Article ; Online: Evolutionary selection against short nucleotide sequences in viruses and their related hosts.
DNA research : an international journal for rapid publication of reports on genes and genomes
2020 Volume 27, Issue 2
Abstract: ... of viruses and their hosts. These sequences cannot be explained by the coding regions' amino acid content ... Viruses are under constant evolutionary pressure to effectively interact with the host ... and a large-scale genomic analysis of 2,625 viruses from all classes infecting 439 host ...
| 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. |
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| MeSH term(s) | Animals ; Bacteria/genetics ; Bacteria/virology ; Biological Coevolution ; Evolution, Molecular ; Female ; Fungi/genetics ; Fungi/virology ; Genome, Viral ; Host-Pathogen Interactions ; Male ; Mice ; Nucleotide Motifs ; Oligonucleotides/genetics ; Plants/genetics ; Plants/virology ; Selection, Genetic ; Systems Biology/methods ; Zika Virus/genetics ; Zika Virus/pathogenicity | |||||
| Chemical Substances | Oligonucleotides | |||||
| Keywords | covid19 | |||||
| Language | English | |||||
| Publishing date | 2020-05-13 | |||||
| Publishing country | England | |||||
| Document type | Journal Article | |||||
| ZDB-ID | 1212508-8 | |||||
| ISSN | 1756-1663 ; 1340-2838 | |||||
| ISSN (online) | 1756-1663 | |||||
| ISSN | 1340-2838 | |||||
| DOI | 10.1093/dnares/dsaa008 | |||||
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| Database | MEDical Literature Analysis and Retrieval System OnLINE |
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