SÁnchez A. Complete mitochondrial genome of the Western Capercaillie Tetrao urogallus (Phasianidae, Tetraoninae). Zootaxa 2019; 4550:585-593. [PMID: 30790836 DOI: 10.11646/zootaxa.4550.4.9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Indexed: 11/04/2022]
Abstract
The Western Capercaillie (Tetrao urogallus) is a galliform bird of boreal climax forests from Scandinavia to eastern Siberia, with a fragmented population in southwestern Europe. We extracted the DNA of T. urogallus aquitanicus and obtained the complete mitochondrial genome (mitogenome) sequence by combining Illumina and Sanger sequencing sequence data. The mitochondrial genome of T. urogallus is 16,683 bp long and is very similar to that of Lyrurus tetrix (16,677 bp). The T. urogallus mitogenome contains the normal 13 protein-coding genes (PCGs), 22 transfer RNAs, 2 ribosomal RNAs, and the control region. The number, order, and orientation of the mitochondrial genes are the same as in L. tetrix and in other species of the same and other bird families. The three domains of the control region contained conserved sequences (ETAS; CSBs), boxes (F, E, D, C, B, BS box), the putative origin of replication of the H-strand (OH) and bidirectional promoters of translation (LSP/HSP).
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Affiliation(s)
- GaËl Aleix-Mata
- Department of Animal and Plant Biology and Ecology, Jaén University, Campus Las Lagunillas, E-23071, Jaén, Spain..
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Ruiz-Ruano FJ, Navarro-Domínguez B, Camacho JPM, Garrido-Ramos MA. Full plastome sequence of the fern Vandenboschia speciosa (Hymenophyllales): structural singularities and evolutionary insights. J Plant Res 2019; 132:3-17. [PMID: 30552526 DOI: 10.1007/s10265-018-1077-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/26/2018] [Indexed: 05/14/2023]
Abstract
We provide here the first full chloroplast genome sequence, i.e., the plastome, for a species belonging to the fern order Hymenophyllales. The phylogenetic position of this order within leptosporangiate ferns, together with the general scarcity of information about fern plastomes, places this research as a valuable study on the analysis of the diversity of plastomes throughout fern evolution. Gene content of V. speciosa plastome was similar to that in most ferns, although there were some characteristic gene losses and lineage-specific differences. In addition, an important number of genes required U to C RNA editing for proper protein translation and two genes showed start codons alternative to the canonical AUG (AUA). Concerning gene order, V. speciosa shared the specific 30-kb inversion of euphyllophytes plastomes and the 3.3-kb inversion of fern plastomes, keeping the ancestral gene order shared by eusporangiate and early leptosporangiate ferns. Conversely, V. speciosa has expanded IR regions comprising the rps7, rps12, ndhB and trnL genes in addition to rRNA and other tRNA genes, a condition shared with several eusporangiate ferns, lycophytes and hornworts, as well as most seed plants.
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Affiliation(s)
- F J Ruiz-Ruano
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - B Navarro-Domínguez
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - J P M Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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25
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Martín-Peciña M, Ruiz-Ruano FJ, Camacho JPM, Dodsworth S. Phylogenetic signal of genomic repeat abundances can be distorted by random homoplasy: a case study from hominid primates. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly077] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- María Martín-Peciña
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | | | - Juan Pedro M Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Steven Dodsworth
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- School of Life Sciences, University of Bedfordshire, University Square, Luton, UK
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26
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Ruiz-Ruano FJ, Castillo-Martínez J, Cabrero J, Gómez R, Camacho JPM, López-León MD. High-throughput analysis of satellite DNA in the grasshopper Pyrgomorpha conica reveals abundance of homologous and heterologous higher-order repeats. Chromosoma 2018; 127:323-340. [PMID: 29549528 DOI: 10.1007/s00412-018-0666-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 02/13/2018] [Accepted: 03/06/2018] [Indexed: 12/25/2022]
Abstract
Satellite DNA (satDNA) constitutes an important fraction of repetitive DNA in eukaryotic genomes, but it is barely known in most species. The high-throughput analysis of satDNA in the grasshopper Pyrgomorpha conica revealed 87 satDNA variants grouped into 76 different families, representing 9.4% of the genome. Fluorescent in situ hybridization (FISH) analysis of the 38 most abundant satDNA families revealed four different patterns of chromosome distribution. Homology search between the 76 satDNA families showed the existence of 15 superfamilies, each including two or more families, with the most abundant superfamily representing more than 80% of all satDNA found in this species. This also revealed the presence of two types of higher-order repeats (HORs), one showing internal homologous subrepeats, as conventional HORs, and an additional type showing non-homologous internal subrepeats, the latter arising by the combination of a given satDNA family with a non-annotated sequence, or with telomeric DNA. Interestingly, the heterologous subrepeats included in these HORs showed higher divergence within the HOR than outside it, suggesting that heterologous HORs show poor homogenization, in high contrast with conventional (homologous) HORs. Finally, heterologous HORs can show high differences in divergence between their constituent subrepeats, suggesting the possibility of regional homogenization.
