1
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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] [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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2
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Borodin PM. Germline-restricted chromosomes of the songbirds. Vavilovskii Zhurnal Genet Selektsii 2023; 27:641-650. [PMID: 38023808 PMCID: PMC10643108 DOI: 10.18699/vjgb-23-75] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 12/01/2023] Open
Abstract
Germline-restricted chromosomes (GRCs) are present in the genomes of germline cells and absent from somatic cells. A GRC is found in all species of the songbirds (Passeri) and in none of the other bird orders studied to date. This indicates that GRC originated in the common ancestor of the songbirds. The germline-restricted chromosome is permanently absent from somatic cells of the songbird, while female germline cells usually contain two copies of GRC and male ones have one copy. In females, GRCs undergo synapsis and restricted recombination in their terminal regions during meiotic prophase. In males, it is almost always eliminated from spermatocytes. Thus, GRC is inherited almost exclusively through the maternal lineage. The germline-restricted chromosome is a necessary genomic element in the germline cells of songbirds. To date, the GRC genetic composition has been studied in four species only. Some GRC genes are actively expressed in female and male gonads, controlling the development of germline cells and synthesis of the proteins involved in the organization of meiotic chromosomes. Songbird species vary in GRC size and genetic composition. The GRC of each bird species consists of amplified and modified copies of genes from the basic genome of that species. The level of homology between GRCs of different species is relatively low, indicating a high rate of genetic evolution of this chromosome. Transmission through the maternal lineage and suppression of the recombination contribute significantly to the accelerated evolution of GRCs. One may suggest that the rapid coordinated evolution between the GRC genes and the genes of the basic genome in the songbirds might be responsible for the explosive speciation and adaptive radiation of this most species-rich and diverse infraorder of birds.
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Affiliation(s)
- P M Borodin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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3
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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] [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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4
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Ayarza E, Cavada G, Arévalo T, Molina A, Berríos S. Quantitative analysis of Robertsonian chromosomes inherited by descendants from multiple Rb heterozygotes of Mus m. Domesticus. Front Cell Dev Biol 2022; 10:1050556. [PMID: 36506103 PMCID: PMC9732535 DOI: 10.3389/fcell.2022.1050556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/14/2022] [Indexed: 11/26/2022] Open
Abstract
Robertsonian translocation is the most common chromosomal rearrangement in mammals, and represents the type of chromosomal change that most effectively contributes to speciation in natural populations. Rb translocations involve double-strand DNA breaks at the centromere level in two telocentric chromosomes, followed by repair ligation of the respective long arms, creating a metacentric Rb chromosome. Many different chromosomal races have been described in Mus musculus domesticus that show reduced chromosome numbers due to the presence of Rb metacentric chromosomes. The crossroads between ancestral telocentrics and the new metacentric chromosomes should be resolved in the meiotic cells of the heterozygote individuals, which form trivalents. The preferential segregation of metacentric chromosomes to the egg during female meiosis I has been proposed to favor their fixation and eventual conversion of a telocentric karyotype to a metacentric karyotype. This biased segregation, a form of meiotic drive, explains the karyotype changes in mammalian species that have accumulated Rb fusions. We studied and compared the number of Rb chromosomes inherited by the offspring of multiple Rb heterozygous of M. domesticus in reciprocal crosses. We did not find that the Rb chromosomes were inherited preferentially with respect to the telocentric chromosomes; therefore, we found no evidence for the meiotic drive, nor was there a random distribution of Rb chromosomes inherited by the descendants.
