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Nikitin P, Sidorov S, Liehr T, Klimina K, Al-Rikabi A, Korchagin V, Kolomiets O, Arakelyan M, Spangenberg V. Variants of a major DNA satellite discriminate parental subgenomes in a hybrid parthenogenetic lizard Darevskia unisexualis (Darevsky, 1966). JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024; 342:368-379. [PMID: 38407543 DOI: 10.1002/jez.b.23244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/12/2023] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
Hybrid parthenogenetic animals are an exceptionally interesting model for studying the mechanisms and evolution of sexual and asexual reproduction. A diploid parthenogenetic lizard Darevskia unisexualis is a result of an ancestral cross between a maternal species Darevskia raddei nairensis and a paternal species Darevskia valentini and presents a unique opportunity for a cytogenetic and computational analysis of a hybrid karyotype. Our previous results demonstrated a significant divergence between the pericentromeric DNA sequences of the parental Darevskia species; however, an in-depth comparative study of their pericentromeres is still lacking. Here, using target sequencing of microdissected pericentromeric regions, we reveal and compare the repertoires of the pericentromeric tandem repeats of the parental Darevskia lizards. We found species-specific sequences of the major pericentromeric tandem repeat CLsat, which allowed computational prediction and experimental validation of fluorescent DNA probes discriminating parental chromosomes within the hybrid karyotype of D. unisexualis. Moreover, we have implemented a generalizable computational method, based on the optimization of the Levenshtein distance between tandem repeat monomers, for finding species-specific fluorescent probes for pericentromere staining. In total, we anticipate that our comparative analysis of Darevskia pericentromeric repeats, the species-specific fluorescent probes that we found and the pipeline that we developed will form a basis for the future detailed cytogenomic studies of a wide range of natural and laboratory hybrids.
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Affiliation(s)
- Pavel Nikitin
- Laboratory of Comparative Ethology and Biocommunication, Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Sviatoslav Sidorov
- Computational Regulatory Genomics, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, London, UK
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Ksenia Klimina
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Ahmed Al-Rikabi
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | | | - Oxana Kolomiets
- Laboratory of Cytogenetics, Vavilov Institute of General Genetics RAS, Moscow, Russia
| | - Marine Arakelyan
- Department of Zoology, Yerevan State University, Yerevan, Armenia
| | - Victor Spangenberg
- Laboratory of Cytogenetics, Vavilov Institute of General Genetics RAS, Moscow, Russia
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Pensabene E, Augstenová B, Kratochvíl L, Rovatsos M. Differentiated sex chromosomes, karyotype evolution, and spontaneous triploidy in carphodactylid geckos. J Hered 2024; 115:262-276. [PMID: 38366660 DOI: 10.1093/jhered/esae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/13/2024] [Indexed: 02/18/2024] Open
Abstract
Geckos exhibit derived karyotypes without a clear distinction between macrochromosomes and microchromosomes and intriguing diversity in sex determination mechanisms. We conducted cytogenetic analyses in six species from the genera Nephrurus, Phyllurus, and Saltuarius of the gecko family Carphodactylidae. We confirmed the presence of a female heterogametic system with markedly differentiated and heteromorphic sex chromosomes in all examined species, typically with the W chromosome notably larger than the Z chromosome. One species, Nephrurus cinctus, possesses unusual multiple Z1Z1Z2Z2/Z1Z2W sex chromosomes. The morphology of the sex chromosomes, along with repetitive DNA content, suggests that the differentiation or emergence of sex chromosomes occurred independently in the genus Phyllurus. Furthermore, our study unveils a case of spontaneous triploidy in a fully grown individual of Saltuarius cornutus (3n = 57) and explores its implications for reproduction in carphodactylid geckos. We revealed that most carphodactylids retain the putative ancestral gekkotan karyotype of 2n = 38, characterized by predominantly acrocentric chromosomes that gradually decrease in size. If present, biarmed chromosomes emerge through pericentric inversions, maintaining the chromosome (and centromere) numbers. However, Phyllurus platurus is a notable exception, with a karyotype of 2n = 22 chromosomes. Its eight pairs of biarmed chromosomes were probably formed by Robertsonian fusions of acrocentric chromosomes. The family underscores a remarkable instance of evolutionary stability in chromosome numbers, followed by a profound transformation through parallel interchromosomal rearrangements. Our study highlights the need to continue generating cytogenetic data in order to test long-standing ideas about reproductive biology and the evolution of genome and sex determination.
