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Genomic evidence of paternal genome elimination in globular springtails

Genomic evidence of paternal genome elimination in globular springtails

Slides to a PopGroup55 lecture by Kamil S Jaron.

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Kamil S Jaroň

January 13, 2022
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Transcript

  1. Genomic evidence of Paternal Genome Elimination in globular springtails Kamil

    S. Jaron Christina N. Hodson Jacintha Ellers Stuart JE Baird Laura Ross @KamilSJaron
  2. genome assembly sequencing reads Genome sequencing

  3. k-mer spectra analysis genome assembly sequencing reads Genome sequencing

  4. Ranallo-Benavidez et al. 2020 k-mer spectra analysis Histogram of coverages

    of all the k-mers
  5. k-mer spectra to explore genomics data

  6. k-mer spectra of male globular springtails ♂ Allacma fusca karyotype

    from Dallai et al. 2000
  7. Two tissue model

  8. Two tissue model c A - autosomal coverage peak c

    X - X-chromosome coverage peak
  9. Two tissue model c A - autosomal coverage peak c

    X - X-chromosome coverage peak f h = 1 - ⅔ = ⅓ ⅔ ⅓
  10. 18.35x 29.65x 1n coverage shift pattern replicated in another male

    autosomes X 57.7x 95.15x ♂
  11. What could be the haploid tissue?

  12. Found in multiple families of globular springtails • ½ sperm

    A00, and degenerate • ½ sperm AX 1 X 2 Aberant spermatogenesis Dallai et al. 2000, Dallai et al. 2001, Dallai et al. 2004
  13. Proposed paternal-genome elimination model Dallai et al. 2000, Dallai et

    al. 2001, Dallai et al. 2004
  14. Two tissue model in globular springtails

  15. Springtails are “jumpy bags of sperm” 38% cells 62% cells

  16. None
  17. Autosomal variants are consistent with PGE

  18. Orchesella cincta - documented regular spermatogenesis - X0 sex determination

    system X alleles have mean coverage exactly in between of the major/minor peaks
  19. Coverage ratio also supports PGE in globular springtails

  20. Globular springtails are the 7th confirmed PGE clade

  21. Fungus gnats carry germ-line restricted chromosomes Christina Hodson

  22. Germ-line library is a mixed-tissue library! GRC X Autosomes Two

    libraries sequenced: 1. “Soma” - pure 2. “Germ” - ~40% germ and ~60% soma
  23. Two tissue model in whole-body samples • scans for certain

    abnormalities in reproduction GRC X Autosomes
  24. Summary • Male globular springtails are full of sperm (~38%)

    • Globular springtails reproduce via paternal genome elimination ◦ 7th confirmed independent origin of PGE • Two tissue model can reveal abnormalities in reproduction
  25. Acknowledgements Ross lab Laura Ross Christina Hodson Jacintha Ellers Stuart

    JE Baird
  26. Questions? Thank you for your attention

  27. Supplementary slides

  28. None
  29. Statistical problem with assuming allele of origin paternal = rnbinom(size

    = 15, mu = 14) maternal = rnbinom(size = 15, mu = 14) paternal maternal 21 14 14 17 13 14 22 7 23 18 16 19 paternal = rnbinom(size = 15, mu = 10) maternal = rnbinom(size = 15, mu = 19) paternal maternal 8 26 11 23 7 24 10 17 8 14 10 9
  30. What about maternal genome elimination? • Exist in rare form

    of androgenesis ◦ freshwater clam Corbicula leana ◦ Australian carp gudgeons • Extremely unlikely in the case of globular springtails as the aberrant spermatogenesis seems to be present already in the common ancestor of globular springtails. By Korea Educational Broadcasting System By Codman
  31. Dallai et al. 2000, Dallai et al. 2001, Dallai et

    al. 2004 Remarkably similar to fungus gnats Figure by Laura Ross Aberant spermatogenesis