An exploration of ambigrammatic sequences in narnaviruses

@article{Derisi2019AnEO,
  title={An exploration of ambigrammatic sequences in narnaviruses},
  author={Joseph L. Derisi and Greg Huber and Amy L Kistler and Hanna Retallack and Michael Wilkinson and David Yllanes},
  journal={Scientific Reports},
  year={2019},
  volume={9}
}
Narnaviruses have been described as positive-sense RNA viruses with a remarkably simple genome of ~3 kb, encoding only a highly conserved RNA-dependent RNA polymerase (RdRp). Many narnaviruses, however, are ‘ambigrammatic’ and harbour an additional uninterrupted open reading frame (ORF) covering almost the entire length of the reverse complement strand. No function has been described for this ORF, yet the absence of stops is conserved across diverse narnaviruses, and in every case the codons in… 
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References

SHOWING 1-10 OF 37 REFERENCES
The family narnaviridae: simplest of RNA viruses.
A case for a reverse-frame coding sequence in a group of positive-sense RNA viruses
TLDR
The genomes of three mosquito-associated narnaviruses are completed, providing the strongest evidence yet of coding capacity on the negative strand of a positive-sense RNA virus.
Antisense overlapping open reading frames in genes from bacteria to humans.
TLDR
Examination of the sequence database for several prokaryotic and eukaryotic organisms, demonstrates that coding sequences with in-phase, 100% overlapping antisense ORFs are present in every genome studied so far.
The evolution of genome compression and genomic novelty in RNA viruses.
TLDR
It is suggested that RNA viruses are a good model system for the investigation of general evolutionary relationship between genome attributes such as mutational robustness, mutation rate, and size.
A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences
TLDR
This work introduces a simple new method for identifying candidate functional overlapping genes using single virus genome sequences and finds that it has both high sensitivity and low false discovery for genes that overlap by at least 50 nucleotides.
Gene overlapping and size constraints in the viral world
TLDR
It is found that the volume utilization of capsids is often low, and greatly varies among viral families, undermining the generality of the compression theory, which emphasizes optimal packing and length dependency to explain overlapping genes and capsid size in viral genomes.
The combinatorics of overlapping genes.
Novel Virus Discovery and Genome Reconstruction from Field RNA Samples Reveals Highly Divergent Viruses in Dipteran Hosts
TLDR
It is clear that viral transmission and maintenance cycles in nature are likely to be significantly more complex and taxonomically diverse than previously expected.
Why genes overlap in viruses
TLDR
It is concluded that gene overlap is unlikely to have evolved as a way of compressing the genome in response to the harmful effect of mutation because RNA viruses, despite having generally higher mutation rates, have less gene overlap on average than DNA viruses of comparable genome length.
Overlapping Genes Produce Proteins with Unusual Sequence Properties and Offer Insight into De Novo Protein Creation
TLDR
Analysis of sequences of the protein products of manually curated overlapping genes from 43 genera of unspliced RNA viruses infecting eukaryotes suggests that some viral overlapping reading frames encoding hypothetical proteins with highly biased composition, often discarded as noncoding, might in fact encode proteins.
...
1
2
3
4
...