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Affiliation(s)
- Eleonora Pensabene
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Barbora Augstenová
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
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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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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: 1.0] [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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Lisachov A, Tishakova K, Romanenko S, Lisachova L, Davletshina G, Prokopov D, Kratochvíl L, O Brien P, Ferguson-Smith M, Borodin P, Trifonov V. Robertsonian fusion triggers recombination suppression on sex chromosomes in Coleonyx geckos. Sci Rep 2023; 13:15502. [PMID: 37726346 PMCID: PMC10509250 DOI: 10.1038/s41598-023-39937-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 08/02/2023] [Indexed: 09/21/2023] Open
Abstract
The classical hypothesis proposes that the lack of recombination on sex chromosomes arises due to selection for linkage between a sex-determining locus and sexually antagonistic loci, primarily facilitated by inversions. However, cessation of recombination on sex chromosomes could be attributed also to neutral processes, connected with other chromosome rearrangements or can reflect sex-specific recombination patterns existing already before sex chromosome differentiation. Three Coleonyx gecko species share a complex X1X1X2X2/X1X2Y system of sex chromosomes evolved via a fusion of the Y chromosome with an autosome. We analyzed synaptonemal complexes and sequenced flow-sorted sex chromosomes to investigate the effect of chromosomal rearrangement on recombination and differentiation of these sex chromosomes. The gecko sex chromosomes evolved from syntenic regions that were also co-opted also for sex chromosomes in other reptiles. We showed that in male geckos, recombination is less prevalent in the proximal regions of chromosomes and is even further drastically reduced around the centromere of the neo-Y chromosome. We highlight that pre-existing recombination patterns and Robertsonian fusions can be responsible for the cessation of recombination on sex chromosomes and that such processes can be largely neutral.
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Affiliation(s)
- Artem Lisachov
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
- Institute of Environmental and Agricultural Biology (X-BIO), University of Tyumen, Tyumen, 625003, Russia.
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia.
| | - Katerina Tishakova
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Svetlana Romanenko
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
| | - Lada Lisachova
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Guzel Davletshina
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
| | - Dmitry Prokopov
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, 12844, Prague, Czech Republic
| | - Patricia O Brien
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Malcolm Ferguson-Smith
- Department of Veterinary Medicine, Cambridge Resource Centre for Comparative Genomics, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Pavel Borodin
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
| | - Vladimir Trifonov
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
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Chmielewska M, Kaźmierczak M, Rozenblut-Kościsty B, Kolenda K, Dudzik A, Dedukh D, Ogielska M. Genome elimination from the germline cells in diploid and triploid male water frogs Pelophylax esculentus. Front Cell Dev Biol 2022; 10:1008506. [PMID: 36313575 PMCID: PMC9615423 DOI: 10.3389/fcell.2022.1008506] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 08/31/2022] [Indexed: 11/18/2022] Open
Abstract
Hybridogenesis is a hemiclonal reproductive strategy in diploid and triploid hybrids. Our study model is a frog P. esculentus (diploid RL and triploids RLL and RRL), a natural hybrid between P. lessonae (LL) and P. ridibundus (RR). Hybridogenesis relies on elimination of one genome (L or R) from gonocytes (G) in tadpole gonads during prespermatogenesis, but not from spermatogonial stem cells (SSCs) in adults. Here we provide the first comprehensive study of testis morphology combined with chromosome composition in the full spectrum of spermatogenic cells. Using genomic in situ hybridization (GISH) and FISH we determined genomes in metaphase plates and interphase nuclei in Gs and SSCs. We traced genomic composition of SSCs, spermatocytes and spermatozoa in individual adult males that were crossed with females of the parental species and gave progeny. Degenerating gonocytes (24%–39%) and SSCs (18%–20%) led to partial sterility of juvenile and adult gonads. We conclude that elimination and endoreplication not properly completed during prespermatogenesis may be halted when gonocytes become dormant in juveniles. After resumption of mitotic divisions by SSCs in adults, these 20% of cells with successful genome elimination and endoreplication continue spermatogenesis, while in about 80% spermatogenesis is deficient. Majority of abnormal cells are eliminated by cell death, however some of them give rise to aneuploid spermatocytes and spermatozoa which shows that hybridogenesis is a wasteful process.