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Affiliation(s)
- Eliana Ayarza
- Departamento de Tecnología Médica, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Gabriel Cavada
- Instituto de Salud Poblacional, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Tamara Arévalo
- Programa Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Alam Molina
- Programa Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Soledad Berríos
- Programa Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile,*Correspondence: Soledad Berríos,
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5
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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] [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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6
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Sotelo-Muñoz M, Poignet M, Albrecht T, Kauzál O, Dedukh D, Schlebusch SA, Janko K, Reifová R. Germline-restricted chromosome shows remarkable variation in size among closely related passerine species. Chromosoma 2022; 131:77-86. [PMID: 35389062 DOI: 10.1007/s00412-022-00771-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/19/2022] [Accepted: 03/22/2022] [Indexed: 12/20/2022]
Abstract
Passerine birds have a supernumerary chromosome in their germ cells called the germline-restricted chromosome (GRC). The GRC was first discovered more than two decades ago in zebra finch but recent studies have suggested that it is likely present in all passerines, the most species rich avian order, encompassing more than half of all modern bird species. Despite its wide taxonomic distribution, studies on this chromosome are still scarce and limited to a few species. Here, we cytogenetically analyzed the GRC in five closely related estrildid finch species of the genus Lonchura. We show that the GRC varies enormously in size, ranging from a tiny micro-chromosome to one of the largest macro-chromosomes in the cell, not only among recently diverged species but also within species and sometimes even between germ cells of a single individual. In Lonchura atricapilla, we also observed variation in GRC copy number among male germ cells of a single individual. Finally, our analysis of hybrids between two Lonchura species with noticeably different GRC size directly supported maternal inheritance of the GRC. Our results reveal the extraordinarily dynamic nature of the GRC, which might be caused by frequent gains and losses of sequences on this chromosome leading to substantial differences in genetic composition of the GRC between and even within species. Such differences might theoretically contribute to reproductive isolation between species and thus accelerate the speciation rate of passerine birds compared to other bird lineages.
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Affiliation(s)
- Manuelita Sotelo-Muñoz
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 12800, Prague, Czech Republic.
| | - Manon Poignet
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 12800, Prague, Czech Republic
| | - Tomáš Albrecht
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 12800, Prague, Czech Republic.,Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 60365, Brno, Czech Republic
| | - Ondřej Kauzál
- Institute of Vertebrate Biology, Czech Academy of Sciences, Květná 8, 60365, Brno, Czech Republic.,Department of Ecology, Faculty of Science, Charles University, Viničná 7, 12800, Prague, Czech Republic
| | - Dmitrij Dedukh
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721, Liběchov, Czech Republic
| | - Stephen A Schlebusch
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 12800, Prague, Czech Republic
| | - Karel Janko
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721, Liběchov, Czech Republic.,Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 12800, Prague, Czech Republic.
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7
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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] [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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8
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Poignet M, Johnson Pokorná M, Altmanová M, Majtánová Z, Dedukh D, Albrecht T, Reif J, Osiejuk TS, Reifová R. Comparison of Karyotypes in Two Hybridizing Passerine Species: Conserved Chromosomal Structure but Divergence in Centromeric Repeats. Front Genet 2021; 12:768987. [PMID: 34938317 PMCID: PMC8687609 DOI: 10.3389/fgene.2021.768987] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/10/2021] [Indexed: 11/23/2022] Open
Abstract
Changes in chromosomal structure involving chromosomal rearrangements or copy number variation of specific sequences can play an important role in speciation. Here, we explored the chromosomal structure of two hybridizing passerine species; the common nightingale (Luscinia megarhynchos) and the thrush nightingale (Luscinia luscinia), using conventional cytogenetic approaches, immunostaining of meiotic chromosomes, fluorescence in situ hybridization as well as comparative genomic hybridization (CGH). We found that the two nightingale species show conserved karyotypes with the same diploid chromosome number of 2n = 84. In addition to standard chromosomes, both species possessed a small germline restricted chromosome of similar size as a microchromosome. Just a few subtle changes in chromosome morphology were observed between the species, suggesting that only a limited number of chromosomal rearrangements occurred after the species divergence. The interspecific CGH experiment suggested that the two nightingale species might have diverged in centromeric repetitive sequences in most macro- and microchromosomes. In addition, some chromosomes showed changes in copy number of centromeric repeats between the species. The observation of very similar karyotypes in the two nightingale species is consistent with a generally slow rate of karyotype evolution in birds. The divergence of centromeric sequences between the two species could theoretically cause meiotic drive or reduced fertility in interspecific hybrids. Nevertheless, further studies are needed to evaluate the potential role of chromosomal structural variations in nightingale speciation.
