Polymorphism of genetic ambigrams.

Gytis Dudas,Michael Wilkinson,Greg Huber,David Yllanes

doi:10.1093/ve/veab038

Gytis Dudas, Michael Wilkinson + Show 2 more

Open Access

https://doi.org/10.1093/ve/veab038

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Abstract

Double synonyms in the genetic code can be used as a tool to test competing hypotheses regarding ambigrammatic narnavirus genomes. Applying the analysis to recent observations of Culex narnavirus 1 and Zhejiang mosquito virus 3 ambigrammatic viruses indicates that the open reading frame on the complementary strand of the segment coding for RNA-dependent RNA polymerase does not code for a functional protein. Culex narnavirus 1 has been shown to possess a second segment, also ambigrammatic, termed ‘Robin’. We find a comparable segment for Zhejiang mosquito virus 3, a moderately diverged relative of Culex narnavirus 1. Our analysis of Robin polymorphisms suggests that its reverse open reading frame also does not code for a functional protein. We make a hypothesis about its role.

Highlights

Of all the various types of viruses catalogued, narnaviruses rank among the simplest and most surprising (Cobian Guemes et al 2016)
We report the results of our studies of polymorphism of the four ambigrammatic narnavirus genes
We have argued that doubly synonymous codons provide a key to understanding whether ambigrammatic viral RNA segments code for two functional proteins

Summary

Introduction

Of all the various types of viruses catalogued, narnaviruses rank among the simplest and most surprising (Cobian Guemes et al 2016). Some narnaviruses have been found to have a genome with an open reading frame (ORF) (i.e. a reading frame without stop codons) on the strand complementary to that coding for the RdRp gene, calling into question the general hypothesis of a one-gene blueprint (Cook et al 2013; DeRisi et al 2019; Dinan et al 2020; Cepelewicz 2020). This reverse ORF (rORF) has codon boundaries aligned with the forward reading frame. Our methods are applied to known ambigrammatic narnavirus genes and to the newly discovered ambigrammatic second segment of some narnaviruses, termed Robin (Batson et al 2021)

Methods

Results

Conclusion