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Affiliation(s)
- Francisco J Ruiz-Ruano
- Departamento de Genética. Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain
| | - Jesús Castillo-Martínez
- Departamento de Genética. Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain.,Facultad de Medicina, Universidad Católica de Valencia, C/Quevedo 2, 46001, Valencia, Spain
| | - Josefa Cabrero
- Departamento de Genética. Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain
| | - Ricardo Gómez
- Departamento de Ciencia y Tecnología Agroforestal, E.T.S. de Ingenieros Agrónomos, Universidad de Castilla La Mancha, 02071, Albacete, Spain
| | - Juan Pedro M Camacho
- Departamento de Genética. Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain
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Fernández-Pérez J, Nantón A, Ruiz-Ruano FJ, Camacho JPM, Méndez J. First complete female mitochondrial genome in four bivalve species genus Donax and their phylogenetic relationships within the Veneroida order. PLoS One 2017; 12:e0184464. [PMID: 28886105 PMCID: PMC5590976 DOI: 10.1371/journal.pone.0184464] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/24/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Four species of the genus Donax (D. semistriatus, D. trunculus, D. variegatus and D. vittatus) are common on Iberian Peninsula coasts. Nevertheless, despite their economic importance and overexploitation, scarce genetic resources are available. In this work, we newly determined the complete mitochondrial genomes of these four representatives of the family Donacidae, with the aim of contributing to unveil phylogenetic relationships within the Veneroida order, and of developing genetic markers being useful in wedge clam identification and authentication, and aquaculture stock management. PRINCIPAL FINDINGS The complete female mitochondrial genomes of the four species vary in size from 17,044 to 17,365 bp, and encode 13 protein-coding genes (including the atp8 gene), 2 rRNAs and 22 tRNAs, all located on the same strand. A long non-coding region was identified in each of the four Donax species between cob and cox2 genes, presumably corresponding to the Control Region. The Bayesian and Maximum Likelihood phylogenetic analysis of the Veneroida order indicate that all four species of Donax form a single clade as a sister group of other bivalves within the Tellinoidea superfamily. However, although Tellinoidea is actually monophyletic, none of its families are monophyletic. CONCLUSIONS Sequencing of complete mitochondrial genomes provides highly valuable information to establish the phylogenetic relationships within the Veneroida order. Furthermore, we provide here significant genetic resources for further research and conservation of this commercially important fishing resource.
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Affiliation(s)
- Jenyfer Fernández-Pérez
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and CICA (Centro de Investigacións Científicas Avanzadas), Universidade da Coruña, Campus de A Zapateira, A Coruña, Spain
| | - Ana Nantón
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and CICA (Centro de Investigacións Científicas Avanzadas), Universidade da Coruña, Campus de A Zapateira, A Coruña, Spain
| | | | - Juan Pedro M. Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Josefina Méndez
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and CICA (Centro de Investigacións Científicas Avanzadas), Universidade da Coruña, Campus de A Zapateira, A Coruña, Spain
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28
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Ruiz-Ruano FJ, Cabrero J, López-León MD, Sánchez A, Camacho JPM. Quantitative sequence characterization for repetitive DNA content in the supernumerary chromosome of the migratory locust. Chromosoma 2017; 127:45-57. [PMID: 28868580 DOI: 10.1007/s00412-017-0644-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 12/23/2022]
Abstract
Repetitive DNA is a major component in most eukaryotic genomes but is ignored in most genome sequencing projects. Here, we report the quantitative composition in repetitive DNA for a supernumerary (B) chromosome, in the migratory locust (Locusta migratoria), by Illumina sequencing of genomic DNA from B-carrying and B-lacking individuals and DNA obtained from a microdissected B chromosome, as well as the physical mapping of some elements. B chromosome DNA of 94.9% was repetitive, in high contrast with the 64.1% of standard (A) chromosomes. B chromosomes are enriched in satellite DNA (satDNA) (65.2% of B-DNA), with a single satellite (LmiSat02-176) comprising 55% of the B. Six satDNAs were visualized by FISH on the B chromosome, and the only A chromosome carrying all these satellites was autosome 9, pointing to this chromosome, along with autosome 8 (which shares histone genes with the B) as putative ancestors of the B chromosome. We found several transposable elements (TEs) showing nucleotidic variation specific to B-carrying individuals, which was also present in B-carrying transcriptomes. Remarkably, an interstitial region of the B chromosome included a 17 kb chimera composed of 29 different TEs, suggesting reiterative TE insertion in this B chromosome region.
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Affiliation(s)
- Francisco J Ruiz-Ruano
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, 18071, Granada, Spain.
