Most eukaryotes maintain the stability of their cellular genome sizes to ensure genome transmission to offspring through sexual reproduction. However, some alter their genome size by selectively eliminating parts or increasing ploidy at specific developmental stages. This phenomenon of genome elimination or whole genome duplication occurs in animal hybrids reproducing asexually. Such genome alterations occur during gonocyte development ensuring successful reproduction of these hybrids. Although multiple examples of genome alterations are known, the underlying molecular and cellular processes involved in selective genome elimination and duplication remain largely unknown. Here, we uncovered the process of selective genome elimination and genome endoreplication in hemiclonal fish hybrids from the genus Hypseleotris. Specifically, we examined parental sexual species H. bucephala and hybrid H. bucephala × H. gymnocephala (HB × HX). We observed micronuclei in the cytoplasm of gonial cells in the gonads of hybrids, but not in the parental sexual species. We also observed misaligned chromosomes during mitosis which were unable to attach to the spindle. Moreover, we found that misaligned chromosomes lag during anaphase and subsequently enclose in the micronuclei. Using whole mount immunofluorescent staining, we showed that chromatid segregation has failed in lagging chromosomes. We also performed three-dimensional comparative genomic hybridization (3D-CGH) using species-specific probes to determine the role of micronuclei in selective genome elimination. We repeatedly observed that misaligned chromosomes of the H. bucephala genome were preferentially enclosed in micronuclei of hybrids. In addition, we detected mitotic cells without a mitotic spindle as a potential cause of genome duplication. We conclude that selective genome elimination in the gonads of hybrids occurs through gradual elimination of individual chromosomes of one parental genome. Such chromosomes, unable to attach to the spindle, lag and become enclosed in micronuclei.

Centre for Applied Water Science Institute for Applied Ecology Faculty of Science and Technology University of Canberra Canberra ACT Australia

Centre for Conservation Ecology and Genomics Institute for Applied Ecology Faculty of Science and Technology University of Canberra Canberra ACT Australia

Laboratory of Fish Genetics Institute of Animal Physiology and Genetics Czech Academy of Sciences Liběchov Czech Republic

Laboratory of Non Mendelian Evolution Institute of Animal Physiology and Genetics Czech Academy of Sciences Liběchov Czech Republic

Erratum v

Sci Rep. 2025 Feb 25;15(1):6785. doi: 10.1038/s41598-025-91480-4. PubMed

Zobrazit více v PubMed

Wang, J. & Davis, R. E. Programmed DNA elimination in multicellular organisms. Curr. Opin. Genet. Dev.27, 26–34 (2014). PubMed PMC

Neaves, W. B. & Baumann, P. Unisexual reproduction among vertebrates. Trends Genet.27, 81–88 (2011). PubMed

Dedukh, D. & Krasikova, A. Delete and survive: Strategies of programmed genetic material elimination in eukaryotes. Biol. Rev.97, 195–216 (2022). PubMed PMC

Stenberg, P. & Saura, A. Meiosis and its deviations in polyploid animals. Cytogenet. Gen. Res.140, 185–203 (2013). PubMed

Smith, J. J., Timoshevskiy, V. A. & Saraceno, C. Programmed DNA elimination in vertebrates. Annu. Rev. Anim. Biosci.9, 173 (2021). PubMed PMC

Lee, H. O., Davidson, J. M. & Duronio, R. J. Endoreplication: polyploidy with purpose. Genes Dev.23, 2461–2477 (2009). PubMed PMC

Calvi, B. R. Making big cells: One size does not fit all. P. Nat. Acad. Sci.110, 9621–9622 (2013). PubMed PMC

Fox, D. T. & Duronio, R. J. Endoreplication and polyploidy: insights into development and disease. Development140, 3–12 (2013). PubMed PMC

Orr-Weaver, T. L. When bigger is better: The role of polyploidy in organogenesis. Trends Genet.31, 307–315 (2015). PubMed PMC

Dawley, R. M. & Bogart, J. P. Evolution and Ecology of Unisexual Vertebrates (New York State Museum, 1989).

