Letter

Paternal chromosome loss and metabolic crisis contribute to hybrid inviability in Xenopus

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Published online:

Abstract

Hybridization of eggs and sperm from closely related species can give rise to genetic diversity, or can lead to embryo inviability owing to incompatibility. Although central to evolution, the cellular and molecular mechanisms underlying post-zygotic barriers that drive reproductive isolation and speciation remain largely unknown1,2. Species of the African clawed frog Xenopus provide an ideal system to study hybridization and genome evolution. Xenopus laevis is an allotetraploid with 36 chromosomes that arose through interspecific hybridization of diploid progenitors, whereas Xenopus tropicalis is a diploid with 20 chromosomes that diverged from a common ancestor approximately 48 million years ago3. Differences in genome size between the two species are accompanied by organism size differences, and size scaling of the egg and subcellular structures such as nuclei and spindles formed in egg extracts4. Nevertheless, early development transcriptional programs, gene expression patterns, and protein sequences are generally conserved5,6. Whereas the hybrid produced when X. laevis eggs are fertilized by X. tropicalis sperm is viable, the reverse hybrid dies before gastrulation7,8. Here we apply cell biological tools and high-throughput methods to study the mechanisms underlying hybrid inviability. We reveal that two specific X. laevis chromosomes are incompatible with the X. tropicalis cytoplasm and are mis-segregated during mitosis, leading to unbalanced gene expression at the maternal to zygotic transition, followed by cell-autonomous catastrophic embryo death. These results reveal a cellular mechanism underlying hybrid incompatibility that is driven by genome evolution and contributes to the process by which biological populations become distinct species.

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Acknowledgements

We thank members of the Heald laboratory, present and past, for support and discussions. We thank the students who helped with some of the experiments: B. Castellano, J. Chen, S. Ramos, A. Sabillo, and K. Shih. We are also grateful to the Marine Biological Laboratory and the National Xenopus Resource for organizing the 2013 Advanced Imaging in Xenopus Workshop where several techniques used here were taught to R.G., and to J. Wallingford and A. Shindo for subsequent support. We thank the Welch, King, Harland, Rokhsar, Barton, and Fletcher laboratories at the University of California, Berkeley (UC Berkeley) for sharing reagents, materials, and expertise, as well as T. Stukenberg and A. Straight for providing us with the Ndc80 and CENP-A antibodies, respectively. We especially thank A. Mudd and D. Rokhsar for providing early access to the X. borealis genome assembly. This work used the Functional Genomics Laboratory, a QB3-Berkeley Core Research Facility at UC Berkeley as well as the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by National Institutes of Health (NIH) S10 OD018174 Instrumentation Grant. The confocal microscopy performed in this work was done at the UC Berkeley CRL Molecular Imaging Center, supported by National Science Foundation DBI-1041078. R.G. was initially supported by EMBO long-term fellowship ALTF 836-2013 and for most of this project by Human Frontier Science Program long-term fellowship LT 0004252014-L. R.A. was supported in part by a National Science Foundation REU Summer Fellowship in 2014. R.H. was supported by NIH R35 GM118183 and the Flora Lamson Hewlett Chair. D.K.N. was supported by NIH R01 CA172667. M.K. was supported by UC Berkeley Department of Molecular and Cell Biology NIH training grant 4T32GM007232-40. T.K. was supported by Basic Science Research Program through the National Research Foundation of Korea funded by the Ministry of Science, ICT and Future Planning (NRF-2016R1C1B2009302), and the UNIST Research Fund (grant number 1.160060.01). G.J.C.V., I.V.K., and G.G. were supported by NIH R01 HD069344.

Author information

Affiliations

  1. Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA

    • Romain Gibeaux
    • , Rachael Acker
    • , Maiko Kitaoka
    •  & Rebecca Heald
  2. Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, 6500 HB Nijmegen, The Netherlands

    • Georgios Georgiou
    • , Ila van Kruijsbergen
    •  & Gert Jan C. Veenstra
  3. Departments of Chemistry and Nutritional Sciences and Toxicology, University of California, Berkeley, California 94720, USA

    • Breanna Ford
    •  & Daniel K. Nomura
  4. Department of Molecular Bioscience, Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA

    • Edward M. Marcotte
  5. Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, South Korea

    • Taejoon Kwon

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Contributions

R.H. and R.G. designed the project. R.G. performed the molecular, cell, and developmental biology experiments, aided by R.A., and analysed the data. M.K., together with R.G., performed the experiments related to X. borealis and analysed the data. G.J.C.V., I.V.K., and G.G. prepared and analysed the hybrid genomes. B.M. and D.K.N. performed the metabolomic profiling of hybrids. T.K. and E.M.M. contributed to the transcriptome data analysis. R.G. prepared the figures and wrote the manuscript with R.H., incorporating feedback from all authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Rebecca Heald.

Reviewer Information Nature thanks E. Amaya and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Supplementary information

PDF files

  1. 1.

    Life Sciences Reporting Summary

Excel files

  1. 1.

    Supplementary Table 1

    This table shows chromosomal distribution of lost vs. remaining DNA in te×ls, tte×ls and te×bs hybrids.

  2. 2.

    Supplementary Table 2

    This table shows transcriptome profiling of te×ls hybrid compared to X. tropicalis embryos at 7 hpf.