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Affiliation(s)
- Manon Poignet
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martina Johnson Pokorná
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Marie Altmanová
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Zuzana Majtánová
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Dmitry Dedukh
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, 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
| | - Jiří Reif
- Institute for Environmental Studies, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Zoology and Laboratory of Ornithology, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Tomasz S. Osiejuk
- Department of Behavioural Ecology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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9
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Torgasheva A, Malinovskaya L, Zadesenets K, Shnaider E, Rubtsov N, Borodin P. Germline-Restricted Chromosome (GRC) in Female and Male Meiosis of the Great Tit (Parus major, Linnaeus, 1758). Front Genet 2021; 12:768056. [PMID: 34759962 PMCID: PMC8573160 DOI: 10.3389/fgene.2021.768056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/28/2021] [Indexed: 11/17/2022] Open
Abstract
All songbirds studied so far have a germline-restricted chromosome (GRC), which is present in the germ cells and absent in the somatic cells. It shows a wide variation in size, morphology, and genetic content between the songbird species. In this paper, we analyzed GRC behavior in female and male meiosis of the great tit, using immunolocalization of meiotic proteins and FISH with GRC-derived DNA probes. We found that, despite dozens of million years of independent evolution, the great tit GRC displays a striking similarity with the GRCs of two species of martins and two species of estrildid finches examined earlier. It was usually present in two copies in females forming recombining bivalent and in one copy in males forming a condensed heterochromatic body with dotted-like axial elements of the synaptonemal complex. We observed mosaicism for the GRC copy number in the female and male great tit. This indicates that one of the GRC copies might be passively lost during premeiotic germ cell divisions. After the meiotic prophase, the GRC was ejected from most male germ cells. The reverse and interspecies FISH with GRC-specific microdissected DNA probes indicates that GRCs of the great tit, pale martin, and zebra finch differ substantially in their genetic content despite similarities in the meiotic behavior.
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Affiliation(s)
- Anna Torgasheva
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Lyubov Malinovskaya
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Kira Zadesenets
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | | | - Nikolai Rubtsov
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Pavel Borodin
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
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10
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The Snakeskin Gourami (Trichopodus pectoralis) Tends to Exhibit XX/XY Sex Determination. FISHES 2021. [DOI: 10.3390/fishes6040043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The snakeskin gourami (Trichopodus pectoralis) has a high meat yield and is one of the top five aquaculture freshwater fishes in Thailand. The species is not externally sexually dimorphic, and its sex determination system is unknown. Understanding the sex determination system of this species will contribute to its full-scale commercialization. In this study, a cytogenetic analysis did not reveal any between-sex differences in chromosomal patterns. However, we used genotyping-by-sequencing to identify 4 male-linked loci and 1 female-linked locus, indicating that the snakeskin gourami tends to exhibit an XX/XY sex determination system. However, we did not find any male-specific loci after filtering the loci for a ratio of 100:0 ratio of males:females. This suggests that the putative Y chromosome is young and that the sex determination region is cryptic. This approach provides solid information that can help identify the sex determination mechanism and potential sex determination regions in the snakeskin gourami, allowing further investigation of genetic improvements in the species.
