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Barley AJ, Cole CJ. Speciation by hybridization: the mind-boggling nature, educational, and research value of the largest group of unisexual vertebrates. Bioscience 2025; 75:331-341. [PMID: 40276476 PMCID: PMC12016801 DOI: 10.1093/biosci/biaf010] [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: 08/22/2024] [Revised: 01/12/2025] [Accepted: 01/17/2025] [Indexed: 04/26/2025] Open
Abstract
Thirteen species of North American lizards are remarkable because only females exist, which reproduce by cloning unfertilized eggs. Their closest relatives reproduce sexually, with eggs fertilized by sperm from males, as in most vertebrates. The unisexual species originated through hybridization, dispensing with sex and males in a single generation. These lizards hold tremendous potential in science education as a fascinating model for learning about fundamental biological concepts, and in research for developing knowledge with medical applications for reproductive biology, embryonic development, and genetic interactions. These lizards maintain genome integrity in a hybrid state in which recombination is absent, but do not suffer from conditions or disorders such as Down's Syndrome or cancer that are caused by aneuploidy in humans. The multifarious impacts of hybridization on the diversity of species in this group present an exceptional opportunity to deepen understanding of the complicated process of evolutionary diversification.
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Affiliation(s)
- Anthony J Barley
- School of Mathematical and Natural Sciences, Arizona State University–West Valley, Glendale, Arizona 85306, United States
| | - Charles J Cole
- Department of Herpetology, American Museum of Natural History, New York, New York 10024, United States
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Boroń A, Grabowska A, Jablonska O, Kirtiklis L, Duda S, Juchno D. Chromosomal rDNA Distribution Patterns in Clonal Cobitis Triploid Hybrids (Teleostei, Cobitidae): Insights into Parental Genomic Contributions. Genes (Basel) 2025; 16:68. [PMID: 39858616 PMCID: PMC11765124 DOI: 10.3390/genes16010068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2024] [Revised: 12/31/2024] [Accepted: 01/05/2025] [Indexed: 01/27/2025] Open
Abstract
Background: Interspecific hybridization between relative species Cobitis taenia (with a diploid genome designated as TT), Cobitis elongatoides (EE) and Cobitis tanaitica (NN) and the successive polyploidization with transitions from sexuality to asexuality experienced by triploid Cobitis hybrids likely influence their chromosomal rearrangements, including rearrangements of ribosomal DNA (rDNA) distribution patterns. Previously, we documented distinct karyotypic differences: C. elongatoides exhibited bi-armed chromosomes while C. taenia showed uni-armed chromosomes with rDNA-positive hybridization signals, respectively. Methods: In this study, fluorescence in situ hybridization (FISH) with 5S rDNA and 28S rDNA probes was used to analyze and compare chromosomal distribution patterns of rDNAs in clonally reproduced triploid Cobitis hybrids of different genomic constitutions ETT, ETN, EEN and EET (referred to using acronyms denoting the haploid genomes of their parent species), and their parental species. Results:Cobitis triploid hybrids exhibited intermediate karyotypes with ribosome synthesis sites on chromosomes inherited from both parents, showing no evidence of nucleolar dominance. The rDNA pattern derived from the C. elongatoides genome was more stable in the hybrids' karyotypes. Two and one submetacentric chromosomes with co-localized rDNAs were effective markers to ascertain C. elongatoides diploid (EE) and haploid (E) genomes within the genome of triploid hybrids, respectively. Fewer 5S rDNA loci were observed in diploid (TT) and haploid (T) chromosome sets from C. taenia in ETT and EET females. C. taenia and C. tanaitica exhibited similar rDNA distribution patterns. Conclusions: The karyotypes of triploid Cobitis hybrids reflect the genomic contributions of their parental species. Variability in rDNA distribution patterns suggests complex genomic interactions in Cobitis hybrids resulting from polyploidization and hybridization, potentially influencing their reproductive potential.
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Affiliation(s)
| | | | | | - Lech Kirtiklis
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; (A.B.); (A.G.); (O.J.); (S.D.); (D.J.)
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Unal Karakus S, Gaffaroğlu M, Karasu Ayata M, Knytl M. A Detailed Karyological Investigation of three Endemic Cobitis Linnaeus, 1758 Species (Teleostei, Cobitidae) in Anatolia, Türkiye. Cytogenet Genome Res 2024; 164:243-256. [PMID: 39622218 PMCID: PMC11825084 DOI: 10.1159/000542804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Accepted: 11/22/2024] [Indexed: 01/11/2025] Open
Abstract
INTRODUCTION Comparative cytogenetics is a vital approach for diagnosing chromosome abnormalities and identifying species-specific patterns. In this study, chromosomal analysis of three Anatolian endemic Cobitis species was performed: Cobitis bilseli, C. fahireae, and C. turcica. METHODS Conventional cytogenetic techniques such as Giemsa staining, C-banding, and Ag-NOR staining were applied, followed by measurements of chromosome arm lengths including analysis of the measured data. RESULTS The diploid chromosome number, 2n = 50, was determined for all three species. The karyotype formulas were as follows: four pairs of metacentric, 5 pairs of submetacentric, and 16 pairs of subtelo-telocentric chromosomes in C. bilseli; 11 pairs of metacentric, 7 pairs of submetacentric, and 7 pairs of subtelo-telocentric chromosomes in C. fahireae; and 4 pairs of metacentric, 4 pairs of submetacentric, and 17 pairs of subtelo-telocentric chromosomes in C. turcica. Dark C-bands were observed on the pericentromeres of nearly all chromosomes in C. bilseli and C. turcica, whereas light C-bands appeared on the pericentromeres of some chromosomes in C. fahireae. Silver-stained metaphases revealed signals on the short arm of a submetacentric chromosome pair in C. fahireae (each homologous chromosome carries one signal), while in C. bilseli and C. turcica, Ag-NOR signals were detected on the long arm of a single metacentric chromosome (only one homologous chromosome carries the signal, and the signal-carrying chromosome is the largest chromosome in the karyotype). CONCLUSION This study provides new cytogenetic data consistent with the phylogenetic distances between the studied species, indicating that pericentric inversions and/or translocations govern the formation of Cobitis karyotypes. INTRODUCTION Comparative cytogenetics is a vital approach for diagnosing chromosome abnormalities and identifying species-specific patterns. In this study, chromosomal analysis of three Anatolian endemic Cobitis species was performed: Cobitis bilseli, C. fahireae, and C. turcica. METHODS Conventional cytogenetic techniques such as Giemsa staining, C-banding, and Ag-NOR staining were applied, followed by measurements of chromosome arm lengths including analysis of the measured data. RESULTS The diploid chromosome number, 2n = 50, was determined for all three species. The karyotype formulas were as follows: four pairs of metacentric, 5 pairs of submetacentric, and 16 pairs of subtelo-telocentric chromosomes in C. bilseli; 11 pairs of metacentric, 7 pairs of submetacentric, and 7 pairs of subtelo-telocentric chromosomes in C. fahireae; and 4 pairs of metacentric, 4 pairs of submetacentric, and 17 pairs of subtelo-telocentric chromosomes in C. turcica. Dark C-bands were observed on the pericentromeres of nearly all chromosomes in C. bilseli and C. turcica, whereas light C-bands appeared on the pericentromeres of some chromosomes in C. fahireae. Silver-stained metaphases revealed signals on the short arm of a submetacentric chromosome pair in C. fahireae (each homologous chromosome carries one signal), while in C. bilseli and C. turcica, Ag-NOR signals were detected on the long arm of a single metacentric chromosome (only one homologous chromosome carries the signal, and the signal-carrying chromosome is the largest chromosome in the karyotype). CONCLUSION This study provides new cytogenetic data consistent with the phylogenetic distances between the studied species, indicating that pericentric inversions and/or translocations govern the formation of Cobitis karyotypes.