Schön, I., Martens, K. & van Dijk, P. Lost Sex: The Evolutionary Biology of Parthenogenesis 1–615 (Springer, 2009).

Stöck, M. et al. Sex chromosomes in meiotic, hemiclonal, clonal and polyploid hybrid vertebrates: Along the ‘extended speciation continuum’. Philos. T. R. Soc. B.376, 20200103 (2021). PubMed PMC

Rieseberg, L. H. Chromosomal rearrangements and speciation. Trends Ecol. Evol.16, 351–358 (2001). PubMed

Mantovani, B. & Scali, V. Hybridogenesis and androgenesis in the stick-insect Bacillus rossius-grandii benazzii (Insecta, Phasmatodea). Evolution46, 783–796 (1992). PubMed

Graf, J. Evolutionary genetics of the Rana esculenta complex. Evolution and Ecology of Unisexual Vertebrates 289–301 (1989).

Tunner, H. G. Die klonale Struktur einer Wasserfroschpopulation 1. J. Zool. Syst. Evol. Res.12, 309–314 (1974).

Schultz, R. J. Hybridization, unisexuality, and polyploidy in the teleost Poeciliopsis (Poeciliidae) and other vertebrates. Am. Nat.103, 605–619 (1969).

Schmidt, D. J., Bond, N. R., Adams, M. & Hughes, J. M. Cytonuclear evidence for hybridogenetic reproduction in natural populations of the Australian carp gudgeon (Hypseleotris: Eleotridae). Mol. Ecol.20, 3367–3380 (2011). PubMed

Munehara, H., Horita, M., Kimura-Kawaguchi, M. R. & Yamazaki, A. Origins of two hemiclonal hybrids among three Hexagrammos species (Teleostei: Hexagrammidae): Genetic diversification through host switching. Ecol. Evol.6, 7126–7140 (2016). PubMed PMC

Cimino, M. C. Egg-production, polyploidization and evolution in a diploid all-female fish of the genus Poeciliopsis. Evolution26, 294–306 (1972). PubMed

Esteban, M., Campos, M., Perondini, A. & Goday, C. Role of microtubules and microtubule organizing centers on meiotic chromosome elimination in Sciara ocellaris. J. Cell Sci.110, 721–730 (1997). PubMed

Zhang, Q., Arai, K. & Yamashita, M. Cytogenetic mechanisms for triploid and haploid egg formation in the triploid loach Misgurnus anguillicaudatus. J. Exp. Zool.281, 608–619 (1998).

Bongiorni, S., Pasqualini, B., Taranta, M., Singh, P. B. & Prantera, G. Epigenetic regulation of facultative heterochromatinisation in Planococcus citri via the Me (3) K9H3-HP1-Me (3) K20H4 pathway. J. Cell Sci.120, 1072–1080 (2007). PubMed

Chmielewska, M. et al. The programmed DNA elimination and formation of micronuclei in germ line cells of the natural hybridogenetic water frog Pelophylax esculentus. Sci. Rep.8, 1–19 (2018). PubMed PMC

Chmielewska, M. et al. Genome elimination from the germline cells in diploid and triploid male water frogs Pelophylax esculentus. Front. Cell Devel. Biol.10 (2022). PubMed PMC

Dedukh, D. et al. Variation in hybridogenetic hybrid emergence between populations of water frogs from the Pelophylax esculentus complex. PLOS ONE14, e0224759 (2019). PubMed PMC

Dedukh, et al. Parthenogenesis as a solution to hybrid sterility: the mechanistic basis of meiotic distortions in clonal and sterile hybrids. Genetics10.1534/genetics.119.302988 (2020). PubMed PMC

Escribá Pérez, M. C., Giardini, M. C. & Goday, C. Histone H3 phosphorylation and non-disjunction of the maternal X chromosome during male meiosis in sciarid flies. J. Cell Sci.124(10), 1715–1725 (2011). PubMed

