The genomic revolution has given us access to inexpensive genetic data for any species. Simultaneously we have lost the ability to easily identify chimerism in samples or some unusual deviations from standard Mendelian genetics. Methods have been developed to identify sex chromosomes, characterise the ploidy, or understand the exact form of parthenogenesis from genomic data. However, we rarely consider that the tissues we extract DNA from could be a mixture of cells with different genotypes or karyotypes. This can nonetheless happen for a variety of (fascinating) reasons such as somatic chromosome elimination, transmissible cancer, or parental genome elimination. Without a dedicated analysis, it is very easy to miss it.
In this preprint, Jaron et al. (2022) used an ingenious analysis of whole individual NGS data to test the hypothesis of paternal genome elimination in the globular springtail Allacma fusca. The authors suspected that a high fraction of the whole body of males is made of sperm in this species and if this species undergoes paternal genome elimination, we would expect that sperm would only contain maternally inherited chromosomes. Given the reference genome was highly fragmented, they developed a two-tissue model to analyse Kmer spectra and obtained confirmation that around one-third of the tissue was sperm in males. This allowed them to test whether coverage patterns were consistent with the species exhibiting paternal genome elimination. They combined their estimation of the fraction of haploid tissue with allele coverages in autosomes and the X chromosome to obtain support for a bias toward one parental allele, suggesting that all sperm carries the same parental haplotype. It could be the maternal or the paternal alleles, but paternal genome elimination is most compatible with the known biology of Arthropods. SNP calling was used to confirm conclusions based on the analysis of the raw pileups.
I found this study to be a good example of how a clever analysis of Kmer spectra and allele coverages can provide information about unusual modes of reproduction in a species, even though it does not have a well-assembled genome yet. As advocated by the authors, routine inspection of Kmer spectra and allelic read-count distributions should be included in the best practice of NGS data analysis. They provide the method to identify paternal genome elimination but also the way to develop similar methods to detect another kind of genetic chimerism in the avalanche of sequence data produced nowadays.
Jaron KS, Hodson CN, Ellers J, Baird SJ, Ross L (2022) Genomic evidence of paternal genome elimination in the globular springtail Allacma fusca. bioRxiv, 2021.11.12.468426, ver. 5 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2021.11.12.468426
DOI or URL of the preprint: https://www.biorxiv.org/content/10.1101/2021.11.12.468426v2
Version of the preprint: 2
Dear Dr Jaron,
Sorry for the delay to process this resubmission. I had problem with emails going in junk mails followed by one referee being off line for a long period, and then me. Referees are happy with the revisions you made and I am pleased to accept your preprint for a recommendation in PCI Evol Biol. I’m working on the recommendation text now. Meanwhile, could you correct the typos identified by referee#2 and resubmit again please?
Thank you for your support of the PCI initiative, and sorry again for the delay.
DOI or URL of the preprint: https://doi.org/10.1101/2021.11.12.468426
Version of the preprint: 1
Dear Dr Jaron,
We have received three thoughtful reviews of your manuscript entitled “Genomic evidence of paternal genome elimination in globular springtails”. The three referees are globally positive, as well as I was when I accepted to handle this preprint for a recommendation. As it is current practice, I’ll ask you to revise your ms according to referees’ concerns and provide a cover letter where you explain how you modified the ms. Referee 1 and 3 have only a few minor concerns to improve clarity that you should easily account for. Referee 2 who signed his review has a longest list of comments. This referee will likely see the revised version. I am looking forward to reading your revised ms and to work on a nice recommendation to advertise your interesting work.