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Affiliation(s)
- Sevgi Unal Karakus
- Department of Molecular Biology and Genetics, Faculty of Science, Bartin University, Bartin, Turkey
| | - Muhammet Gaffaroğlu
- Department of Molecular Biology and Genetics, Faculty of Science and Arts, Kirsehir Ahi Evran University, Kirsehir, Turkey
| | - Muradiye Karasu Ayata
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Kirsehir Ahi Evran University, Kirsehir, Turkey
| | - Martin Knytl
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Biology, McMaster University, Hamilton, ON, Canada
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Dedukh D, Marta A, Myung RY, Ko MH, Choi DS, Won YJ, Janko K. A cyclical switch of gametogenic pathways in hybrids depends on the ploidy level. Commun Biol 2024; 7:424. [PMID: 38589507 PMCID: PMC11001910 DOI: 10.1038/s42003-024-05948-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 02/21/2024] [Indexed: 04/10/2024] Open
Abstract
The cellular and molecular mechanisms governing sexual reproduction are conserved across eukaryotes. Nevertheless, hybridization can disrupt these mechanisms, leading to asexual reproduction, often accompanied by polyploidy. In this study, we investigate how ploidy level and ratio of parental genomes in hybrids affect their reproductive mode. We analyze the gametogenesis of sexual species and their diploid and triploid hybrids from the freshwater fish family Cobitidae, using newly developed cytogenetic markers. We find that diploid hybrid females possess oogonia and oocytes with original (diploid) and duplicated (tetraploid) ploidy. Diploid oocytes cannot progress beyond pachytene due to aberrant pairing. However, tetraploid oocytes, which emerge after premeiotic genome endoreplication, exhibit normal pairing and result in diploid gametes. Triploid hybrid females possess diploid, triploid, and haploid oogonia and oocytes. Triploid and haploid oocytes cannot progress beyond pachytene checkpoint due to aberrant chromosome pairing, while diploid oocytes have normal pairing in meiosis, resulting in haploid gametes. Diploid oocytes emerge after premeiotic elimination of a single-copied genome. Triploid hybrid males are sterile due to aberrant pairing and the failure of chromosomal segregation during meiotic divisions. Thus, changes in ploidy and genome dosage may lead to cyclical alteration of gametogenic pathways in hybrids.
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Affiliation(s)
- Dmitrij Dedukh
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics of the CAS, Liběchov, Czech Republic.
| | - Anatolie Marta
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics of the CAS, Liběchov, Czech Republic
| | - Ra-Yeon Myung
- Division of EcoScience, Ewha Womans University, Seoul, South Korea
| | | | - Da-Song Choi
- Division of EcoScience, Ewha Womans University, Seoul, South Korea
| | - Yong-Jin Won
- Division of EcoScience, Ewha Womans University, Seoul, South Korea
| | - Karel Janko
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics of the CAS, Liběchov, Czech Republic.
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.
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Dudzik A, Dedukh D, Crochet PA, Rozenblut-Kościsty B, Rybka H, Doniol-Valcroze P, Choleva L, Ogielska M, Chmielewska M. Cytogenetics of the Hybridogenetic Frog Pelophylax grafi and Its Parental Species Pelophylax perezi. Genome Biol Evol 2023; 15:evad215. [PMID: 38015654 PMCID: PMC10715190 DOI: 10.1093/gbe/evad215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 11/10/2023] [Accepted: 11/19/2023] [Indexed: 11/30/2023] Open
Abstract
Hybrid taxa from the genus Pelophylax can propagate themselves in a modified way of sexual reproduction called hybridogenesis ensuring the formation of clonal gametes containing the genome of only one parental (host) species. Pelophylax grafi from South-Western Europe is a hybrid composed of P. ridibundus and P. perezi genomes and it lives with a host species P. perezi (P-G system). Yet it is unknown, whether non-Mendelian inheritance is fully maintained in such populations. In this study, we characterize P. perezi and P. grafi somatic karyotypes by using comparative genomic hybridization, genomic in situ hybridization, fluorescent in situ hybridization, and actinomycin D-DAPI. Here, we show the homeology of P. perezi and P. grafi somatic karyotypes to other Pelophylax taxa with 2n = 26 and equal contribution of ridibundus and perezi chromosomes in P. grafi which supports F1 hybrid genome constitution as well as a hemiclonal genome inheritance. We show that ridibundus chromosomes have larger regions of interstitial (TTAGGG)n repeats flanking the nucleolus organizing region on chromosome no. 10 and a high quantity of AT pairs in the centromeric regions. In P. perezi, we found species-specific sequences in metaphase chromosomes and marker structures in lampbrush chromosomes. Pericentromeric RrS1 repeat sequence was present in perezi and ridibundus chromosomes, but the blocks were stronger in ridibundus. Various cytogenetic techniques applied to the P-G system provide genome discrimination between ridibundus and perezi chromosomal sets. They could be used in studies of germ-line cells to explain patterns of clonal gametogenesis in P. grafi and broaden the knowledge about reproductive strategies in hybrid animals.
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Affiliation(s)
- Anna Dudzik
- Amphibian Biology Group, Department of Evolutionary Biology and Conservation of Vertebrates, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - Dmitrij Dedukh
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | | | - Beata Rozenblut-Kościsty
- Amphibian Biology Group, Department of Evolutionary Biology and Conservation of Vertebrates, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - Hanna Rybka
- Amphibian Biology Group, Department of Evolutionary Biology and Conservation of Vertebrates, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | | | - Lukáš Choleva
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Maria Ogielska
- Amphibian Biology Group, Department of Evolutionary Biology and Conservation of Vertebrates, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - Magdalena Chmielewska
- Amphibian Biology Group, Department of Evolutionary Biology and Conservation of Vertebrates, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
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Marta A, Tichopád T, Bartoš O, Klíma J, Shah MA, Bohlen VŠ, Bohlen J, Halačka K, Choleva L, Stöck M, Dedukh D, Janko K. Genetic and karyotype divergence between parents affect clonality and sterility in hybrids. eLife 2023; 12:RP88366. [PMID: 37930936 PMCID: PMC10627513 DOI: 10.7554/elife.88366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
Asexual reproduction can be triggered by interspecific hybridization, but its emergence is supposedly rare, relying on exceptional combinations of suitable genomes. To examine how genomic and karyotype divergence between parental lineages affect the incidence of asexual gametogenesis, we experimentally hybridized fishes (Cobitidae) across a broad phylogenetic spectrum, assessed by whole exome data. Gametogenic pathways generally followed a continuum from sexual reproduction in hybrids between closely related evolutionary lineages to sterile or inviable crosses between distant lineages. However, most crosses resulted in a combination of sterile males and asexually reproducing females. Their gametes usually experienced problems in chromosome pairing, but females also produced a certain proportion of oocytes with premeiotically duplicated genomes, enabling their development into clonal eggs. Interspecific hybridization may thus commonly affect cell cycles in a specific way, allowing the formation of unreduced oocytes. The emergence of asexual gametogenesis appears tightly linked to hybrid sterility and constitutes an inherent part of the extended speciation continuum.
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Affiliation(s)
- Anatolie Marta
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics of the CASLibechovCzech Republic
| | - Tomáš Tichopád
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics of the CASLibechovCzech Republic
| | - Oldřich Bartoš
- Military Health Institute, Military Medical AgencyPragueCzech Republic
| | - Jiří Klíma
- Laboratory of Cell Regeneration and Plasticity, Institute of Animal Physiology and Genetics of the CASLiběchovCzech Republic
| | - Mujahid Ali Shah
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in Ceske BudejoviceVodnanyCzech Republic
| | - Vendula Šlechtová Bohlen
- Laboratory of Fish genetics, Institute of Animal Physiology and Genetics of the CASLiběchovCzech Republic
| | - Joerg Bohlen
- Laboratory of Fish genetics, Institute of Animal Physiology and Genetics of the CASLiběchovCzech Republic
| | - Karel Halačka
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics of the CASLibechovCzech Republic
| | - Lukáš Choleva
- Department of Biology and Ecology, Faculty of Science, University of OstravaOstravaCzech Republic
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGBBerlinGermany
| | - Dmitrij Dedukh
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics of the CASLibechovCzech Republic
| | - Karel Janko
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics of the CASLibechovCzech Republic
- Department of Biology and Ecology, Faculty of Science, University of OstravaOstravaCzech Republic
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Bartoš O, Bohlen J, Šlechtová VB, Kočí J, Röslein J, Janko K. Sequence capture: Obsolete or irreplaceable? A thorough validation across phylogenetic distances and its applicability to hybrids and allopolyploids. Mol Ecol Resour 2023. [PMID: 37122140 DOI: 10.1111/1755-0998.13806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 05/02/2023]
Abstract
As whole-genome sequencing has become pervasive, some have suggested that reduced genomic representation approaches, for example, sequence capture, are becoming obsolete. In the present study, we argue that these techniques still provide excellent tools in terms of price and quality of data as well as in their ability to provide markers with specific features, as required, for example, in phylogenomics. A potential drawback of the wide-scale application of reduced representation approaches could be their drop in efficiency with increasing phylogenetic distance from the reference species. While some studies have focused on the degree and performance of reduced representation techniques in such situations, to our knowledge, none of them evaluated their applicability to inter-specific hybrids and polyploids. This highlights a significant gap in current knowledge since there is increasing evidence for the frequent occurrence of natural hybrids and polyploids, as well as for the major importance of both phenomena in evolution. The main aim of the present study was to carry out a thorough validation of SEQcap applicability to (1) a set of non-model taxa with a wide range of phylogenetic relatedness and (2) inter-specific hybrids of various ploidies and genomic compositions. Considering the latter point, we especially focused on mechanisms causing allelic bias and consequent allelic dropout, as these could have confounding effects with respect to the evolutionary genomic dynamics of hybrids, especially in asexuals, which virtually reproduce as a frozen F1 generation.