Escribá Pérez, M. C. & Goday, C. Histone h3 phosphorylation and elimination of paternal X chromosomes at early cleavages in sciarid flies. J. Cell Sci.126(14), 3214–3222 (2013). PubMed

Del Priore, L. & Pigozzi, M. I. Histone modifications related to chromosome silencing and elimination during male meiosis in Bengalese finch. Chromosoma123, 293–302 (2014). PubMed

Liu, Y. et al. RNAi-dependent H3K27 methylation is required for heterochromatin formation and DNA elimination in Tetrahymena. Genes Dev.21, 1530–1545 (2007). PubMed PMC

Herdy, J. R. Small RNA Expression During Programmed Rearragement of a Vertebrate Genome (University of Kentucky, 2014).

Timoshevskiy, V. A., Herdy, J. R., Keinath, M. C. & Smith, J. J. Cellular and molecular features of developmentally programmed genome rearrangement in a vertebrate (sea lamprey: Petromyzon marinus). PLOS Genet.12, e1006103 (2016). PubMed PMC

Perondini, A. & Ribeiro, A. Chromosome elimination in germ cells of Sciara embryos: Involvement of the nuclear envelope. Invertebr. Reprod. Dev.32, 131–141 (1997).

Ogielska, M. Nucleus-like bodies in gonial cells of Rana esculenta [Amphibia, Anura] tadpoles-a putative way of chromosome elimination. Zool. Poloniae39 (1994).

Gernand, D., Rutten, T., Pickering, R. & Houben, A. Elimination of chromosomes in Hordeum vulgare × H. bulbosum crosses at mitosis and interphase involves micronucleus formation and progressive heterochromatinization. Cytogen. Gen. Res.114, 169–174 (2006). PubMed

Gernand, D. et al. Uniparental chromosome elimination at mitosis and interphase in wheat and pearl millet crosses involves micronucleus formation, progressive heterochromatinization, and DNA fragmentation. Plant Cell17, 2431–2438 (2005). PubMed PMC

Thacker, C. & Unmack, P. J. Phylogeny and biogeography of the eleotrid genus Hypseleotris (Teleostei: Gobioidei: Eleotridae), with redescription of H. cyprinoides. Rec. Aust. Mus.57, 1 (2005).

Thacker, C. E., Geiger, D. L. & Unmack, P. J. Species delineation and systematics of a hemiclonal hybrid complex in Australian freshwaters (Gobiiformes: Gobioidei: Eleotridae: Hypseleotris). R. Soc. Open Sci.9, 220201 (2022). PubMed PMC

Lehtonen, J., Schmidt, D. J., Heubel, K. & Kokko, H. Evolutionary and ecological implications of sexual parasitism. Tree28, 297–306 (2013). PubMed

Majtánová, Z. et al. Uniparental genome elimination in Australian carp gudgeons. Gen. Biol. Evol.13, evab030 (2021). PubMed PMC

Unmack, P. J. et al. Perspectives on the clonal persistence of presumed ‘ghost’ genomes in unisexual or allopolyploid taxa arising via hybridization. Sci. Rep.9, 4730 (2019). PubMed PMC

Begum, S., Gnanasree, S. M., Anusha, N. & Senthilkumaran, B. Germ cell markers in fishes-a review. Aquac. Fish7, 540–552 (2022).

Gustafson, E. A. & Wessel, G. M. Vasa genes: Emerging roles in the germ line and in multipotent cells. Bioessays32, 626–637 (2010). PubMed PMC

Goto, H. et al. Identification of a novel phosphorylation site on histone H3 coupled with mitotic chromosome condensation. J. Biol. Chem.274, 25543–25549 (1999). PubMed

Giet, R. & Glover, D. M. Drosophila aurora B kinase is required for histone H3 phosphorylation and condensin recruitment during chromosome condensation and to organize the central spindle during cytokinesis. J. Cell Biol.152, 669–682 (2001). PubMed PMC

