Genomic evidence of paternal genome elimination in globular springtails

Slides to a PopGroup55 lecture by Kamil S Jaron.

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
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
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