Computational methods for inferring location and genealogy of overlapping genes in virus genomes: approaches and applications.
Journal
Current opinion in virology
ISSN: 1879-6265
Titre abrégé: Curr Opin Virol
Pays: Netherlands
ID NLM: 101560941
Informations de publication
Date de publication:
02 2022
02 2022
Historique:
received:
04
09
2021
revised:
21
10
2021
accepted:
22
10
2021
pubmed:
20
11
2021
medline:
17
2
2022
entrez:
19
11
2021
Statut:
ppublish
Résumé
Viruses may evolve to increase the amount of encoded genetic information by means of overlapping genes, which utilize several reading frames. Such overlapping genes may be especially impactful for genomes of small size, often serving a source of novel accessory proteins, some of which play a crucial role in viral pathogenicity or in promoting the systemic spread of virus. Diverse genome-based metrics were proposed to facilitate recognition of overlapping genes that otherwise may be overlooked during genome annotation. They can detect the atypical codon bias associated with the overlap (e.g. a statistically significant reduction in variability at synonymous sites) or other sequence-composition features peculiar to overlapping genes. In this review, I compare nine computational methods, discuss their strengths and limitations, and survey how they were applied to detect candidate overlapping genes in the genome of SARS-CoV-2, the etiological agent of COVID-19 pandemic.
Identifiants
pubmed: 34798370
pii: S1879-6257(21)00131-0
doi: 10.1016/j.coviro.2021.10.009
pmc: PMC8594276
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
1-8Informations de copyright
Copyright © 2021 Elsevier B.V. All rights reserved.
Références
Trends Biochem Sci. 2004 Jun;29(6):279-81
pubmed: 15276178
Virology. 2021 Jun;558:145-151
pubmed: 33774510
J Gen Virol. 2016 Sep;97(9):2333-2345
pubmed: 27325292
Evolution. 2000 Jun;54(3):731-9
pubmed: 10937248
Genome Biol Evol. 2014 Dec 31;7(1):381-90
pubmed: 25552532
PLoS One. 2018 Oct 19;13(10):e0202513
pubmed: 30339683
Virology. 2021 Oct;562:149-157
pubmed: 34339929
Chem Rev. 2014 Jul 9;114(13):6589-631
pubmed: 24773235
EMBO Rep. 2005 Dec;6(12):1149-55
pubmed: 16270100
Cell. 2003 Dec 26;115(7):799-811
pubmed: 14697199
Nature. 2020 Mar;579(7798):270-273
pubmed: 32015507
Nucleic Acids Res. 2014 Nov 10;42(20):12425-39
pubmed: 25326325
Genome Res. 2007 Oct;17(10):1496-504
pubmed: 17785537
PLoS One. 2011;6(10):e25697
pubmed: 22022432
Virol J. 2020 Aug 27;17(1):131
pubmed: 32854725
J Gen Virol. 2020 Oct;101(10):1085-1089
pubmed: 32667280
Elife. 2020 Oct 01;9:
pubmed: 33001029
Nat Med. 2001 Dec;7(12):1306-12
pubmed: 11726970
Nucleic Acids Res. 2015 May 26;43(10):4800-13
pubmed: 25904630
PeerJ. 2019 Jan 10;6:e6176
pubmed: 30647994
Genes (Basel). 2021 May 26;12(6):
pubmed: 34073395
Nat Commun. 2021 May 11;12(1):2642
pubmed: 33976134
Virus Evol. 2020 Feb 13;6(1):veaa009
pubmed: 32071766
Bioinformatics. 2011 Jul 1;27(13):i275-82
pubmed: 21685081
PLoS Comput Biol. 2013;9(8):e1003162
pubmed: 23966842
Proc Natl Acad Sci U S A. 1992 Oct 15;89(20):9489-93
pubmed: 1329098
PLoS Pathog. 2011 Dec;7(12):e1002413
pubmed: 22174679
Structure. 2006 Jul;14(7):1157-65
pubmed: 16843897
Cell Rep. 2020 Sep 22;32(12):108185
pubmed: 32941788
Nature. 2021 Jan;589(7840):125-130
pubmed: 32906143
J Gen Virol. 2006 Apr;87(Pt 4):1013-1017
pubmed: 16528052
Genome Biol. 2015 Feb 17;16:38
pubmed: 25853568
Nat Rev Genet. 2021 Oct 5;:
pubmed: 34611352
Science. 2012 Jul 13;337(6091):199-204
pubmed: 22745253
J Virol. 2009 Oct;83(20):10719-36
pubmed: 19640978
Nat Microbiol. 2020 Apr;5(4):536-544
pubmed: 32123347
J Mol Evol. 2000 Mar;50(3):284-95
pubmed: 10754072
Nucleic Acids Res. 2016 Jan 8;44(1):14-23
pubmed: 26578573
Mol Biol Evol. 2020 Aug 1;37(8):2440-2449
pubmed: 32243542
Proc Biol Sci. 2010 Dec 22;277(1701):3809-17
pubmed: 20610432
Mol Biol Evol. 2018 Oct 1;35(10):2572-2581
pubmed: 30099499
Nucleic Acids Res. 2015 Jan;43(Database issue):D571-7
pubmed: 25428358
Nat Commun. 2020 Aug 13;11(1):4070
pubmed: 32792502
Virology. 2020 Jul;546:51-66
pubmed: 32452417