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11
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Dedukh D, Krasikova A. Delete and survive: strategies of programmed genetic material elimination in eukaryotes. Biol Rev Camb Philos Soc 2021; 97:195-216. [PMID: 34542224 PMCID: PMC9292451 DOI: 10.1111/brv.12796] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 02/06/2023]
Abstract
Genome stability is a crucial feature of eukaryotic organisms because its alteration drastically affects the normal development and survival of cells and the organism as a whole. Nevertheless, some organisms can selectively eliminate part of their genomes from certain cell types during specific stages of ontogenesis. This review aims to describe the phenomenon of programmed DNA elimination, which includes chromatin diminution (together with programmed genome rearrangement or DNA rearrangements), B and sex chromosome elimination, paternal genome elimination, parasitically induced genome elimination, and genome elimination in animal and plant hybrids. During programmed DNA elimination, individual chromosomal fragments, whole chromosomes, and even entire parental genomes can be selectively removed. Programmed DNA elimination occurs independently in different organisms, ranging from ciliate protozoa to mammals. Depending on the sequences destined for exclusion, programmed DNA elimination may serve as a radical mechanism of dosage compensation and inactivation of unnecessary or dangerous genetic entities. In hybrids, genome elimination results from competition between parental genomes. Despite the different consequences of DNA elimination, all genetic material destined for elimination must be first recognised, epigenetically marked, separated, and then removed and degraded.
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Affiliation(s)
- Dmitrij Dedukh
- Saint-Petersburg State University, 7/9 Universitetskaya Embankment, Saint-Petersburg, 199034, Russia
| | - Alla Krasikova
- Saint-Petersburg State University, 7/9 Universitetskaya Embankment, Saint-Petersburg, 199034, Russia
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12
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Kratochvíl L, Stöck M, Rovatsos M, Bullejos M, Herpin A, Jeffries DL, Peichel CL, Perrin N, Valenzuela N, Pokorná MJ. Expanding the classical paradigm: what we have learnt from vertebrates about sex chromosome evolution. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200097. [PMID: 34304593 PMCID: PMC8310716 DOI: 10.1098/rstb.2020.0097] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2021] [Indexed: 12/15/2022] Open
Abstract
Until recently, the field of sex chromosome evolution has been dominated by the canonical unidirectional scenario, first developed by Muller in 1918. This model postulates that sex chromosomes emerge from autosomes by acquiring a sex-determining locus. Recombination reduction then expands outwards from this locus, to maintain its linkage with sexually antagonistic/advantageous alleles, resulting in Y or W degeneration and potentially culminating in their disappearance. Based mostly on empirical vertebrate research, we challenge and expand each conceptual step of this canonical model and present observations by numerous experts in two parts of a theme issue of Phil. Trans. R. Soc. B. We suggest that greater theoretical and empirical insights into the events at the origins of sex-determining genes (rewiring of the gonadal differentiation networks), and a better understanding of the evolutionary forces responsible for recombination suppression are required. Among others, crucial questions are: Why do sex chromosome differentiation rates and the evolution of gene dose regulatory mechanisms between male versus female heterogametic systems not follow earlier theory? Why do several lineages not have sex chromosomes? And: What are the consequences of the presence of (differentiated) sex chromosomes for individual fitness, evolvability, hybridization and diversification? We conclude that the classical scenario appears too reductionistic. Instead of being unidirectional, we show that sex chromosome evolution is more complex than previously anticipated and principally forms networks, interconnected to potentially endless outcomes with restarts, deletions and additions of new genomic material. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
| | - Mónica Bullejos
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Las Lagunillas Campus S/N, 23071 Jaén, Spain
| | - Amaury Herpin
- INRAE, LPGP, 35000 Rennes, France
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, People's Republic of China
| | - Daniel L. Jeffries
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Catherine L. Peichel
- Institute of Ecology and Evolution, University of Bern, CH-3012 Bern, Switzerland
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Martina Johnson Pokorná
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague, Czech Republic
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
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13
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Abstract
Female meiotic drive is the phenomenon where a selfish genetic element alters chromosome segregation during female meiosis to segregate to the egg and transmit to the next generation more frequently than Mendelian expectation. While several examples of female meiotic drive have been known for many decades, a molecular understanding of the underlying mechanisms has been elusive. Recent advances in this area in several model species prompts a comparative re-examination of these drive systems. In this review, we compare female meiotic drive of several animal and plant species, highlighting pertinent similarities.