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Affiliation(s)
- Magdalena Chmielewska
- Amphibian Biology Group, Department of Evolutionary Biology and Conservation of Vertebrates, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
- *Correspondence: Magdalena Chmielewska,
| | - Mikołaj Kaźmierczak
- Amphibian Biology Group, Department of Evolutionary Biology and Conservation of Vertebrates, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
- Department of Medicine Biology, The Cardinal Wyszyński National Institute of Cardiology, Warsaw, Poland
| | - Beata Rozenblut-Kościsty
- Amphibian Biology Group, Department of Evolutionary Biology and Conservation of Vertebrates, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - Krzysztof Kolenda
- Amphibian Biology Group, Department of Evolutionary Biology and Conservation of Vertebrates, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
| | - 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
| | - Maria Ogielska
- Amphibian Biology Group, Department of Evolutionary Biology and Conservation of Vertebrates, Faculty of Biological Sciences, University of Wrocław, Wrocław, Poland
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Dedukh D, da Cruz I, Kneitz S, Marta A, Ormanns J, Tichopád T, Lu Y, Alsheimer M, Janko K, Schartl M. Achiasmatic meiosis in the unisexual Amazon molly, Poecilia formosa. Chromosome Res 2022; 30:443-457. [PMID: 36459298 PMCID: PMC9771850 DOI: 10.1007/s10577-022-09708-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/30/2022] [Accepted: 10/27/2022] [Indexed: 12/03/2022]
Abstract
Unisexual reproduction, which generates clonal offspring, is an alternative strategy to sexual breeding and occurs even in vertebrates. A wide range of non-sexual reproductive modes have been described, and one of the least understood questions is how such pathways emerged and how they mechanistically proceed. The Amazon molly, Poecilia formosa, needs sperm from males of related species to trigger the parthenogenetic development of diploid eggs. However, the mechanism, of how the unreduced female gametes are produced, remains unclear. Cytological analyses revealed that the chromosomes of primary oocytes initiate pachytene but do not proceed to bivalent formation and meiotic crossovers. Comparing ovary transcriptomes of P. formosa and its sexual parental species revealed expression levels of meiosis-specific genes deviating from P. mexicana but not from P. latipinna. Furthermore, several meiosis genes show biased expression towards one of the two alleles from the parental genomes. We infer from our data that in the Amazon molly diploid oocytes are generated by apomixis due to a failure in the synapsis of homologous chromosomes. The fact that this failure is not reflected in the differential expression of known meiosis genes suggests the underlying molecular mechanism may be dysregulation on the protein level or misexpression of a so far unknown meiosis gene, and/or hybrid dysgenesis because of compromised interaction of proteins from diverged genomes.
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Affiliation(s)
- Dmitrij Dedukh
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21 Czech Republic
| | - Irene da Cruz
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Susanne Kneitz
- Biochemistry and Cell Biology, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Anatolie Marta
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21 Czech Republic ,Institute of Zoology, Academiei 1, 2001, MD-2028 Chisinau, Moldova
| | - Jenny Ormanns
- Biochemistry and Cell Biology, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany
| | - Tomáš Tichopád
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21 Czech Republic ,Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Zátiší 728/II, 389 25 Vodňany, Czech Republic
| | - Yuan Lu
- Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX 78666 USA
| | - Manfred Alsheimer
- Cell and Developmental Biology, University of Wuerzburg, Am Hubland, 97074 BiocenterWuerzburg, Germany
| | - Karel Janko
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21 Czech Republic ,Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany ,Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX 78666 USA
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