Karyorelict ciliates use an ambiguous genetic code with context-dependent stop/sense codonsuse asterix (*) to get italics

Brandon Kwee Boon Seah, Aditi Singh, Estienne Carl SwartPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"

2022

<p style="text-align: justify;">In ambiguous stop/sense genetic codes, the stop codon(s) not only terminate translation but can also encode amino acids. Such codes have evolved at least four times in eukaryotes, twice among ciliates (<em>Condylostoma magnum</em> and <em>Parduczia</em> sp.). These have appeared to be isolated cases whose next closest relatives use conventional stop codons. However, little genomic data have been published for the Karyorelictea, the ciliate class that contains <em>Parduczia</em> sp., and previous studies may have overlooked ambiguous codes because of their apparent rarity. We therefore analyzed single-cell transcriptomes from four of the six karyorelict families to determine their genetic codes. Reassignment of canonical stops to sense codons was inferred from codon frequencies in conserved protein domains, while the actual stop codon was predicted from full-length transcripts with intact 3'-UTRs. We found that all available karyorelicts use the <em>Parduczia</em> code, where canonical stops UAA and UAG are reassigned to glutamine, and UGA encodes either tryptophan or stop. Furthermore, a small minority of transcripts may use an ambiguous stop-UAA instead of stop-UGA. Given the ubiquity of karyorelicts in marine coastal sediments, ambiguous genetic codes are not mere marginal curiosities but a defining feature of a globally distributed and diverse group of eukaryotes.</p>

https://www.ebi.ac.uk/ena/browser/view/PRJEB50648, https://doi.org/10.17617/3.XWMBKT, https://doi.org/10.17617/3.QLWR38You should fill this box only if you chose 'All or part of the results presented in this preprint are based on data'. URL must start with http:// or https://

https://doi.org/10.5281/zenodo.6784075, https://doi.org/10.5281/zenodo.6647650, https://doi.org/10.5281/zenodo.6647652, https://doi.org/10.5281/zenodo.6647679You should fill this box only if you chose 'Scripts were used to obtain or analyze the results'. URL must start with http:// or https://

https://github.com/Swart-lab/PORCYou should fill this box only if you chose 'Codes have been used in this study'. URL must start with http:// or https://

genetic code, codons, single cell transcriptomics, eukaryotic microbiology, protists, ciliates

NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).

Bioinformatics, Evolutionary genomics

Tsvetan R. Bachvaroff [bachvarofft@umces.edu], Pavel Baranov [p.baranov@ucc.ie], Andre Cavalcanti [aroc@pomona.edu], Marek Eliáš [marek.elias@osu.cz], Natalia Ivanova [NNIvanova@lbl.gov], Stefanie Mühlhausen [me@stefaniemuehlhausen.de]

e.g. John Doe john@doe.com

No need for them to be recommenders of PCI Genomics. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct

Laura A Katz [lkatz@smith.edu]e.g. John Doe john@doe.com

2022-05-02 11:06:10

Iker Irisarri