Ruchaud, S., Carmena, M. & Earnshaw, W. C. Chromosomal passengers: conducting cell division. Nat. Rev. Mol. Cell Biol.8, 798–812 (2007). PubMed

Zhou, V. W., Goren, A. & Bernstein, B. E. Charting histone modifications and the functional organization of mammalian genomes. Nat. Rev. Genet.12, 7–18 (2011). PubMed

Preuss, U., Landsberg, G. & Scheidtmann, K. H. Novel mitosis-specific phosphorylation of histone H3 at Thr11 mediated by Dlk/ZIP kinase. Nucleic Acids Res.31, 878–885 (2003). PubMed PMC

Dedukh, D., Litvinchuk, S., Rosanov, J., Shabanov, D. & Krasikova, A. Mutual maintenance of di-and triploid Pelophylax esculentus hybrids in RE systems: results from artificial crossings experiments. BMC Evol. Biol.17, 1–15 (2017). PubMed PMC

Dedukh, D. et al. Micronuclei in germ cells of hybrid frogs from Pelophylax esculentus complex contain gradually eliminated chromosomes. Sci. Rep.10, 8720 (2020). PubMed PMC

Dedukh, D. et al. A cyclical switch of gametogenic pathways in hybrids depends on the ploidy level. Commun. Biol.7, 1–14 (2024). PubMed PMC

Wei, Y., Mizzen, C. A., Cook, R. G., Gorovsky, M. A. & Allis, C. D. Phosphorylation of histone H3 at serine 10 is correlated with chromosome condensation during mitosis and meiosis in Tetrahymena. Proc. Nat. Acad. Sci.95, 7480–7484 (1998). PubMed PMC

Ruban, A. et al. Supernumerary B chromosomes of Aegilops speltoides undergo precise elimination in roots early in embryo development. Nat. Com.11, 1–12 (2020). PubMed PMC

Staiber, W. Chromosome elimination in germ line–soma differentiation of Acricotopus lucidus (Diptera, Chironomidae). Genome49, 269–274 (2006). PubMed

Sotelo-Muñoz, M. et al. Germline-restricted chromosome shows remarkable variation in size among closely related passerine species. Chromosoma131, 77–86 (2022). PubMed

Janssen, A., van der Burg, M., Szuhai, K., Kops, G. J. P. L. & Medema, R. H. Chromosome segregation errors as a cause of DNA damage and structural chromosome aberrations. Science333, 1895–1898 (2011). PubMed

Cheeseman, I. M. The Kinetochore. Cold Spring Harb. Perspect Biol.6, a015826 (2014). PubMed PMC

Cimini, D. et al. Merotelic kinetochore orientation is a major mechanism of aneuploidy in mitotic mammalian tissue cells. J. Cell Biol.153, 517–528 (2001). PubMed PMC

Colicino, E. G. et al. Chromosome misalignment is associated with PLK1 activity at cenexin-positive mitotic centrosomes. Mol. Biol. Cell30, 1598–1609 (2019). PubMed PMC

Sanei, M., Pickering, R., Kumke, K., Nasuda, S. & Houben, A. Loss of centromeric histone H3 (CENH3) from centromeres precedes uniparental chromosome elimination in interspecific barley hybrids. P. Nat. Acad. Sci.108, E498–E505 (2011). PubMed PMC

Kang, Y. et al. Differential chromosomal localization of centromeric histone CENP-A contributes to nematode programmed DNA elimination. Cell Rep.16, 2308–2316 (2016). PubMed PMC

Bongiorni, S., Pasqualini, B., Taranta, M., Singh, P. B. & Prantera, G. Epigenetic regulation of facultative heterochromatinisation in Planococcus citri via the Me(3)K9H3-HP1-Me(3)K20H4 pathway. J. Cell Sci.120, 1072–1080 (2007). PubMed