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Affiliation(s)
- Frances E. Clark
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Takashi Akera
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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14
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Stöck M, Kratochvíl L, Kuhl H, Rovatsos M, Evans BJ, Suh A, Valenzuela N, Veyrunes F, Zhou Q, Gamble T, Capel B, Schartl M, Guiguen Y. A brief review of vertebrate sex evolution with a pledge for integrative research: towards ' sexomics'. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200426. [PMID: 34247497 PMCID: PMC8293304 DOI: 10.1098/rstb.2020.0426] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2021] [Indexed: 02/07/2023] Open
Abstract
Triggers and biological processes controlling male or female gonadal differentiation vary in vertebrates, with sex determination (SD) governed by environmental factors or simple to complex genetic mechanisms that evolved repeatedly and independently in various groups. Here, we review sex evolution across major clades of vertebrates with information on SD, sexual development and reproductive modes. We offer an up-to-date review of divergence times, species diversity, genomic resources, genome size, occurrence and nature of polyploids, SD systems, sex chromosomes, SD genes, dosage compensation and sex-biased gene expression. Advances in sequencing technologies now enable us to study the evolution of SD at broader evolutionary scales, and we now hope to pursue a sexomics integrative research initiative across vertebrates. The vertebrate sexome comprises interdisciplinary and integrated information on sexual differentiation, development and reproduction at all biological levels, from genomes, transcriptomes and proteomes, to the organs involved in sexual and sex-specific processes, including gonads, secondary sex organs and those with transcriptional sex-bias. The sexome also includes ontogenetic and behavioural aspects of sexual differentiation, including malfunction and impairment of SD, sexual differentiation and fertility. Starting from data generated by high-throughput approaches, we encourage others to contribute expertise to building understanding of the sexomes of many key vertebrate species. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.
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Affiliation(s)
- Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries—IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czech Republic
| | - Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries—IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
| | - Michail Rovatsos
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Ben J. Evans
- Department of Biology, McMaster University, Life Sciences Building Room 328, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
- Department of Organismal Biology—Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Frédéric Veyrunes
- Institut des Sciences de l'Evolution de Montpellier, ISEM UMR 5554 (CNRS/Université de Montpellier/IRD/EPHE), Montpellier, France
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
- Department of Neuroscience and Developmental Biology, University of Vienna, A-1090 Vienna, Austria
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
| | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Würzburg, 97074 Würzburg, Germany
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
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15
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Torgasheva A, Malinovskaya L, Zadesenets KS, Slobodchikova A, Shnaider E, Rubtsov N, Borodin P. Highly Conservative Pattern of Sex Chromosome Synapsis and Recombination in Neognathae Birds. Genes (Basel) 2021; 12:1358. [PMID: 34573341 PMCID: PMC8465153 DOI: 10.3390/genes12091358] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/16/2021] [Accepted: 08/27/2021] [Indexed: 01/22/2023] Open
Abstract
We analyzed the synapsis and recombination between Z and W chromosomes in the oocytes of nine neognath species: domestic chicken Gallus gallus domesticus, grey goose Anser anser, black tern Chlidonias niger, common tern Sterna hirundo, pale martin Riparia diluta, barn swallow Hirundo rustica, European pied flycatcher Ficedula hypoleuca, great tit Parus major and white wagtail Motacilla alba using immunolocalization of SYCP3, the main protein of the lateral elements of the synaptonemal complex, and MLH1, the mismatch repair protein marking mature recombination nodules. In all species examined, homologous synapsis occurs in a short region of variable size at the ends of Z and W chromosomes, where a single recombination nodule is located. The remaining parts of the sex chromosomes undergo synaptic adjustment and synapse non-homologously. In 25% of ZW bivalents of white wagtail, synapsis and recombination also occur at the secondary pairing region, which probably resulted from autosome-sex chromosome translocation. Using FISH with a paint probe specific to the germline-restricted chromosome (GRC) of the pale martin on the oocytes of the pale martin, barn swallow and great tit, we showed that both maternally inherited songbird chromosomes (GRC and W) share common sequences.