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Affiliation(s)
- Oldřich Bartoš
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Libechov, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jörg Bohlen
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Libechov, Czech Republic
| | - Vendula Bohlen Šlechtová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Libechov, Czech Republic
| | - Jan Kočí
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Libechov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jan Röslein
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Libechov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, Libechov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
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Janko K, Bartoš O, Kočí J, Roslein J, Drdová EJ, Kotusz J, Eisner J, Mokrejš M, Štefková-Kašparová E. Genome Fractionation and Loss of Heterozygosity in Hybrids and Polyploids: Mechanisms, Consequences for Selection, and Link to Gene Function. Mol Biol Evol 2021; 38:5255-5274. [PMID: 34410426 PMCID: PMC8662595 DOI: 10.1093/molbev/msab249] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Hybridization and genome duplication have played crucial roles in the evolution of many animal and plant taxa. The subgenomes of parental species undergo considerable changes in hybrids and polyploids, which often selectively eliminate segments of one subgenome. However, the mechanisms underlying these changes are not well understood, particularly when the hybridization is linked with asexual reproduction that opens up unexpected evolutionary pathways. To elucidate this problem, we compared published cytogenetic and RNAseq data with exome sequences of asexual diploid and polyploid hybrids between three fish species; Cobitis elongatoides, C. taenia, and C. tanaitica. Clonal genomes remained generally static at chromosome-scale levels but their heterozygosity gradually deteriorated at the level of individual genes owing to allelic deletions and conversions. Interestingly, the impact of both processes varies among animals and genomic regions depending on ploidy level and the properties of affected genes. Namely, polyploids were more tolerant to deletions than diploid asexuals where conversions prevailed, and genomic restructuring events accumulated preferentially in genes characterized by high transcription levels and GC-content, strong purifying selection and specific functions like interacting with intracellular membranes. Although hybrids were phenotypically more similar to C. taenia, we found that they preferentially retained C. elongatoides alleles. This demonstrates that favored subgenome is not necessarily the transcriptionally dominant one. This study demonstrated that subgenomes in asexual hybrids and polyploids evolve under a complex interplay of selection and several molecular mechanisms whose efficiency depends on the organism's ploidy level, as well as functional properties and parental ancestry of the genomic region.
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Affiliation(s)
- Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Oldřich Bartoš
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Kočí
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jan Roslein
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Edita Janková Drdová
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jan Kotusz
- Museum of Natural History, University of Wroclaw, Wroclaw, Poland
| | - Jan Eisner
- Department of Mathematics, Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
| | - Martin Mokrejš
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- IT4Innovations, VŠB—Technical University of Ostrava, Ostrava-Poruba, Czech Republic
| | - Eva Štefková-Kašparová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Liběchov, Czech Republic
- Department of Genetics and Breeding, FAFNR, Czech University of Life Sciences Prague, Czech Republic
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9
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Dedukh D, Marta A, Janko K. Challenges and Costs of Asexuality: Variation in Premeiotic Genome Duplication in Gynogenetic Hybrids from Cobitis taenia Complex. Int J Mol Sci 2021; 22:ijms222212117. [PMID: 34830012 PMCID: PMC8622741 DOI: 10.3390/ijms222212117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/25/2021] [Accepted: 11/04/2021] [Indexed: 02/07/2023] Open
Abstract
The transition from sexual reproduction to asexuality is often triggered by hybridization. The gametogenesis of many hybrid asexuals involves premeiotic genome endoreplication leading to bypass hybrid sterility and forming clonal gametes. However, it is still not clear when endoreplication occurs, how many gonial cells it affects and whether its rate differs among clonal lineages. Here, we investigated meiotic and premeiotic cells of diploid and triploid hybrids of spined loaches (Cypriniformes: Cobitis) that reproduce by gynogenesis. We found that in naturally and experimentally produced F1 hybrids asexuality is achieved by genome endoreplication, which occurs in gonocytes just before entering meiosis or, rarely, one or a few divisions before meiosis. However, genome endoreplication was observed only in a minor fraction of the hybrid's gonocytes, while the vast majority of gonocytes were unable to duplicate their genomes and consequently could not proceed beyond pachytene due to defects in bivalent formation. We also noted that the rate of endoreplication was significantly higher among gonocytes of hybrids from natural clones than of experimentally produced F1 hybrids. Thus, asexuality and hybrid sterility are intimately related phenomena and the transition from sexual reproduction to asexuality must overcome significant problems with genome incompatibilities with a possible impact on reproductive potential.
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Affiliation(s)
- Dmitrij Dedukh
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the CAS, Rumburská 89, 277 21 Liběchov, Czech Republic;
- Correspondence: (D.D.); (K.J.)
| | - Anatolie Marta
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the CAS, Rumburská 89, 277 21 Liběchov, Czech Republic;
- Department of Zoology, Faculty of Science, Charles University in Prague, 128 00 Prague, Czech Republic
- Institute of Zoology, MD-2028, Academiei 1, 2001 Chisinau, Moldova
| | - Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics of the CAS, Rumburská 89, 277 21 Liběchov, Czech Republic;
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
- Correspondence: (D.D.); (K.J.)
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Stöck M, Dedukh D, Reifová R, Lamatsch DK, Starostová Z, Janko K. Sex chromosomes in meiotic, hemiclonal, clonal and polyploid hybrid vertebrates: along the 'extended speciation continuum'. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200103. [PMID: 34304588 PMCID: PMC8310718 DOI: 10.1098/rstb.2020.0103] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2021] [Indexed: 12/15/2022] Open
Abstract
We review knowledge about the roles of sex chromosomes in vertebrate hybridization and speciation, exploring a gradient of divergences with increasing reproductive isolation (speciation continuum). Under early divergence, well-differentiated sex chromosomes in meiotic hybrids may cause Haldane-effects and introgress less easily than autosomes. Undifferentiated sex chromosomes are more susceptible to introgression and form multiple (or new) sex chromosome systems with hardly predictable dominance hierarchies. Under increased divergence, most vertebrates reach complete intrinsic reproductive isolation. Slightly earlier, some hybrids (linked in 'the extended speciation continuum') exhibit aberrant gametogenesis, leading towards female clonality. This facilitates the evolution of various allodiploid and allopolyploid clonal ('asexual') hybrid vertebrates, where 'asexuality' might be a form of intrinsic reproductive isolation. A comprehensive list of 'asexual' hybrid vertebrates shows that they all evolved from parents with divergences that were greater than at the intraspecific level (K2P-distances of greater than 5-22% based on mtDNA). These 'asexual' taxa inherited genetic sex determination by mostly undifferentiated sex chromosomes. Among the few known sex-determining systems in hybrid 'asexuals', female heterogamety (ZW) occurred about twice as often as male heterogamety (XY). We hypothesize that pre-/meiotic aberrations in all-female ZW-hybrids present Haldane-effects promoting their evolution. Understanding the preconditions to produce various clonal or meiotic allopolyploids appears crucial for insights into the evolution of sex, 'asexuality' and polyploidy. 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)
- 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
| | - Dmitrij Dedukh
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, 277 21 Libechov, Czech Republic
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 00, Czech Republic
| | - Dunja K. Lamatsch
- Research Department for Limnology, University of Innsbruck, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Zuzana Starostová
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, Prague 2, 128 00, Czech Republic
| | - Karel Janko
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, 277 21 Libechov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 701 03 Ostrava, Czech Republic
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11
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Majtánová Z, Dedukh D, Choleva L, Adams M, Ráb P, Unmack PJ, Ezaz T. Uniparental Genome Elimination in Australian Carp Gudgeons. Genome Biol Evol 2021; 13:6137838. [PMID: 33591327 PMCID: PMC8245195 DOI: 10.1093/gbe/evab030] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2021] [Indexed: 12/15/2022] Open
Abstract
Metazoans usually reproduce sexually, blending the unique identity of parental genomes for the next generation through functional crossing-over and recombination in meiosis. However, some metazoan lineages have evolved reproductive systems where offspring are either full (clonal) or partial (hemiclonal) genetic replicas. In the latter group, the process of uniparental genome elimination selectively eliminates either the maternal or paternal genome from germ cells, and only one parental genome is selected for transmission. Although fairly common in plants, hybridogenesis (i.e., clonal haploidization via chromosome elimination) remains a poorly understood process in animals. Here, we explore the proximal cytogenomic mechanisms of somatic and germ cell chromosomes in sexual and hybrid genotypes of Australian carp gudgeons (Hypseleotris) by tracing the fate of each set during mitosis (in somatic tissues) and meiosis (in gonads). Our comparative study of diploid hybrid and sexual individuals revealed visually functional gonads in male and female hybrid genotypes and generally high karyotype variability, although the number of chromosome arms remains constant. Our results delivered direct evidence for classic hybridogenesis as a reproductive mode in carp gudgeons. Two parental sets with integral structure in the hybrid soma (the F1 constitution) contrasted with uniparental chromosomal inheritance detected in gonads. The inheritance mode happens through premeiotic genome duplication of the parental genome to be transmitted, whereas the second parental genome is likely gradually eliminated already in juvenile individuals. The role of metacentric chromosomes in hybrid evolution is also discussed.