Timoshevskiy, V. A., Herdy, J. R., Keinath, M. C. & Smith, J. J. Cellular and molecular features of developmentally programmed genome rearrangement in a vertebrate (Sea lamprey: Petromyzon marinus). PLOS Genet.12, 1–20 (2016). PubMed PMC

Goday, C. & Esteban, M. R. Chromosome elimination in sciarid flies. BioEssays23, 242–250 (2001). PubMed

Utani, K., Kohno, Y., Okamoto, A. & Shimizu, N. Emergence of micronuclei and their effects on the fate of cells under replication stress. PLOS ONE5, e10089 (2010). PubMed PMC

Tan, E. H. et al. Catastrophic chromosomal restructuring during genome elimination in plants. eLife4, e06516 (2015). PubMed PMC

Peng, Q. et al. Coordinated histone modifications and chromatin reorganization in a single cell revealed by FRET biosensors. Proc. Natl. Acad. Sci. U S A115, E11681-E11690, E (2018). PubMed PMC

Macgregor, H. & Uzzell, T. M. Gynogenesis in salamanders related to Ambystoma jeffersonianum. Science143, 1043–1045 (1964). PubMed

Itono, M. et al. Premeiotic endomitosis produces diploid eggs in the natural clone loach, Misgurnus anguillicaudatus (Teleostei: Cobitidae). J. Exp. Zool. Part A Comp. Exp. Biol.305, 513–523 (2006). PubMed

Lutes, A. A., Neaves, W. B., Baumann, D. P., Wiegraebe, W. & Baumann, P. Sister chromosome pairing maintains heterozygosity in parthenogenetic lizards. Nature464, 283–286 (2010). PubMed PMC

Stöck, M. et al. Simultaneous Mendelian and clonal genome transmission in a sexually reproducing, all-triploid vertebrate. P. Roy. Soc. B: Biol. Sci.279, 1293–1299 (2012). PubMed PMC

Dedukh, D., Litvinchuk, S., Rosanov, J., Mazepa, G., Saifitdinova, A., Shabanov, D. & Krasikova, A. Optional endoreplication and selective elimination of parental genomes during oogenesis in diploid and triploid hybrid European water frogs. PLOS ONE10(4), e0123304 (2015). PubMed PMC

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.22, 12117 (2021). PubMed PMC

Dedukh, D., Altmanová, M., Klíma, J. & Kratochvíl, L. Premeiotic endoreplication is essential for obligate parthenogenesis in geckos. Development149, 200345 (2022). PubMed

Juchno, D. et al. Evidence of the sterility of allotetraploid Cobitis loaches (Teleostei, Cobitidae) using testes ultrastructure. J. Exp. Zool. Part A Ecol. Integrat. Physiology327, 66–74 (2017). PubMed

Kuroda, M., Fujimoto, T., Murakami, M., Yamaha, E. & Arai, K. Aberrant meiotic configurations cause sterility in clone-origin triploid and inter-group hybrid males of the Dojo Loach, Misgurnus anguillicaudatus. Cytogenet. Gen. Res.158, 46–54 (2019). PubMed

Wang, J. et al. Cell fusion as the formation mechanism of unreduced gametes in the gynogenetic diploid hybrid fish. Sci. Rep.6, 1–12 (2016). PubMed PMC

Kilian, A. et al. Diversity arrays technology: a generic genome profiling technology on open platforms. Methods Mol. Biol.888, 67–89 (2012). PubMed

Gruber, B., Unmack, P. J., Berry, O. F. & Georges, A. dartr: An R package to facilitate analysis of SNP data generated from reduced representation genome sequencing. Mol. Ecol. Resour.18, 691–699 (2018). PubMed

Georges, A. et al. Genomewide SNP markers breathe new life into phylogeography and species delimitation for the problematic short-necked turtles (Chelidae: Emydura) of eastern Australia. Mol. Ecol.27, 5195–5213 (2018). PubMed

Gower, J. C. Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika53, 325–338 (1966).

Cattell, R. B. The scree test for the number of factors. Multivar. Behav. Res.1, 245–276 (1966). PubMed