| | - Josefa Cabrero
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, 18071, Granada, Spain
| | - María Dolores López-León
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, 18071, Granada, Spain
| | - Antonio Sánchez
- Departamento de Biología Experimental, Universidad de Jaén, Jaén, Spain
| | - Juan Pedro M Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, 18071, Granada, Spain
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29
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Utsunomia R, Ruiz-Ruano FJ, Silva DMZA, Serrano ÉA, Rosa IF, Scudeler PES, Hashimoto DT, Oliveira C, Camacho JPM, Foresti F. A Glimpse into the Satellite DNA Library in Characidae Fish (Teleostei, Characiformes). Front Genet 2017; 8:103. [PMID: 28855916 PMCID: PMC5557728 DOI: 10.3389/fgene.2017.00103] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/26/2017] [Indexed: 01/21/2023] Open
Abstract
Satellite DNA (satDNA) is an abundant fraction of repetitive DNA in eukaryotic genomes and plays an important role in genome organization and evolution. In general, satDNA sequences follow a concerted evolutionary pattern through the intragenomic homogenization of different repeat units. In addition, the satDNA library hypothesis predicts that related species share a series of satDNA variants descended from a common ancestor species, with differential amplification of different satDNA variants. The finding of a same satDNA family in species belonging to different genera within Characidae fish provided the opportunity to test both concerted evolution and library hypotheses. For this purpose, we analyzed here sequence variation and abundance of this satDNA family in ten species, by a combination of next generation sequencing (NGS), PCR and Sanger sequencing, and fluorescence in situ hybridization (FISH). We found extensive between-species variation for the number and size of pericentromeric FISH signals. At genomic level, the analysis of 1000s of DNA sequences obtained by Illumina sequencing and PCR amplification allowed defining 150 haplotypes which were linked in a common minimum spanning tree, where different patterns of concerted evolution were apparent. This also provided a glimpse into the satDNA library of this group of species. In consistency with the library hypothesis, different variants for this satDNA showed high differences in abundance between species, from highly abundant to simply relictual variants.
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Affiliation(s)
- Ricardo Utsunomia
- Department of Morphology, Institute of Biosciences, São Paulo State UniversityBotucatu, Brazil
| | | | - Duílio M Z A Silva
- Department of Morphology, Institute of Biosciences, São Paulo State UniversityBotucatu, Brazil
| | - Érica A Serrano
- Department of Morphology, Institute of Biosciences, São Paulo State UniversityBotucatu, Brazil
| | - Ivana F Rosa
- Department of Morphology, Institute of Biosciences, São Paulo State UniversityBotucatu, Brazil
| | - Patrícia E S Scudeler
- Department of Morphology, Institute of Biosciences, São Paulo State UniversityBotucatu, Brazil
| | | | - Claudio Oliveira
- Department of Morphology, Institute of Biosciences, São Paulo State UniversityBotucatu, Brazil
| | - Juan Pedro M Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de GranadaGranada, Spain
| | - Fausto Foresti
- Department of Morphology, Institute of Biosciences, São Paulo State UniversityBotucatu, Brazil
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Navarro-Domínguez B, Ruiz-Ruano FJ, Cabrero J, Corral JM, López-León MD, Sharbel TF, Camacho JPM. Protein-coding genes in B chromosomes of the grasshopper Eyprepocnemis plorans. Sci Rep 2017; 7:45200. [PMID: 28367986 PMCID: PMC5377258 DOI: 10.1038/srep45200] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 02/22/2017] [Indexed: 01/20/2023] Open
Abstract
For many years, parasitic B chromosomes have been considered genetically inert elements. Here we show the presence of ten protein-coding genes in the B chromosome of the grasshopper Eyprepocnemis plorans. Four of these genes (CIP2A, GTPB6, KIF20A, and MTG1) were complete in the B chromosome whereas the six remaining (CKAP2, CAP-G, HYI, MYCB2, SLIT and TOP2A) were truncated. Five of these genes (CIP2A, CKAP2, CAP-G, KIF20A, and MYCB2) were significantly up-regulated in B-carrying individuals, as expected if they were actively transcribed from the B chromosome. This conclusion is supported by three truncated genes (CKAP2, CAP-G and MYCB2) which showed up-regulation only in the regions being present in the B chromosome. Our results indicate that B chromosomes are not so silenced as was hitherto believed. Interestingly, the five active genes in the B chromosome code for functions related with cell division, which is the main arena where B chromosome destiny is played. This suggests that B chromosome evolutionary success can lie on its gene content.
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Affiliation(s)
| | - Francisco J Ruiz-Ruano
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Josefa Cabrero
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - José María Corral
- Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany.,Department of Bioanalytics, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | | | - Timothy F Sharbel
- Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany.,Global Institute for Food Security, 110 Gymnasium Place, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 4J8, Canada
| | - Juan Pedro M Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
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31
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Silva DMZDA, Utsunomia R, Ruiz-Ruano FJ, Oliveira C, Foresti F. The complete mitochondrial genome sequence of Astyanax paranae(Teleostei: characiformes). Mitochondrial DNA B Resour 2016; 1:586-587. [PMID: 33490410 PMCID: PMC7800300 DOI: 10.1080/23802359.2016.1222251] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Complete mitochondrial genome of the characiform fish Astyanax paranae was characterized in the present study. The whole mitogenome was 16,707 bp long and consisted of 13 protein-coding genes, 22 tRNAs, 2 rRNAs genes, a control region and origin of light-strand replication. The gene order is similar to those of the congeneric blind cavefish A. mexicanus. The nucleotide content of A. paranae mitogenome was 29.5% for A, 27.6% for T, 15.8% for G, 27.1% for C. Nucleotide identity between A. paranae and A. mexicanus across all the 37 genic regions ranged from 74.9% (ND2) to 90.3% (COX3).