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Affiliation(s)
- Zuzana Majtánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Dmitrij Dedukh
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Lukáš Choleva
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic.,Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Mark Adams
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA, Australia.,School of Biological Sciences, The University of Adelaide, SA, Australia
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Peter J Unmack
- Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra, ACT, Australia
| | - Tariq Ezaz
- Centre for Conservation Ecology and Genetics, Institute for Applied Ecology, University of Canberra, ACT, Australia
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12
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Comparative analysis of the morphology, karyotypes and biochemical composition of muscle in Siniperca chuatsi, Siniperca scherzeri and the F1 hybrid (S. chuatsi ♀ × S. scherzeri ♂). AQUACULTURE AND FISHERIES 2020. [DOI: 10.1016/j.aaf.2020.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Kočí J, Röslein J, Pačes J, Kotusz J, Halačka K, Koščo J, Fedorčák J, Iakovenko N, Janko K. No evidence for accumulation of deleterious mutations and fitness degradation in clonal fish hybrids: Abandoning sex without regrets. Mol Ecol 2020; 29:3038-3055. [PMID: 32627290 PMCID: PMC7540418 DOI: 10.1111/mec.15539] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/18/2020] [Accepted: 06/22/2020] [Indexed: 02/07/2023]
Abstract
Despite its inherent costs, sexual reproduction is ubiquitous in nature, and the mechanisms to protect it from a competitive displacement by asexuality remain unclear. Popular mutation-based explanations, like the Muller's ratchet and the Kondrashov's hatchet, assume that purifying selection may not halt the accumulation of deleterious mutations in the nonrecombining genomes, ultimately leading to their degeneration. However, empirical evidence is scarce and it remains particularly unclear whether mutational degradation proceeds fast enough to ensure the decay of clonal organisms and to prevent them from outcompeting their sexual counterparts. To test this hypothesis, we jointly analysed the exome sequences and the fitness-related phenotypic traits of the sexually reproducing fish species and their clonal hybrids, whose evolutionary ages ranged from F1 generations to 300 ky. As expected, mutations tended to accumulate in the clonal genomes in a time-dependent manner. However, contrary to the predictions, we found no trend towards increased nonsynonymity of mutations acquired by clones, nor higher radicality of their amino acid substitutions. Moreover, there was no evidence for fitness degeneration in the old clones compared with that in the younger ones. In summary, although an efficacy of purifying selection may still be reduced in the asexual genomes, our data indicate that its efficiency is not drastically decreased. Even the oldest investigated clone was found to be too young to suffer fitness consequences from a mutation accumulation. This suggests that mechanisms other than mutation accumulation may be needed to explain the competitive advantage of sex in the short term.
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Affiliation(s)
- Jan Kočí
- Department of Biology and Ecology, University of Ostrava, Ostrava, Czechia.,Institute of Animal Physiology and Genetics, Czech Academy of Science, Liběchov, Czechia
| | - Jan Röslein
- Department of Biology and Ecology, University of Ostrava, Ostrava, Czechia.,Institute of Animal Physiology and Genetics, Czech Academy of Science, Liběchov, Czechia
| | - Jan Pačes
- Institute of Animal Physiology and Genetics, Czech Academy of Science, Liběchov, Czechia.,Institute of Molecular Genetics, Czech Academy of Science, Prague, Czechia
| | - Jan Kotusz
- Museum of Natural History, University of Wrocław, Wrocław, Poland
| | - Karel Halačka
- Institute of Vertebrate Biology, Czech Academy of Science, Brno, Czechia
| | - Ján Koščo
- Department of Ecology, University of Prešov, Prešov, Slovakia
| | - Jakub Fedorčák
- Department of Ecology, University of Prešov, Prešov, Slovakia
| | - Nataliia Iakovenko
- Department of Biology and Ecology, University of Ostrava, Ostrava, Czechia.,Institute of Animal Physiology and Genetics, Czech Academy of Science, Liběchov, Czechia
| | - Karel Janko
- Department of Biology and Ecology, University of Ostrava, Ostrava, Czechia.,Institute of Animal Physiology and Genetics, Czech Academy of Science, Liběchov, Czechia
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14
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Dalziel AC, Tirbhowan S, Drapeau HF, Power C, Jonah LS, Gbotsyo YA, Dion‐Côté A. Using asexual vertebrates to study genome evolution and animal physiology: Banded ( Fundulus diaphanus) x Common Killifish ( F. heteroclitus) hybrid lineages as a model system. Evol Appl 2020; 13:1214-1239. [PMID: 32684956 PMCID: PMC7359844 DOI: 10.1111/eva.12975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 12/27/2022] Open
Abstract
Wild, asexual, vertebrate hybrids have many characteristics that make them good model systems for studying how genomes evolve and epigenetic modifications influence animal physiology. In particular, the formation of asexual hybrid lineages is a form of reproductive incompatibility, but we know little about the genetic and genomic mechanisms by which this mode of reproductive isolation proceeds in animals. Asexual lineages also provide researchers with the ability to produce genetically identical individuals, enabling the study of autonomous epigenetic modifications without the confounds of genetic variation. Here, we briefly review the cellular and molecular mechanisms leading to asexual reproduction in vertebrates and the known genetic and epigenetic consequences of the loss of sex. We then specifically discuss what is known about asexual lineages of Fundulus diaphanus x F. heteroclitus to highlight gaps in our knowledge of the biology of these clones. Our preliminary studies of F. diaphanus and F. heteroclitus karyotypes from Porter's Lake (Nova Scotia, Canada) agree with data from other populations, suggesting a conserved interspecific chromosomal arrangement. In addition, genetic analyses suggest that: (a) the same major clonal lineage (Clone A) of F. diaphanus x F. heteroclitus has remained dominant over the past decade, (b) some minor clones have also persisted, (c) new clones may have recently formed, and iv) wild clones still mainly descend from F. diaphanus ♀ x F. heteroclitus ♂ crosses (96% in 2017-2018). These data suggest that clone formation may be a relatively rare, but continuous process, and there are persistent environmental or genetic factors causing a bias in cross direction. We end by describing our current research on the genomic causes and consequences of a transition to asexuality and the potential physiological consequences of epigenetic variation.
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Affiliation(s)
| | - Svetlana Tirbhowan
- Department of BiologySaint Mary's UniversityHalifaxNSCanada
- Département de biologieUniversité de MonctonMonctonNBCanada
| | | | - Claude Power
- Département de biologieUniversité de MonctonMonctonNBCanada
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15
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Parthenogenesis as a Solution to Hybrid Sterility: The Mechanistic Basis of Meiotic Distortions in Clonal and Sterile Hybrids. Genetics 2020; 215:975-987. [PMID: 32518062 PMCID: PMC7404241 DOI: 10.1534/genetics.119.302988] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 06/03/2020] [Indexed: 11/25/2022] Open
Abstract
Hybrid sterility is a hallmark of speciation, but the underlying molecular mechanisms remain poorly understood. Here, we report that speciation may regularly proceed through a stage at which gene flow is completely interrupted, but hybrid sterility occurs only in male hybrids whereas female hybrids reproduce asexually. We analyzed gametogenic pathways in hybrids between the fish species Cobitis elongatoides and C. taenia, and revealed that male hybrids were sterile owing to extensive asynapsis and crossover reduction among heterospecific chromosomal pairs in their gametes, which was subsequently followed by apoptosis. We found that polyploidization allowed pairing between homologous chromosomes and therefore partially rescued the bivalent formation and crossover rates in triploid hybrid males. However, it was not sufficient to overcome sterility. In contrast, both diploid and triploid hybrid females exhibited premeiotic genome endoreplication, thereby ensuring proper bivalent formation between identical chromosomal copies. This endoreplication ultimately restored female fertility but it simultaneously resulted in the obligate production of clonal gametes, preventing any interspecific gene flow. In conclusion, we demonstrate that the emergence of asexuality can remedy hybrid sterility in a sex-specific manner and contributes to the speciation process.