Videos

  1. 1.

    Characterization of te×ls hybrid embryo death; X. tropicalis vs. te×ls

    X. tropicalis eggs were fertilized with X. tropicalis (left) or X. laevis sperm (right) and simultaneously imaged in separate dishes. The video plays 20h in 15s (rate of 120 fps) and the scale bar corresponds to 200 μm.

  2. 2.

    Cell death in te×ls hybrid animal cap; X. tropicalis vs. te×ls

    X. tropicalis eggs were fertilized with X. tropicalisX. tropicalis sperm (left) or X. laevis sperm (right). At stage 8, animal caps were isolated and simultaneously imaged in separate dishes. The video plays 20h in 15s (rate of 120 fps) and the scale bar corresponds to 200 μm.

  3. 3.

    Role of X. laevis DNA in te×ls hybrid embryo death te×ls vs. te×[ls]

    X. tropicalis eggs were fertilized with X. laevis sperm (left) or UV-irradiated X. laevis sperm (right) and simultaneously imaged in separate dishes. The video plays 20h in 15s (rate of 120 fps) and the scale bar corresponds to 200 μm.

  4. 4.

    Development of X. tropicalis haploid embryos; te×[ts] vs. te×[ls]

    X. tropicalis eggs were fertilized with UV-irradiated X. tropicalis sperm (left) or UV-irradiated X. laevis sperm (right) and simultaneously imaged in separate dishes. The video plays 20h in 15s (rate of 120 fps) and the scale bar corresponds to 200 μm.

  5. 5.

    Mitosis in te×ls hybrid animal cap

    X. tropicalis eggs were fertilized with X. laevis sperm. In vitro transcribed mRNA coding for the microtubule end binding protein EB3 labeled with GFP and histone H2B labeled with RFP was injected into stage 2 embryos. At stage 8, animal caps were isolated, mounted and imaged using live confocal microscopy. Histone H2B-RFP (shown in magenta) and EB3-GFP (shown in green) signals were imaged in a single plane with a frame size of 1024x1024 pixels, every 5s. The movie plays 20 min in 8s (rate of 30 fps). The time is in mm:ss and the scale bar is 20 µm.

  6. 6.

    Phenotype of embryo death induced by inhibition of protein synthesis

    X. tropicalis eggs were fertilized with X. tropicalis sperm and imaged while incubated from stage 6.5 in 1/10X MMR containing 0.1 mg/ml cycloheximide. The video plays 20h in 15s (rate of 120 fps) and the scale bar corresponds to 200 μm.

  7. 7.

    Phenotype of embryo death induced by inhibition of DNA replication

    X. tropicalis eggs were fertilized with X. tropicalis sperm and imaged while incubated from stage 3 in 1/10X MMR containing 30 mM hydroxyurea. The video plays 20h in 15s (rate of 120 fps) and the scale bar corresponds to 200 μm.

  8. 8.

    Phenotype of embryo death induced by inhibiting transcription using triptolide

    X. tropicalis eggs were fertilized with X. tropicalis sperm and imaged in separate dishes while incubated from stage 2 in 1/10X MMR containing 25 μM triptolide (left) or a corresponding amount of DMSO (right). The video plays 20h in 15s (rate of 120 fps) and the scale bar corresponds to 200 μm.

  9. 9.

    Effect of triptolide treatment on te×ls hybrid embryos

    X. tropicalis eggs were fertilized with X. laevis sperm and imaged in separate dishes while incubated from stage 2 in 1/10X MMR containing 25 μM triptolide (left) or a corresponding amount of DMSO (right). The video plays 20h in 15s (rate of 120 fps) and the scale bar corresponds to 200 μm.

  10. 10.

    Effect of inhibiting ATP synthase on X. tropicalis embryos

    X. tropicalis eggs were fertilized with X. tropicalis sperm and imaged in separate dishes while incubated from stage 2 in 1/10X MMR containing 40 μM oligomycin (left) or a corresponding amount of DMSO (right). The video plays 20h in 15s (rate of 120 fps) and the scale bar corresponds to 200 μm.

  11. 11.

    Effect of inhibiting glyceraldehyde-3-P dehydrogenase on X. tropicalis embryos

    X. tropicalis eggs were fertilized with X. tropicalis sperm and imaged in separate dishes while incubated from stage 2 in 1/10X MMR containing 50 mM iodoacetic acid (left) or a corresponding amount of ddH2O (right). The video plays 20h in 15s (rate of 120 fps) and the scale bar corresponds to 200 μm.

  12. 12.

    Effect of inhibiting glycogen phosphorylase on X. tropicalis embryos.

    X. tropicalis eggs were fertilized with X. tropicalis sperm and imaged in separate dishes while incubated from stage 2 in 1/10X MMR containing 270 μM CP-91,149 (left) or a corresponding amount of DMSO (right). The video plays 20h in 15s (rate of 120 fps) and the scale bar corresponds to 200 μm.

  13. 13.

    Characterization of te×bs hybrid embryo inviability; X. tropicalis vs. te×bs.

    X. tropicalis eggs were fertilized with X. borealis sperm (left) or X. tropicalis sperm (right) and simultaneously imaged in separate dishes. The video plays 20h in 15s (rate of 120 fps) and the scale bar corresponds to 200 μm.

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