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Affiliation(s)
- Duílio M Z de A Silva
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Ricardo Utsunomia
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | | | - Cláudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, SP, Brazil
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Ruiz-Ruano FJ, López-León MD, Cabrero J, Camacho JPM. High-throughput analysis of the satellitome illuminates satellite DNA evolution. Sci Rep 2016; 6:28333. [PMID: 27385065 PMCID: PMC4935994 DOI: 10.1038/srep28333] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 06/02/2016] [Indexed: 12/22/2022] Open
Abstract
Satellite DNA (satDNA) is a major component yet the great unknown of eukaryote genomes and clearly underrepresented in genome sequencing projects. Here we show the high-throughput analysis of satellite DNA content in the migratory locust by means of the bioinformatic analysis of Illumina reads with the RepeatExplorer and RepeatMasker programs. This unveiled 62 satDNA families and we propose the term "satellitome" for the whole collection of different satDNA families in a genome. The finding that satDNAs were present in many contigs of the migratory locust draft genome indicates that they show many genomic locations invisible by fluorescent in situ hybridization (FISH). The cytological pattern of five satellites showing common descent (belonging to the SF3 superfamily) suggests that non-clustered satDNAs can become into clustered through local amplification at any of the many genomic loci resulting from previous dissemination of short satDNA arrays. The fact that all kinds of satDNA (micro- mini- and satellites) can show the non-clustered and clustered states suggests that all these elements are mostly similar, except for repeat length. Finally, the presence of VNTRs in bacteria, showing similar properties to non-clustered satDNAs in eukaryotes, suggests that this kind of tandem repeats show common properties in all living beings.
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Affiliation(s)
| | | | - Josefa Cabrero
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Juan Pedro M. Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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de A Silva DMZ, Daniel SN, Camacho JPM, Utsunomia R, Ruiz-Ruano FJ, Penitente M, Pansonato-Alves JC, Hashimoto DT, Oliveira C, Porto-Foresti F, Foresti F. Origin of B chromosomes in the genus Astyanax (Characiformes, Characidae) and the limits of chromosome painting. Mol Genet Genomics 2016; 291:1407-18. [PMID: 26984341 DOI: 10.1007/s00438-016-1195-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 03/02/2016] [Indexed: 11/25/2022]
Abstract
Eukaryote genomes are frequently burdened with the presence of supernumerary (B) chromosomes. Their origin is frequently investigated by chromosome painting, under the hypothesis that sharing the repetitive DNA sequences contained in the painting probes is a sign of common descent. However, the intragenomic mobility of many anonymous DNA sequences contained in these probes (e.g., transposable elements) adds high uncertainty to this conclusion. Here we test the validity of chromosome painting to investigate B chromosome origin by comparing its results for seven B chromosome types in two fish species genus Astyanax, with those obtained (1) by means of the physical mapping of 18S ribosomal DNA (rDNA), H1 histone genes, the As51 satellite DNA and the (AC)15 microsatellite, and (2) by comparing the nucleotide sequence of one of these families (ITS regions from ribosomal DNA) between genomic DNA from B-lacking individuals in both species and the microdissected DNA from two metacentric B chromosomes found in these same species. Intra- and inter-specific painting suggested that all B chromosomes that were assayed shared homologous DNA sequences among them, as well as with a variable number of A chromosomes in each species. This finding would be consistent with a common origin for all seven B chromosomes analyzed. By contrast, the physical mapping of repetitive DNA sequences failed to give support to this hypothesis, as no more than two B-types shared a given repetitive DNA. Finally, sequence analysis of the ITS regions suggested that at least some of the B chromosomes could have had a common origin.
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Affiliation(s)
- Duílio M Z de A Silva
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, 18618-970, Brazil.
| | - Sandro Natal Daniel
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, Campus de Bauru., Bauru, SP, 17033-360, Brazil
| | | | - Ricardo Utsunomia
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, 18618-970, Brazil
| | | | - Manolo Penitente
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, Campus de Bauru., Bauru, SP, 17033-360, Brazil
| | - José Carlos Pansonato-Alves
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, 18618-970, Brazil
| | - Diogo Teruo Hashimoto
- CAUNESP, Universidade Estadual Paulista, Campus Jaboticabal, Jaboticabal, SP, 14884-900, Brazil
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, 18618-970, Brazil
| | - Fábio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, Campus de Bauru., Bauru, SP, 17033-360, Brazil
| | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, s/n, Botucatu, SP, 18618-970, Brazil
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Utsunomia R, Silva DMZDA, Ruiz-Ruano FJ, Araya-Jaime C, Pansonato-Alves JC, Scacchetti PC, Hashimoto DT, Oliveira C, Trifonov VA, Porto-Foresti F, Camacho JPM, Foresti F. Uncovering the Ancestry of B Chromosomes in Moenkhausia sanctaefilomenae (Teleostei, Characidae). PLoS One 2016; 11:e0150573. [PMID: 26934481 PMCID: PMC4775049 DOI: 10.1371/journal.pone.0150573] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/17/2016] [Indexed: 11/19/2022] Open
Abstract
B chromosomes constitute a heterogeneous mixture of genomic parasites that are sometimes derived intraspecifically from the standard genome of the host species, but result from interspecific hybridization in other cases. The mode of origin determines the DNA content, with the B chromosomes showing high similarity with the A genome in the first case, but presenting higher similarity with a different species in the second. The characid fish Moenkhausia sanctaefilomenae harbours highly invasive B chromosomes, which are present in all populations analyzed to date in the Parana and Tietê rivers. To investigate the origin of these B chromosomes, we analyzed two natural populations: one carrying B chromosomes and the other lacking them, using a combination of molecular cytogenetic techniques, nucleotide sequence analysis and high-throughput sequencing (Illumina HiSeq2000). Our results showed that i) B chromosomes have not yet reached the Paranapanema River basin; ii) B chromosomes are mitotically unstable; iii) there are two types of B chromosomes, the most frequent of which is lightly C-banded (similar to euchromatin in A chromosomes) (B1), while the other is darkly C-banded (heterochromatin-like) (B2); iv) the two B types contain the same tandem repeat DNA sequences (18S ribosomal DNA, H3 histone genes, MS3 and MS7 satellite DNA), with a higher content of 18S rDNA in the heterochromatic variant; v) all of these repetitive DNAs are present together only in the paracentromeric region of autosome pair no. 6, suggesting that the B chromosomes are derived from this A chromosome; vi) the two B chromosome variants show MS3 sequences that are highly divergent from each other and from the 0B genome, although the B2-derived sequences exhibit higher similarity with the 0B genome (this suggests an independent origin of the two B variants, with the less frequent, B2 type presumably being younger); and vii) the dN/dS ratio for the H3.2 histone gene is almost 4–6 times higher for B chromosomes than for A chromosome sequences, suggesting that purifying selection is relaxed for the DNA sequences located on the B chromosomes, presumably because they are mostly inactive.