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16
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Marta A, Dedukh D, Bartoš O, Majtánová Z, Janko K. Cytogenetic Characterization of Seven Novel satDNA Markers in Two Species of Spined Loaches ( Cobitis) and Their Clonal Hybrids. Genes (Basel) 2020; 11:genes11060617. [PMID: 32512717 PMCID: PMC7348982 DOI: 10.3390/genes11060617] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/31/2020] [Accepted: 06/02/2020] [Indexed: 01/11/2023] Open
Abstract
Interspecific hybridization is a powerful evolutionary force. However, the investigation of hybrids requires the application of methodologies that provide efficient and indubitable identification of both parental subgenomes in hybrid individuals. Repetitive DNA, and especially the satellite DNA sequences (satDNA), can rapidly diverge even between closely related species, hence providing a useful tool for cytogenetic investigations of hybrids. Recent progress in whole-genome sequencing (WGS) offers unprecedented possibilities for the development of new tools for species determination, including identification of species-specific satDNA markers. In this study, we focused on spined loaches (Cobitis, Teleostei), a group of fishes with frequent interspecific hybridization. Using the WGS of one species, C. elongatoides, we identified seven satDNA markers, which were mapped by fluorescence in situ hybridization on mitotic and lampbrush chromosomes of C. elongatoides, C. taenia and their triploid hybrids (C. elongatoides × 2C. taenia). Two of these markers were chromosome-specific in both species, one had centromeric localization in multiple chromosomes and four had variable patterns between tested species. Our study provided a novel set of cytogenetic markers for Cobitis species and demonstrated that NGS-based development of satDNA cytogenetic markers may provide a very efficient and easy tool for the investigation of hybrid genomes, cell ploidy, and karyotype evolution.
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Affiliation(s)
- Anatolie Marta
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (D.D.); (O.B.); (Z.M.); (K.J.)
- Department of Zoology, Faculty of Science, Charles University in Prague, 128 00 Prague, Czech Republic
- Institute of Zoology, Academy of Science of Moldova, MD-2028, Academiei 1, 2001 Chisinau, Moldova
- Correspondence:
| | - Dmitry Dedukh
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (D.D.); (O.B.); (Z.M.); (K.J.)
| | - Oldřich Bartoš
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (D.D.); (O.B.); (Z.M.); (K.J.)
- Department of Zoology, Faculty of Science, Charles University in Prague, 128 00 Prague, Czech Republic
| | - Zuzana Majtánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (D.D.); (O.B.); (Z.M.); (K.J.)
| | - Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (D.D.); (O.B.); (Z.M.); (K.J.)
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
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17
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Abstract
Darevskia rock lizards is a unique complex taxa, including more than thirty species, seven of which are parthenogenetic. In mixed populations of Darevskia lizards, tri- and tetraploid forms can be found. The most important issues in the theory of reticulate evolution of Darevskia lizards are the origin of parthenogenetic species and their taxonomic position. However, there is little data on how meiosis proceeds in these species. The present work reports the complex results of cytogenetics in a diploid parthenogenetic species – D. unisexualis. Here we detail the meiotic prophase I progression and the specific features оf mitotic chromosomes organization. The stages of meiosis prophase I were investigated by immunocytochemical analysis of preparations obtained from isolated primary oocytes of D. unisexualis in comparison with maternal species D. raddei nairensis. It has been shown that in D. unisexualis at the leptotene-zygotene stages the axial elements and the synaptonemal complex (SC) form typical “bouquets”. At the pachytene-diplotene stage, 18 autosomal SC-bivalents and thickened asynapted sex Z and w univalents were observed. The presence of SYCP1 protein between the lateral elements of autosomal chromosomes proved the formation of assembled SCs. Comparative genomic hybridization (CGH) on the mitotic metaphase chromosomes of D. unisexualis was carried out using the genomic DNA isolated from the parental species D. raddei nairensis and D. valentini. In the pericentromeric regions of half of the mitotic chromosomes of D. unisexualis, specific regions inherited from maternal species have been found. Following our results, we suggest a model for diploid germ cells formation from diploid oocytes without premeiotic duplication of chromosomes in the oogenesis of diploid parthenogenetic lizards D. unisexualis. Taken as a whole, our findings confirm the hybrid nature of D. unisexualis and shed light on heterozygosity and automixis in diploid parthenogenetic forms.
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18
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Bartoš O, Röslein J, Kotusz J, Paces J, Pekárik L, Petrtýl M, Halačka K, Štefková Kašparová E, Mendel J, Boroń A, Juchno D, Leska A, Jablonska O, Benes V, Šídová M, Janko K. The Legacy of Sexual Ancestors in Phenotypic Variability, Gene Expression, and Homoeolog Regulation of Asexual Hybrids and Polyploids. Mol Biol Evol 2020; 36:1902-1920. [PMID: 31077330 PMCID: PMC6735777 DOI: 10.1093/molbev/msz114] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Hybridization and polyploidization are important evolutionary processes whose impacts range from the alteration of gene expression and phenotypic variation to the triggering of asexual reproduction. We investigated fishes of the Cobitis taenia-elongatoides hybrid complex, which allowed us to disentangle the direct effects of both processes, due to the co-occurrence of parental species with their diploid and triploid hybrids. Employing morphological, ecological, and RNAseq approaches, we investigated the molecular determinants of hybrid and polyploid forms. In contrast with other studies, hybridization and polyploidy induced relatively very little transgressivity. Instead, Cobitis hybrids appeared intermediate with a clear effect of genomic dosing when triploids expressed higher similarity to the parent contributing two genome sets. This dosage effect was symmetric in the germline (oocyte gene expression), interestingly though, we observed an overall bias toward C. taenia in somatic tissues and traits. At the level of individual genes, expression-level dominance vastly prevailed over additivity or transgressivity. Also, trans-regulation of gene expression was less efficient in diploid hybrids than in triploids, where the expression modulation of homoeologs derived from the "haploid" parent was stronger than those derived from the "diploid" parent. Our findings suggest that the apparent intermediacy of hybrid phenotypes results from the combination of individual genes with dominant expression rather than from simple additivity. The efficiency of cross-talk between trans-regulatory elements further appears dosage dependent. Important effects of polyploidization may thus stem from changes in relative concentrations of trans-regulatory elements and their binding sites between hybridizing genomes. Links between gene regulation and asexuality are discussed.
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Affiliation(s)
- Oldřich Bartoš
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic.,Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Röslein
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic.,Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jan Kotusz
- Museum of Natural History, University of Wroclaw, Wroclaw, Poland
| | - Jan Paces
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic.,Institute of Molecular Genetics, Laboratory of Genomics and Bioinformatics, The Czech Academy of Sciences, Prague, Czech Republic
| | - Ladislav Pekárik
- Plant Science and Biodiversity Center, Institute of Botany, Slovak Academy of Sciences, Bratislava, Slovakia.,Faculty of Education, Trnava University, Trnava, Slovakia
| | - Miloslav Petrtýl
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic.,Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Karel Halačka
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Eva Štefková Kašparová
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic
| | - Jan Mendel
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Alicja Boroń
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Dorota Juchno
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Anna Leska
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Olga Jablonska
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Monika Šídová
- Institute of Biotechnology of the Czech Academy of Sciences - BIOCEV, Vestec, Czech Republic
| | - Karel Janko
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Libechov, Czech Republic.,Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
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19
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Grabowska AI, Boroń A, Kirtiklis L, Spóz A, Juchno D, Kotusz J. Chromosomal inheritance of parental rDNAs distribution pattern detected by FISH in diploid F 1 hybrid progeny of Cobitis (Teleostei, Cobitidae) species has non-Mendelian character. JOURNAL OF FISH BIOLOGY 2020; 96:261-273. [PMID: 31755097 DOI: 10.1111/jfb.14216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/21/2019] [Indexed: 06/10/2023]
Abstract
This study was conducted to describe the major and the minor rDNA chromosome distribution in the spined loach Cobitis taenia (2n = 48) and the Danubian loach Cobitis elongatoides (2n = 50), and their laboratory-produced diploid reciprocal F1 hybrid progeny. It was tested by fluorescence in situ hybridisation (FISH) whether the number of 28s and 5s rDNA sites in the karyotypes of diploid hybrids corresponds to the expectations resulting from Mendelian ratio and if nucleolar organiser regions (NOR)were inherited from both parents or nucleolar dominance can be observed in the induced F1 hybrid progeny. Ten (females) or twelve (males) 28s rDNA loci were located in nine uniarm chromosomes of C. taenia. Two of such loci terminally bounded on one acrocentric chromosome were unique and indicated as specific for this species. Large 5s rDNA clusters were located on two acrocentric chromosomes. In C. elongatoides of both sexes, six NOR sites in terminal regions on six meta-submetacentric chromosomes and two 5s rDNA sites on large submetacentrics were detected. The F1 hybrid progeny (2n = 49) was characterised by the intermediate karyotype with the sites of ribosome synthesis on chromosomes inherited from both parents without showing nucleolar dominance. 5s rDNA sites were detected on large submetacentric and two acrocentric chromosomes. The observed number of both 28s and 5s rDNAs signals in F1 diploid Cobitis hybrids was disproportionally inherited from the two parental species, showing inconsistency with the Mendelian ratios. The presented rDNA patterns indicate some marker chromosomes that allow the species of the parental male and female to be recognised in hybrid progeny. The 5s rDNA was found to be a particularly effective diagnostic marker of C. elongatoides to partially discern genomic composition of diploid Cobitis hybrids and presumably allopolyploids resulting from their backcrossing with one of the parental species. Thus, the current study provides insight into the extent of rDNA heredity in Cobitis chromosomes and their cytotaxonomic character.