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Affiliation(s)
- Anna Torgasheva
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia; (A.T.); (L.M.); (K.S.Z.); (A.S.); (N.R.)
- Department of Cytology and Genetics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Lyubov Malinovskaya
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia; (A.T.); (L.M.); (K.S.Z.); (A.S.); (N.R.)
- Department of Cytology and Genetics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Kira S. Zadesenets
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia; (A.T.); (L.M.); (K.S.Z.); (A.S.); (N.R.)
| | - Anastasia Slobodchikova
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia; (A.T.); (L.M.); (K.S.Z.); (A.S.); (N.R.)
- Department of Cytology and Genetics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Elena Shnaider
- Bird of Prey Rehabilitation Centre, 630090 Novosibirsk, Russia;
| | - Nikolai Rubtsov
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia; (A.T.); (L.M.); (K.S.Z.); (A.S.); (N.R.)
- Department of Cytology and Genetics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Pavel Borodin
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia; (A.T.); (L.M.); (K.S.Z.); (A.S.); (N.R.)
- Department of Cytology and Genetics, Novosibirsk State University, 630090 Novosibirsk, Russia
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16
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Pajpach F, Wu T, Shearwin-Whyatt L, Jones K, Grützner F. Flavors of Non-Random Meiotic Segregation of Autosomes and Sex Chromosomes. Genes (Basel) 2021; 12:genes12091338. [PMID: 34573322 PMCID: PMC8471020 DOI: 10.3390/genes12091338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 12/14/2022] Open
Abstract
Segregation of chromosomes is a multistep process occurring both at mitosis and meiosis to ensure that daughter cells receive a complete set of genetic information. Critical components in the chromosome segregation include centromeres, kinetochores, components of sister chromatid and homologous chromosomes cohesion, microtubule organizing centres, and spindles. Based on the cytological work in the grasshopper Brachystola, it has been accepted for decades that segregation of homologs at meiosis is fundamentally random. This ensures that alleles on chromosomes have equal chance to be transmitted to progeny. At the same time mechanisms of meiotic drive and an increasing number of other examples of non-random segregation of autosomes and sex chromosomes provide insights into the underlying mechanisms of chromosome segregation but also question the textbook dogma of random chromosome segregation. Recent advances provide a better understanding of meiotic drive as a prominent force where cellular and chromosomal changes allow autosomes to bias their segregation. Less understood are mechanisms explaining observations that autosomal heteromorphism may cause biased segregation and regulate alternating segregation of multiple sex chromosome systems or translocation heterozygotes as an extreme case of non-random segregation. We speculate that molecular and cytological mechanisms of non-random segregation might be common in these cases and that there might be a continuous transition between random and non-random segregation which may play a role in the evolution of sexually antagonistic genes and sex chromosome evolution.
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Affiliation(s)
- Filip Pajpach
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (F.P.); (L.S.-W.)
| | - Tianyu Wu
- Department of Central Laboratory, Clinical Laboratory, Jing’an District Centre Hospital of Shanghai and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China;
| | - Linda Shearwin-Whyatt
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (F.P.); (L.S.-W.)
| | - Keith Jones
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RH, UK;
| | - Frank Grützner
- School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; (F.P.); (L.S.-W.)