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Affiliation(s)
- Ricardo Utsunomia
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
- * E-mail:
| | | | | | - Cristian Araya-Jaime
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - José Carlos Pansonato-Alves
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Priscilla Cardim Scacchetti
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | | | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | | | - Fábio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, Bauru, São Paulo, Brazil
| | | | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências de Botucatu, Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
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Doña J, Ruiz-Ruano FJ, Jovani R. DNA barcoding of Iberian Peninsula and North Africa Tawny Owls Strix aluco suggests the Strait of Gibraltar as an important barrier for phylogeography. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4475-4478. [PMID: 26465068 DOI: 10.3109/19401736.2015.1089573] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Eight subspecies have been proposed within the Tawny Owl (Strix aluco) species. However, recent molecular data have challenged this view, encouraging further work in this species complex. Here we reevaluated the taxonomic status between the North-Western African Tawny Owl, S. a. mauritanica, and its closest Iberian Tawny Owl population (from the S. a. sylvatica to S. a. aluco clade) separated by the Strait of Gibraltar. The Tawny Owl is a non-migratory and territorial species, and juvenile dispersal is restricted to a few kilometers around the natal site. This limited dispersal and the barrier imposed by the Strait of Gibraltar predicted a strong differentiation between the two populations. We tested this using DNA barcoding, Bayesian phylogenetic and species delimitation analysis. We found that an 81.1% of variation is due to the intergroups variation. In addition, the inter-intraspecific distances distribution revealed a barcoding gap among the two subspecies. Also, posterior probabilities and the PAB value allowed to reject the hypothesis that observed degree of distinctiveness is due to random coalescence processes. These findings clearly support the Strait of Gibraltar as an isolating barrier for this species. The subspecific status is confirmed and species status is even suggested for S. a. mauritanica.
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Affiliation(s)
- Jorge Doña
- a Department of Evolutionary Ecology , Estación Biológica de Doñana (CSIC) , Avda. Americo Vespucio S/N , Sevilla , Spain and
| | | | - Roger Jovani
- a Department of Evolutionary Ecology , Estación Biológica de Doñana (CSIC) , Avda. Americo Vespucio S/N , Sevilla , Spain and
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Ruiz-Estévez M, Ruiz-Ruano FJ, Cabrero J, Bakkali M, Perfectti F, López-León MD, Camacho JPM. Non-random expression of ribosomal DNA units in a grasshopper showing high intragenomic variation for the ITS2 region. Insect Mol Biol 2015; 24:319-330. [PMID: 25565136 DOI: 10.1111/imb.12158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We analyse intragenomic variation of the ITS2 internal transcribed spacer of ribosomal DNA (rDNA) in the grasshopper Eyprepocnemis plorans, by means of tagged PCR 454 amplicon sequencing performed on both genomic DNA (gDNA) and RNA-derived complementary DNA (cDNA), using part of the ITS2 flanking coding regions (5.8S and 28S rDNA) as an internal control for sequencing errors. Six different ITS2 haplotypes (i.e. variants for at least one nucleotide in the complete ITS2 sequence) were found in a single population, one of them (Hap4) being specific to a supernumerary (B) chromosome. The analysis of both gDNA and cDNA from the same individuals provided an estimate of the expression efficiency of the different haplotypes. We found random expression (i.e. about similar recovery in gDNA and cDNA) for three haplotypes (Hap1, Hap2 and Hap5), but significant underexpression for three others (Hap3, Hap4 and Hap6). Hap4 was the most extremely underexpressed and, remarkably, it showed the lowest sequence conservation for the flanking 5.8-28S coding regions in the gDNA reads but the highest conservation (100%) in the cDNA ones, suggesting the preferential expression of mutation-free rDNA units carrying this ITS2 haplotype. These results indicate that the ITS2 region of rDNA is far from complete homogenization in this species, and that the different rDNA units are not expressed at random, with some of them being severely downregulated.