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Affiliation(s)
- Anna I Grabowska
- Department of Zoology, University of Warmia and Mazury, Olsztyn, Poland
| | - Alicja Boroń
- Department of Zoology, University of Warmia and Mazury, Olsztyn, Poland
| | - Lech Kirtiklis
- Department of Zoology, University of Warmia and Mazury, Olsztyn, Poland
| | - Aneta Spóz
- Department of Zoology, University of Warmia and Mazury, Olsztyn, Poland
| | - Dorota Juchno
- Department of Zoology, University of Warmia and Mazury, Olsztyn, Poland
| | - Jan Kotusz
- Museum of Natural History, University of Wroclaw, Wroclaw, Poland
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20
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Sousa RPCDE, Sodré D, Costa RMDA, Vallinoto M, Oliveira EHC, Silva-Oliveira GC, Sampaio I, Guimarães-Costa A. Range distribution and contributions to taxonomy of Elops smithi (ELOPIFORMES: ELOPIDAE). AN ACAD BRAS CIENC 2019; 91:e20181240. [PMID: 31800702 DOI: 10.1590/0001-3765201920181240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 08/29/2019] [Indexed: 05/30/2023] Open
Abstract
This study presents the first record of Elops smithi for northern Brazil. The evidence suggests this species is being misidentified incorrectly as Elops saurus in estuaries of the Western Atlantic Ocean. Here, morphological, molecular, and cytogenetic evidence identified all ladyfish specimens from one estuary in the region as E. smithi. Thus, at least Elops smithi occurs in the northern coast of Brazil and it is recommended that specimens from this region identified as E. saurus be further investigated with genetic and cytogenetic tools in order to assure a correct species identification.
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Affiliation(s)
- Rodrigo P C DE Sousa
- Universidade Federal do Pará, Laboratório de Evolução, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
| | - Denise Sodré
- Universidade Federal do Pará, Laboratório de Plâncton e Cultivo de Microalgas. Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
| | - Rauquírio M DA Costa
- Universidade Federal do Pará, Laboratório de Plâncton e Cultivo de Microalgas. Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
| | - Marcelo Vallinoto
- Universidade Federal do Pará, Laboratório de Evolução, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil.,CIBIO/InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Universidade do Porto, 4485-661, Vairão, Portugal
| | - Edivaldo H C Oliveira
- Instituto Evandro Chagas, Laboratório de Cultura de Tecidos e Citogenética Animal, Rodovia BR-316 Km 7, s/n, Levilândia, 67030-000 Ananindeua, PA, Brazil
| | - Gláucia C Silva-Oliveira
- Universidade Federal do Pará, Laboratório de Evolução, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
| | - Iracilda Sampaio
- Universidade Federal do Pará, Laboratório de Genética e Biologia Molecular, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
| | - Aurycéia Guimarães-Costa
- Universidade Federal do Pará, Laboratório de Genética e Biologia Molecular, Alameda Leandro Ribeiro, s/n, Aldeia, 68600-000 Bragança, PA, Brazil
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21
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Hnátková E, Triantaphyllidis C, Ozouf-Costaz C, Lukáš Choleva, Majtánová Z, Bohlen J, Ráb P. Karyotype and chromosomal characteristics of rDNA of Cobitisstrumicae Karaman, 1955 (Teleostei, Cobitidae) from Lake Volvi, Greece. COMPARATIVE CYTOGENETICS 2018; 12:483-491. [PMID: 30498563 PMCID: PMC6251958 DOI: 10.3897/compcytogen.v12i4.28068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/26/2018] [Indexed: 10/05/2023]
Abstract
The karyotype of Greek cobitid fish Cobitisstrumicae Karaman, 1955, from Lake Volvi, Greece, a representative of one of its two major intraspecific phylogenetic lineages, was analysed by means of sequential Giemsa-staining, C-banding, silver-staining, CMA3 fluorescence banding and also by in situ hybridization (FISH) with rDNA probe. The diploid chromosome number was 2n = 50, karyotype composed of 10 pairs of metacentric to submetacentric and 15 pairs of subtelocentric to acrocentric chromosomes. The nucleolus organizer regions (NORs) as revealed by Ag- and CMA3 staining and FISH were situated in the telomeric region of the fourth submetacentric chromosome pair. The chromosomes contained very low content of C-positive heterochromatin. No heteromorphic sex chromosomes were detected. This first karyotype report for any species of lineage Bicanestrinia Băcescu, 1962 shows a simple karyotype dominated by acrocentric chromosomes and possessing single NOR-bearing chromosome pair. Cytotaxonomic implications of this finding for the taxonomy of the genus Cobitis Linnaeus, 1758 are further discussed.
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Affiliation(s)
- Eva Hnátková
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, 165 00 Prague, Kamýcká 129, Czech RepublicCzech University of Life SciencesPragueCzech Republic
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of Czech Republic, 277 21 Liběchov, Czech RepublicInstitute of Animal Physiology and Genetics, Academy of Sciences of Czech RepublicLibĕchovCzech Republic
| | - Costas Triantaphyllidis
- Department of Genetics, Development and Molecular Biology, Faculty of Sciences, School of Biology, Aristotle University of Thessaloniki, University Campus, 54124 Thessaloniki, GreeceAristotle University of ThessalonikiThessalonikiGreece
| | - Catherine Ozouf-Costaz
- Institut de Biologie Paris Seine, UMR 7138 “Evolution”, Sorbonne Universités, Case 5, 7 quai St Bernard, 75952 Paris cedex 05, Paris, FranceSorbonne UniversitésParisFrance
| | - Lukáš Choleva
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of Czech Republic, 277 21 Liběchov, Czech RepublicInstitute of Animal Physiology and Genetics, Academy of Sciences of Czech RepublicLibĕchovCzech Republic
| | - Zuzana Majtánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of Czech Republic, 277 21 Liběchov, Czech RepublicInstitute of Animal Physiology and Genetics, Academy of Sciences of Czech RepublicLibĕchovCzech Republic
| | - Joerg Bohlen
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of Czech Republic, 277 21 Liběchov, Czech RepublicInstitute of Animal Physiology and Genetics, Academy of Sciences of Czech RepublicLibĕchovCzech Republic
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of Czech Republic, 277 21 Liběchov, Czech RepublicInstitute of Animal Physiology and Genetics, Academy of Sciences of Czech RepublicLibĕchovCzech Republic
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22
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Reil JB, Doorenweerd C, San Jose M, Sim SB, Geib SM, Rubinoff D. Transpacific coalescent pathways of coconut rhinoceros beetle biotypes: Resistance to biological control catalyses resurgence of an old pest. Mol Ecol 2018; 27:4459-4474. [DOI: 10.1111/mec.14879] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/07/2018] [Accepted: 09/07/2018] [Indexed: 01/13/2023]
Affiliation(s)
- Jonathan Bradley Reil
- Department of Plant and Environmental Protection Sciences; University of Hawaii at Manoa; Honolulu Hawaii
| | - Camiel Doorenweerd
- Department of Plant and Environmental Protection Sciences; University of Hawaii at Manoa; Honolulu Hawaii
| | - Michael San Jose
- Department of Plant and Environmental Protection Sciences; University of Hawaii at Manoa; Honolulu Hawaii
| | - Sheina B. Sim
- Department of Plant and Environmental Protection Sciences; University of Hawaii at Manoa; Honolulu Hawaii
- Tropical Crop and Commodity Protection Research Unit; Daniel K Inouye U.S. Pacific Basin Agricultural Research Center; USDA, Agricultural Research Services; Hilo Hawaii
| | - Scott M. Geib
- Tropical Crop and Commodity Protection Research Unit; Daniel K Inouye U.S. Pacific Basin Agricultural Research Center; USDA, Agricultural Research Services; Hilo Hawaii
| | - Daniel Rubinoff
- Department of Plant and Environmental Protection Sciences; University of Hawaii at Manoa; Honolulu Hawaii
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23
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Kuroda M, Fujimoto T, Murakami M, Yamaha E, Arai K. Clonal reproduction assured by sister chromosome pairing in dojo loach, a teleost fish. Chromosome Res 2018; 26:243-253. [DOI: 10.1007/s10577-018-9581-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/12/2018] [Accepted: 05/15/2018] [Indexed: 01/13/2023]
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24
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Sember A, Bohlen J, Šlechtová V, Altmanová M, Pelikánová Š, Ráb P. Dynamics of tandemly repeated DNA sequences during evolution of diploid and tetraploid botiid loaches (Teleostei: Cobitoidea: Botiidae). PLoS One 2018; 13:e0195054. [PMID: 29590207 PMCID: PMC5874072 DOI: 10.1371/journal.pone.0195054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/15/2018] [Indexed: 12/16/2022] Open
Abstract
Polyploidization has played an important role in the evolution of vertebrates, particularly at the base of Teleostei-an enormously successful ray-finned fish group with additional genome doublings on lower taxonomic levels. The investigation of post-polyploid genome dynamics might provide important clues about the evolution and ecology of respective species and can help to decipher the role of polyploidy per se on speciation. Few studies have attempted to investigate the dynamics of repetitive DNA sequences in the post-polyploid genome using molecular cytogenetic tools in fishes, though recent efforts demonstrated their usefulness. The demonstrably monophyletic freshwater loach family Botiidae, branching to evolutionary diploid and tetraploid lineages separated >25 Mya, offers a suited model group for comparing the long-term repetitive DNA evolution. For this, we integrated phylogenetic analyses with cytogenetical survey involving Giemsa- and Chromomycin A3 (CMA3)/DAPI stainings and fluorescence in situ hybridization with 5S/45S rDNA, U2 snDNA and telomeric probes in representative sample of 12 botiid species. The karyotypes of all diploids were composed of 2n = 50 chromosomes, while majority of tetraploids had 2n = 4x = 100, with only subtle interspecific karyotype differences. The exceptional karyotype of Botia dario (2n = 4x = 96) suggested centric fusions behind the 2n reduction. Variable patterns of FISH signals revealed cases of intraspecific polymorphisms, rDNA amplification, variable degree of correspondence with CMA3+ sites and almost no phylogenetic signal. In tetraploids, either additivity or loci gain/loss was recorded. Despite absence of classical interstitial telomeric sites, large blocks of interspersed rDNA/telomeric regions were found in diploids only. We uncovered different molecular drives of studied repetitive DNA classes within botiid genomes as well as the advanced stage of the re-diploidization process in tetraploids. Our results may contribute to link genomic approach with molecular cytogenetic analyses in addressing the origin and mechanism of this polyploidization event.