- Correspondence:
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17
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Asalone KC, Takkar AK, Saldanha CJ, Bracht JR. A Transcriptomic Pipeline Adapted for Genomic Sequence Discovery of Germline-Restricted Sequence in Zebra Finch, Taeniopygia guttata. Genome Biol Evol 2021; 13:evab088. [PMID: 33905492 PMCID: PMC8245190 DOI: 10.1093/gbe/evab088] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2021] [Indexed: 11/24/2022] Open
Abstract
Songbirds have an unusual genomic element which is only found in their germline cells, known as the germline-restricted chromosome (GRC). Because germ cells contain both GRC and non-GRC (or A-chromosome) sequences, confidently identifying the GRC-derived elements from genome assemblies has proven difficult. Here, we introduce a new application of a transcriptomic method for GRC sequence identification. By adapting the Stringtie/Ballgown pipeline to use somatic and germline DNA reads, we find that the ratio of fragments per kilobase per million mapped reads can be used to confidently assign contigs to the GRC. Using this comparative coverage analysis, we successfully identify 733 contigs as high confidence GRC sequences (720 newly identified in this study) and 51 contigs which were validated using quantitative polymerase chain reaction. We also identified two new GRC genes, one hypothetical protein and one gene encoding an RNase H-like domain, and placed 16 previously identified but unplaced genes onto their host contigs. With the current focus on sequencing GRCs from different songbirds, our work adds to the genomic toolkit to identify GRC elements, and we provide a detailed protocol and GitHub repository at https://github.com/brachtlab/Comparative_Coverage_Analysis (last accessed May 12, 2021).
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Affiliation(s)
- Kathryn C Asalone
- Department of Biology, American University, Washington, District of Columbia, USA
| | - Ajuni K Takkar
- Department of Biology, American University, Washington, District of Columbia, USA
| | - Colin J Saldanha
- Department of Neuroscience, American University, Washington, District of Columbia, USA
- Center for Neuroscience and Behavior, American University, Washington, District of Columbia, USA
| | - John R Bracht
- Department of Biology, American University, Washington, District of Columbia, USA
- Center for Neuroscience and Behavior, American University, Washington, District of Columbia, USA
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18
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Abstract
Over the last few decades, an increasing number of vertebrate taxa have been identified that undergo programmed genome rearrangement, or programmed DNA loss, during development. In these organisms, the genome of germ cells is often reproducibly different from the genome of all other cells within the body. Although we clearly have not identified all vertebrate taxa that undergo programmed genome loss, the list of species known to undergo loss now represents ∼10% of vertebrate species, including several basally diverging lineages. Recent studies have shed new light on the targets and mechanisms of DNA loss and their association with canonical modes of DNA silencing. Ultimately, expansion of these studies into a larger collection of taxa will aid in reconstructing patterns of shared/independent ancestry of programmed DNA loss in the vertebrate lineage, as well as more recent evolutionary events that have shaped the structure and content of eliminated DNA.
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Affiliation(s)
- Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA; , ,
| | | | - Cody Saraceno
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA; , ,
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19
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Heterochiasmy and Sexual Dimorphism: The Case of the Barn Swallow ( Hirundo rustica, Hirundinidae, Aves). Genes (Basel) 2020; 11:genes11101119. [PMID: 32987748 PMCID: PMC7650650 DOI: 10.3390/genes11101119] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 11/23/2022] Open
Abstract
Heterochiasmy, a sex-based difference in recombination rate, has been detected in many species of animals and plants. Several hypotheses about evolutionary causes of heterochiasmy were proposed. However, there is a shortage of empirical data. In this paper, we compared recombination related traits in females and males of the barn swallow Hirundo rustica (Linnaeus, 1758), the species under strong sexual selection, with those in the pale martin Riparia diluta (Sharpe and Wyatt, 1893), a related and ecologically similar species with the same karyotype (2N = 78), but without obvious sexual dimorphism. Recombination traits were examined in pachytene chromosome spreads prepared from spermatocytes and oocytes. Synaptonemal complexes and mature recombination nodules were visualized with antibodies to SYCP3 and MLH1 proteins, correspondingly. Recombination rate was significantly higher (p = 0.0001) in barn swallow females (55.6 ± 6.3 recombination nodules per autosomal genome), caused by the higher number of nodules at the macrochromosomes, than in males (49.0 ± 4.5). They also showed more even distribution of recombination nodules along the macrochromosomes. At the same time, in the pale martin, sexual differences in recombination rate and distributions were rather small. We speculate that an elevated recombination rate in the female barn swallows might have evolved as a compensatory reaction to runaway sexual selection in males.
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