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Affiliation(s)
- M Ruiz-Estévez
- Departamento de Genética, Universidad de Granada, Granada, Spain
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37
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Montiel EE, Ruiz-Ruano FJ, Cabrero J, Marchal JA, Sánchez A, Perfectti F, López-León MD, Camacho JPM. Intragenomic distribution of RTE retroelements suggests intrachromosomal movement. Chromosome Res 2015; 23:211-23. [PMID: 25605325 DOI: 10.1007/s10577-014-9461-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 11/25/2014] [Accepted: 12/18/2014] [Indexed: 11/25/2022]
Abstract
Much is known about the abundance of transposable elements (TEs) in eukaryotic genomes, but much is still unknown on their behaviour within cells. We employ here a combination of cytological, molecular and genomic approaches providing information on the intragenomic distribution and behaviour of non-long terminal repeat (LTR) retrotransposon-like elements (RTE). We microdissected every chromosome in a single first meiotic metaphase cell of the grasshopper Eyprepocnemis plorans and polymerase chain reaction (PCR) amplified a fragment of the RTE reverse transcriptase gene with specific primers. PCR products were cloned and 139 clones were sequenced. Analysis of molecular variance (AMOVA) showed significant intragenomic structure for these elements, with 4.6 % of molecular variance being found between chromosomes. A maximum likelihood tree built with the RTE sequences revealed the frequent presence of two or more elements showing very high similarity and being located on the same chromosome, thus suggesting intrachromosome movement. The 454 pyrosequencing of genomic DNA gave strong support to the microdissection results and provided evidence for the existence of 5' truncated elements. Our results thus indicate a tendency of RTE elements to reinsert into the same chromosome from where they were transcribed, which could be achieved if retrotranscription and insertion takes place immediately after transcription.
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Affiliation(s)
- Eugenia E Montiel
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, 18071, Spain,
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Guillén Y, Rius N, Delprat A, Williford A, Muyas F, Puig M, Casillas S, Ràmia M, Egea R, Negre B, Mir G, Camps J, Moncunill V, Ruiz-Ruano FJ, Cabrero J, de Lima LG, Dias GB, Ruiz JC, Kapusta A, Garcia-Mas J, Gut M, Gut IG, Torrents D, Camacho JP, Kuhn GCS, Feschotte C, Clark AG, Betrán E, Barbadilla A, Ruiz A. Genomics of ecological adaptation in cactophilic Drosophila. Genome Biol Evol 2014; 7:349-66. [PMID: 25552534 PMCID: PMC4316639 DOI: 10.1093/gbe/evu291] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Cactophilic Drosophila species provide a valuable model to study gene–environment interactions and ecological adaptation. Drosophila buzzatii and Drosophila mojavensis are two cactophilic species that belong to the repleta group, but have very different geographical distributions and primary host plants. To investigate the genomic basis of ecological adaptation, we sequenced the genome and developmental transcriptome of D. buzzatii and compared its gene content with that of D. mojavensis and two other noncactophilic Drosophila species in the same subgenus. The newly sequenced D. buzzatii genome (161.5 Mb) comprises 826 scaffolds (>3 kb) and contains 13,657 annotated protein-coding genes. Using RNA sequencing data of five life-stages we found expression of 15,026 genes, 80% protein-coding genes, and 20% noncoding RNA genes. In total, we detected 1,294 genes putatively under positive selection. Interestingly, among genes under positive selection in the D. mojavensis lineage, there is an excess of genes involved in metabolism of heterocyclic compounds that are abundant in Stenocereus cacti and toxic to nonresident Drosophila species. We found 117 orphan genes in the shared D. buzzatii–D. mojavensis lineage. In addition, gene duplication analysis identified lineage-specific expanded families with functional annotations associated with proteolysis, zinc ion binding, chitin binding, sensory perception, ethanol tolerance, immunity, physiology, and reproduction. In summary, we identified genetic signatures of adaptation in the shared D. buzzatii–D. mojavensis lineage, and in the two separate D. buzzatii and D. mojavensis lineages. Many of the novel lineage-specific genomic features are promising candidates for explaining the adaptation of these species to their distinct ecological niches.