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Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Jörg Bohlen
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Vendula Šlechtová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Marie Altmanová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, Czech Republic
| | - Šárka Pelikánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
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25
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Karyotype Variability and Inter-Population Genomic Differences in Freshwater Ostracods (Crustacea) Showing Geographical Parthenogenesis. Genes (Basel) 2018. [PMID: 29518021 PMCID: PMC5867871 DOI: 10.3390/genes9030150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Transitions from sexual to asexual reproduction are often associated with polyploidy and increased chromosomal plasticity in asexuals. We investigated chromosomes in the freshwater ostracod species Eucypris virens (Jurine, 1820), where sexual, asexual and mixed populations can be found. Our initial karyotyping of multiple populations from Europe and North Africa, both sexual and asexual, revealed a striking variability in chromosome numbers. This would suggest that chromosomal changes are likely to be accelerated in asexuals because the constraints of meiosis are removed. Hence, we employed comparative genomic hybridization (CGH) within and among sexual and asexual populations to get insights into E. virens genome arrangements. CGH disclosed substantial genomic imbalances among the populations analyzed, and three patterns of genome arrangement between these populations: 1. Only putative ribosomal DNA (rDNA)-bearing regions were conserved in the two populations compared indicating a high sequence divergence between these populations. This pattern is comparable with our findings at the interspecies level of comparison; 2. Chromosomal regions were shared by both populations to a varying extent with a distinct copy number variation in pericentromeric and presumable rDNA-bearing regions. This indicates a different rate of evolution in repetitive sequences; 3. A mosaic pattern of distribution of genomic material that can be explained as non-reciprocal genetic introgression and evidence of a hybrid origin of these individuals. We show an overall increased chromosomal dynamics in E. virens that is complementary with available phylogenetic and population genetic data reporting highly differentiated diploid sexual and asexual lineages with a wide variety of genetic backgrounds.
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Sember A, Bertollo LAC, Ráb P, Yano CF, Hatanaka T, de Oliveira EA, Cioffi MDB. Sex Chromosome Evolution and Genomic Divergence in the Fish Hoplias malabaricus (Characiformes, Erythrinidae). Front Genet 2018; 9:71. [PMID: 29556249 PMCID: PMC5845122 DOI: 10.3389/fgene.2018.00071] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 02/16/2018] [Indexed: 11/13/2022] Open
Abstract
The Erythrinidae family (Teleostei: Characiformes) is a small Neotropical fish group with a wide distribution throughout South America, where Hoplias malabaricus corresponds to the most widespread and cytogenetically studied taxon. This species possesses significant genetic variation, as well as huge karyotype diversity among populations, as reflected by its seven major karyotype forms (i.e., karyomorphs A-G) identified up to now. Although morphological differences in their bodies are not outstanding, H. malabaricus karyomorphs are easily identified by differences in 2n, morphology and size of chromosomes, as well as by distinct evolutionary steps of sex chromosomes development. Here, we performed comparative genomic hybridization (CGH) to analyse both the intra- and inter-genomic status in terms of repetitive DNA divergence among all but one (E) H. malabaricus karyomorphs. Our results indicated that they have close relationships, but with evolutionary divergences among their genomes, yielding a range of non-overlapping karyomorph-specific signals. Besides, male-specific regions were uncovered on the sex chromosomes, confirming their differential evolutionary trajectories. In conclusion, the hypothesis that H. malabaricus karyomorphs are result of speciation events was strengthened.
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Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czechia
| | - Luiz A. C. Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czechia
| | - Cassia F. Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Ezequiel A. de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
- Secretaria de Estado de Educação de Mato Grosso (SEDUC-MT), Cuiabá, Brazil
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27
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Symonová R, Howell WM. Vertebrate Genome Evolution in the Light of Fish Cytogenomics and rDNAomics. Genes (Basel) 2018; 9:genes9020096. [PMID: 29443947 PMCID: PMC5852592 DOI: 10.3390/genes9020096] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 12/19/2022] Open
Abstract
To understand the cytogenomic evolution of vertebrates, we must first unravel the complex genomes of fishes, which were the first vertebrates to evolve and were ancestors to all other vertebrates. We must not forget the immense time span during which the fish genomes had to evolve. Fish cytogenomics is endowed with unique features which offer irreplaceable insights into the evolution of the vertebrate genome. Due to the general DNA base compositional homogeneity of fish genomes, fish cytogenomics is largely based on mapping DNA repeats that still represent serious obstacles in genome sequencing and assembling, even in model species. Localization of repeats on chromosomes of hundreds of fish species and populations originating from diversified environments have revealed the biological importance of this genomic fraction. Ribosomal genes (rDNA) belong to the most informative repeats and in fish, they are subject to a more relaxed regulation than in higher vertebrates. This can result in formation of a literal 'rDNAome' consisting of more than 20,000 copies with their high proportion employed in extra-coding functions. Because rDNA has high rates of transcription and recombination, it contributes to genome diversification and can form reproductive barrier. Our overall knowledge of fish cytogenomics grows rapidly by a continuously increasing number of fish genomes sequenced and by use of novel sequencing methods improving genome assembly. The recently revealed exceptional compositional heterogeneity in an ancient fish lineage (gars) sheds new light on the compositional genome evolution in vertebrates generally. We highlight the power of synergy of cytogenetics and genomics in fish cytogenomics, its potential to understand the complexity of genome evolution in vertebrates, which is also linked to clinical applications and the chromosomal backgrounds of speciation. We also summarize the current knowledge on fish cytogenomics and outline its main future avenues.
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Affiliation(s)
- Radka Symonová
- Faculty of Science, Department of Biology, University of Hradec Králové, 500 03 Hradec Králové, Czech Republic.
| | - W Mike Howell
- Department of Biological and Environmental Sciences, Samford University, Birmingham, AL 35229, USA.
