Document Type
Article
Journal/Book Title/Conference
DNA Research
Volume
27
Issue
2
Publisher
Oxford University Press
Publication Date
4-27-2020
First Page
1
Last Page
16
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License
Abstract
Viruses are under constant evolutionary pressure to effectively interact with the host intracellular factors, while evading its immune system. Understanding how viruses co-evolve with their hosts is a fundamental topic in molecular evolution and may also aid in developing novel viral based applications such as vaccines, oncologic therapies, and anti-bacterial treatments. Here, based on a novel statistical framework and a large-scale genomic analysis of 2,625 viruses from all classes infecting 439 host organisms from all kingdoms of life, we identify short nucleotide sequences that are under-represented in the coding regions of viruses and their hosts. These sequences cannot be explained by the coding regions’ amino acid content, codon, and dinucleotide frequencies. We specifically show that short homooligonucleotide and palindromic sequences tend to be under-represented in many viruses probably due to their effect on gene expression regulation and the interaction with the host immune system. In addition, we show that more sequences tend to be under-represented in dsDNA viruses than in other viral groups. Finally, we demonstrate, based on in vitro and in vivo experiments, how under-represented sequences can be used to attenuated Zika virus strains.
Recommended Citation
Yoram Zarai, Zohar Zafrir, Bunpote Siridechadilok, Amporn Suphatrakul, Modi Roopin, Justin Julander, Tamir Tuller, Evolutionary selection against short nucleotide sequences in viruses and their related hosts, DNA Research, Volume 27, Issue 2, April 2020, dsaa008, https://doi.org/10.1093/dnares/dsaa008