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Affiliation(s)
- Yolanda Guillén
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain
| | - Núria Rius
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain
| | - Alejandra Delprat
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain
| | | | - Francesc Muyas
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain
| | - Marta Puig
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain
| | - Sònia Casillas
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Spain
| | - Miquel Ràmia
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Spain
| | - Raquel Egea
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Spain
| | - Barbara Negre
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Gisela Mir
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Barcelona, Spain The Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Jordi Camps
- Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Torre I, Barcelona, Spain
| | - Valentí Moncunill
- Barcelona Supercomputing Center (BSC), Edifici TG (Torre Girona), Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Josefa Cabrero
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Spain
| | - Leonardo G de Lima
- Instituto de Ciências Biológicas, Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Guilherme B Dias
- Instituto de Ciências Biológicas, Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Jeronimo C Ruiz
- Informática de Biossistemas, Centro de Pesquisas René Rachou-Fiocruz Minas, Belo Horizonte, MG, Brazil
| | - Aurélie Kapusta
- Department of Human Genetics, University of Utah School of Medicine
| | - Jordi Garcia-Mas
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Barcelona, Spain
| | - Marta Gut
- Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Torre I, Barcelona, Spain
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, Torre I, Barcelona, Spain
| | - David Torrents
- Barcelona Supercomputing Center (BSC), Edifici TG (Torre Girona), Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Juan P Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Spain
| | - Gustavo C S Kuhn
- Instituto de Ciências Biológicas, Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University
| | - Esther Betrán
- Department of Biology, University of Texas at Arlington
| | - Antonio Barbadilla
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Spain
| | - Alfredo Ruiz
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Spain
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Camacho JPM, Ruiz-Ruano FJ, Martín-Blázquez R, López-León MD, Cabrero J, Lorite P, Cabral-de-Mello DC, Bakkali M. A step to the gigantic genome of the desert locust: chromosome sizes and repeated DNAs. Chromosoma 2014; 124:263-75. [PMID: 25472934 DOI: 10.1007/s00412-014-0499-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 11/24/2014] [Accepted: 11/25/2014] [Indexed: 10/24/2022]
Abstract
The desert locust (Schistocerca gregaria) has been used as material for numerous cytogenetic studies. Its genome size is estimated to be 8.55 Gb of DNA comprised in 11 autosomes and the X chromosome. Its X0/XX sex chromosome determinism therefore results in females having 24 chromosomes whereas males have 23. Surprisingly, little is known about the DNA content of this locust's huge chromosomes. Here, we use the Feulgen Image Analysis Densitometry and C-banding techniques to respectively estimate the DNA quantity and heterochromatin content of each chromosome. We also identify three satellite DNAs using both restriction endonucleases and next-generation sequencing. We then use fluorescent in situ hybridization to determine the chromosomal location of these satellite DNAs as well as that of six tandem repeat DNA gene families. The combination of the results obtained in this work allows distinguishing between the different chromosomes not only by size, but also by the kind of repetitive DNAs that they contain. The recent publication of the draft genome of the migratory locust (Locusta migratoria), the largest animal genome hitherto sequenced, invites for sequencing even larger genomes. S. gregaria is a pest that causes high economic losses. It is thus among the primary candidates for genome sequencing. But this species genome is about 50 % larger than that of L. migratoria, and although next-generation sequencing currently allows sequencing large genomes, sequencing it would mean a greater challenge. The chromosome sizes and markers provided here should not only help planning the sequencing project and guide the assembly but would also facilitate assigning assembled linkage groups to actual chromosomes.
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Affiliation(s)
- J P M Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Fuentenueva S/N, 18071, Granada, Spain
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Ruiz-Ruano FJ, Cuadrado Á, Montiel EE, Camacho JPM, López-León MD. Next generation sequencing and FISH reveal uneven and nonrandom microsatellite distribution in two grasshopper genomes. Chromosoma 2014; 124:221-34. [PMID: 25387401 DOI: 10.1007/s00412-014-0492-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 10/17/2014] [Accepted: 10/29/2014] [Indexed: 11/29/2022]
Abstract
Simple sequence repeats (SSRs), also known as microsatellites, are one of the prominent DNA sequences shaping the repeated fraction of eukaryotic genomes. In spite of their profuse use as molecular markers for a variety of genetic and evolutionary studies, their genomic location, distribution, and function are not yet well understood. Here we report the first thorough joint analysis of microsatellite motifs at both genomic and chromosomal levels in animal species, by a combination of 454 sequencing and fluorescent in situ hybridization (FISH) techniques performed on two grasshopper species. The in silico analysis of the 454 reads suggested that microsatellite expansion is not driving size increase of these genomes, as SSR abundance was higher in the species showing the smallest genome. However, the two species showed the same uneven and nonrandom location of SSRs, with clear predominance of dinucleotide motifs and association with several types of repetitive elements, mostly histone gene spacers, ribosomal DNA intergenic spacers (IGS), and transposable elements (TEs). The FISH analysis showed a dispersed chromosome distribution of microsatellite motifs in euchromatic regions, in coincidence with chromosome location patterns previously observed for many mobile elements in these species. However, some SSR motifs were clustered, especially those located in the histone gene cluster.
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Affiliation(s)
- Francisco J Ruiz-Ruano
- Departamento de Genética Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain
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Silva DMZDA, Pansonato-Alves JC, Utsunomia R, Araya-Jaime C, Ruiz-Ruano FJ, Daniel SN, Hashimoto DT, Oliveira C, Camacho JPM, Porto-Foresti F, Foresti F. Delimiting the origin of a B chromosome by FISH mapping, chromosome painting and DNA sequence analysis in Astyanax paranae (Teleostei, Characiformes). PLoS One 2014; 9:e94896. [PMID: 24736529 PMCID: PMC3988084 DOI: 10.1371/journal.pone.0094896] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 03/19/2014] [Indexed: 12/19/2022] Open
Abstract
Supernumerary (B) chromosomes have been shown to contain a wide variety of repetitive sequences. For this reason, fluorescent in situ hybridisation (FISH) is a useful tool for ascertaining the origin of these genomic elements, especially when combined with painting from microdissected B chromosomes. In order to investigate the origin of B chromosomes in the fish species Astyanax paranae, these two approaches were used along with PCR amplification of specific DNA sequences obtained from the B chromosomes and its comparison with those residing in the A chromosomes. Remarkably, chromosome painting with the one-arm metacentric B chromosome probe showed hybridization signals on entire B chromosome, while FISH mapping revealed the presence of H1 histone and 18S rDNA genes symmetrically placed in both arms of the B chromosome. These results support the hypothesis that the B chromosome of A. paranae is an isochromosome. Additionally, the chromosome pairs Nos. 2 or 23 are considered the possible B chromosome ancestors since both contain syntenic H1 and 18S rRNA sequences. The analysis of DNA sequence fragments of the histone and rRNA genes obtained from the microdissected B chromosomes showed high similarity with those obtained from 0B individuals, which supports the intraspecific origin of B chromosomes in A. paranae. Finally, the population hereby analysed showed a female-biased B chromosome presence suggesting that B chromosomes in this species could influence sex determinism.