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28
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Betto-Colliard C, Hofmann S, Sermier R, Perrin N, Stöck M. Profound genetic divergence and asymmetric parental genome contributions as hallmarks of hybrid speciation in polyploid toads. Proc Biol Sci 2018; 285:rspb.2017.2667. [PMID: 29436499 PMCID: PMC5829204 DOI: 10.1098/rspb.2017.2667] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/17/2018] [Indexed: 01/19/2023] Open
Abstract
The evolutionary causes and consequences of allopolyploidization, an exceptional pathway to instant hybrid speciation, are poorly investigated in animals. In particular, when and why hybrid polyploids versus diploids are produced, and constraints on sources of paternal and maternal ancestors, remain underexplored. Using the Palearctic green toad radiation (including bisexually reproducing species of three ploidy levels) as model, we generate a range-wide multi-locus phylogeny of 15 taxa and present four new insights: (i) at least five (up to seven) distinct allotriploid and allotetraploid taxa have evolved in the Pleistocene; (ii) all maternal and paternal ancestors of hybrid polyploids stem from two deeply diverged nuclear clades (6 Mya, 3.1-9.6 Mya), with distinctly greater divergence than the parental species of diploid hybrids found at secondary contact zones; (iii) allotriploid taxa possess two conspecific genomes and a deeply diverged allospecific one, suggesting that genomic imbalance and divergence are causal for their partly clonal reproductive mode; (iv) maternal versus paternal genome contributions exhibit asymmetry, with the maternal nuclear (and mitochondrial) genome of polyploids always coming from the same clade, and the paternal genome from the other. We compare our findings with similar patterns in diploid/polyploid vertebrates, and suggest deep ancestral divergence as a precondition for successful allopolyploidization.
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Affiliation(s)
- Caroline Betto-Colliard
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Sylvia Hofmann
- Department of Conservation Biology, UFZ Helmholtz-Centre for Environmental Research, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Roberto Sermier
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587 Berlin, Germany
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29
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Janko K, Pačes J, Wilkinson‐Herbots H, Costa RJ, Roslein J, Drozd P, Iakovenko N, Rídl J, Hroudová M, Kočí J, Reifová R, Šlechtová V, Choleva L. Hybrid asexuality as a primary postzygotic barrier between nascent species: On the interconnection between asexuality, hybridization and speciation. Mol Ecol 2018; 27:248-263. [PMID: 28987005 PMCID: PMC6849617 DOI: 10.1111/mec.14377] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/25/2017] [Accepted: 09/05/2017] [Indexed: 12/30/2022]
Abstract
Although sexual reproduction is ubiquitous throughout nature, the molecular machinery behind it has been repeatedly disrupted during evolution, leading to the emergence of asexual lineages in all eukaryotic phyla. Despite intensive research, little is known about what causes the switch from sexual reproduction to asexuality. Interspecific hybridization is one of the candidate explanations, but the reasons for the apparent association between hybridization and asexuality remain unclear. In this study, we combined cross-breeding experiments with population genetic and phylogenomic approaches to reveal the history of speciation and asexuality evolution in European spined loaches (Cobitis). Contemporary species readily hybridize in hybrid zones, but produce infertile males and fertile but clonally reproducing females that cannot mediate introgressions. However, our analysis of exome data indicates that intensive gene flow between species has occurred in the past. Crossings among species with various genetic distances showed that, while distantly related species produced asexual females and sterile males, closely related species produce sexually reproducing hybrids of both sexes. Our results suggest that hybridization leads to sexual hybrids at the initial stages of speciation, but as the species diverge further, the gradual accumulation of reproductive incompatibilities between species could distort their gametogenesis towards asexuality. Interestingly, comparative analysis of published data revealed that hybrid asexuality generally evolves at lower genetic divergences than hybrid sterility or inviability. Given that hybrid asexuality effectively restricts gene flow, it may establish a primary reproductive barrier earlier during diversification than other "classical" forms of postzygotic incompatibilities. Hybrid asexuality may thus indirectly contribute to the speciation process.
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Affiliation(s)
- Karel Janko
- Institute of Animal Physiology and GeneticsLaboratory of Fish GeneticsThe Czech Academy of SciencesLibechovCzech Republic
- Department of Biology and EcologyFaculty of ScienceUniversity of OstravaOstravaCzech Republic
| | - Jan Pačes
- Institute of Animal Physiology and GeneticsLaboratory of Fish GeneticsThe Czech Academy of SciencesLibechovCzech Republic
- Institute of Molecular GeneticsLaboratory of Genomics and BioinformaticsThe Czech Academy of SciencesPragueCzech Republic
| | | | - Rui J. Costa
- Department of Statistical ScienceUniversity College LondonLondonUK
| | - Jan Roslein
- Institute of Animal Physiology and GeneticsLaboratory of Fish GeneticsThe Czech Academy of SciencesLibechovCzech Republic
- Department of Biology and EcologyFaculty of ScienceUniversity of OstravaOstravaCzech Republic
- Department of Fish EcologyInstitute of Vertebrate BiologyThe Czech Academy of SciencesBrnoCzech Republic
| | - Pavel Drozd
- Department of Biology and EcologyFaculty of ScienceUniversity of OstravaOstravaCzech Republic
| | - Nataliia Iakovenko
- Institute of Animal Physiology and GeneticsLaboratory of Fish GeneticsThe Czech Academy of SciencesLibechovCzech Republic
- Department of Biology and EcologyFaculty of ScienceUniversity of OstravaOstravaCzech Republic
- Schmalhausen Institute of Zoology of NAS of UkraineKyivUkraine
| | - Jakub Rídl
- Institute of Molecular GeneticsLaboratory of Genomics and BioinformaticsThe Czech Academy of SciencesPragueCzech Republic
| | - Miluše Hroudová
- Institute of Molecular GeneticsLaboratory of Genomics and BioinformaticsThe Czech Academy of SciencesPragueCzech Republic
| | - Jan Kočí
- Institute of Animal Physiology and GeneticsLaboratory of Fish GeneticsThe Czech Academy of SciencesLibechovCzech Republic
- Department of Biology and EcologyFaculty of ScienceUniversity of OstravaOstravaCzech Republic
| | - Radka Reifová
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Věra Šlechtová
- Institute of Animal Physiology and GeneticsLaboratory of Fish GeneticsThe Czech Academy of SciencesLibechovCzech Republic
| | - Lukáš Choleva
- Institute of Animal Physiology and GeneticsLaboratory of Fish GeneticsThe Czech Academy of SciencesLibechovCzech Republic
- Department of Biology and EcologyFaculty of ScienceUniversity of OstravaOstravaCzech Republic
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30
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Carvalho PC, de Oliveira EA, Bertollo LAC, Yano CF, Oliveira C, Decru E, Jegede OI, Hatanaka T, Liehr T, Al-Rikabi ABH, Cioffi MDB. First Chromosomal Analysis in Hepsetidae (Actinopterygii, Characiformes): Insights into Relationship between African and Neotropical Fish Groups. Front Genet 2017; 8:203. [PMID: 29312435 PMCID: PMC5733008 DOI: 10.3389/fgene.2017.00203] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 11/22/2017] [Indexed: 01/27/2023] Open
Abstract
Hepsetidae is a small fish family with only the genus Hepsetus, with six described species distributed throughout the South, Central and Western regions of Africa, showing a close relationship with the Alestidae and some Neotropical fish families. However, no cytogenetic information is available for both Hepsetidae and Alestidae species, thus preventing any evolutionary comparative studies at the chromosomal level. In the present study, we are providing new cytogenetic data for Hepsetus odoe, including the standard karyotype, C-banding, repetitive DNAs mapping, comparative genomic hybridization (CGH) and whole chromosome painting (WCP), providing chromosomal patterns and subsidies for comparative cytogenetics with other characiform families. Both males and females H. odoe have 2n = 58 chromosomes (10m + 28sm + 20st/a), with most of the C-band positive heterochromatin localized in the centromeric and subtelomeric regions. Only one pair of chromosomes bears proximal 5S rDNA sites in the short arms, contrasting with the 18S rDNA sequences which are located in the terminal regions of four chromosome pairs. Clear interstitial hybridization signals are evidenced for the U1 and U2 snDNA probes, but in only one and two chromosome pairs, respectively. Microsatellite motifs are widely distributed in the karyotype, with exception for the (CGG)10, (GAA)10 and (GAG)10 probes, which highlight conspicuous interstitial signals on an unique pair of chromosomes. Comparative data from conventional and molecular cytogenetics, including CGH and WCP experiments, indicate that H. odoe and some Erythrinidae species, particularly Erythrinus erythrinus, share similar chromosomal sequences suggesting some relatedness among them, although bearing genomic specificities in view of their divergent evolutionary histories.
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Affiliation(s)
- Pedro C Carvalho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Ezequiel A de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil.,Secretaria de Estado de Educação de Mato Grosso (Seduc-MT), Cuiabá, Brazil
| | - Luiz A C Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Cassia F Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Eva Decru
- Section Vertebrates, Ichthyology, Royal Museum for Central Africa, Tervuren, Belgium
| | - Oladele I Jegede
- Department of Fisheries and Aquaculture, Adamawa State University, Mubi, Nigeria
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | | | - Marcelo de B Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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