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Affiliation(s)
- Duílio M. Z. de A. Silva
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, Botucatu, São Paulo, Brazil
| | - José Carlos Pansonato-Alves
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, Botucatu, São Paulo, Brazil
| | - Ricardo Utsunomia
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, Botucatu, São Paulo, Brazil
| | - Cristian Araya-Jaime
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, Botucatu, São Paulo, Brazil
| | | | - Sandro Natal Daniel
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, Campus de Bauru, Bauru, São Paulo, Brazil
| | - Diogo Teruo Hashimoto
- CAUNESP, Universidade Estadual Paulista, Campus Jaboticabal, Jaboticabal, São Paulo, Brazil
| | - Cláudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, Botucatu, São Paulo, Brazil
| | | | - Fábio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, Campus de Bauru, Bauru, São Paulo, Brazil
| | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, Botucatu, São Paulo, Brazil
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Bessa J, Luengo M, Rivero-Gil S, Ariza-Cosano A, Maia AHF, Ruiz-Ruano FJ, Caballero P, Naranjo S, Carvajal JJ, Gómez-Skarmeta JL. A mobile insulator system to detect and disrupt cis-regulatory landscapes in vertebrates. Genome Res 2013; 24:487-95. [PMID: 24277716 PMCID: PMC3941113 DOI: 10.1101/gr.165654.113] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In multicellular organisms, cis-regulation controls gene expression in space and time. Despite the essential implication of cis-regulation in the development and evolution of organisms and in human diseases, our knowledge about regulatory sequences largely derives from analyzing their activity individually and outside their genomic context. Indeed, the contribution of these sequences to the expression of their target genes in their genomic context is still largely unknown. Here we present a novel genetic screen designed to visualize and interrupt gene regulatory landscapes in vertebrates. In this screen, based on the random insertion of an engineered Tol2 transposon carrying a strong insulator separating two fluorescent reporter genes, we isolated hundreds of zebrafish lines containing insertions that disrupt the cis-regulation of tissue-specific expressed genes. We therefore provide a new easy-to-handle tool that will help to disrupt and chart the regulatory activity spread through the vast noncoding regions of the vertebrate genome.
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Affiliation(s)
- José Bessa
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville 41013, Spain
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Ruiz-Ruano FJ, Ruiz-Estévez M, Rodríguez-Pérez J, López-Pino JL, Cabrero J, Camacho JPM. DNA amount of X and B chromosomes in the grasshoppers Eyprepocnemis plorans and Locusta migratoria. Cytogenet Genome Res 2011; 134:120-6. [PMID: 21389690 DOI: 10.1159/000324690] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2010] [Indexed: 11/19/2022] Open
Abstract
We analyzed the DNA amount in X and B chromosomes of 2 XX/X0 grasshopper species (Eyprepocnemis plorans and Locusta migratoria), by means of Feulgen image analysis densitometry (FIAD), using previous estimates in L. migratoria as standard (5.89 pg). We first analyzed spermatids of 0B males and found a bimodal distribution of integrated optical densities (IODs), suggesting that one peak corresponded to +X and the other to -X spermatids. The difference between the 2 peaks corresponded to the X chromosome DNA amount, which was 1.28 pg in E. plorans and 0.80 pg in L. migratoria. In addition, the +X peak in E. plorans gave an estimate of the C-value in this species (10.39 pg). We next analyzed diplotene cells from 1B males in E. plorans and +B males in L. migratoria (a species where Bs are mitotically unstable and no integer B number can be defined for an individual) and measured B chromosome IOD relative to X chromosome IOD, within the same cell, taking advantage of the similar degree of condensation for both positively heteropycnotic chromosomes at this meiotic stage. From this proportion, we estimated the DNA amount for 3 different B chromosome variants found in individuals from 3 E. plorans Spanish populations (0.54 pg for B1 from Saladares, 0.51 pg for B2 from Salobreña and 0.64 for B24 from Torrox). Likewise, we estimated the DNA amount of the B chromosome in L. migratoria to be 0.15 pg. To automate measurements, we wrote a GPL3 licensed Python program (pyFIA). We discuss the utility of the present approach for estimating X and B chromosome DNA amount in a variety of situations, and the meaning of the DNA amount estimates for X and B chromosomes in these 2 species.
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Affiliation(s)
- F J Ruiz-Ruano
- Departamento de Genética, Universidad de Granada, Granada, España
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