Evolution shapes and conserves genomic signatures in viruses.
Journal
Communications biology
ISSN: 2399-3642
Titre abrégé: Commun Biol
Pays: England
ID NLM: 101719179
Informations de publication
Date de publication:
30 Oct 2024
30 Oct 2024
Historique:
received:
22
12
2023
accepted:
17
10
2024
medline:
31
10
2024
pubmed:
31
10
2024
entrez:
31
10
2024
Statut:
epublish
Résumé
The genomic signature of an organism captures the characteristics of repeated oligonucleotide patterns in its genome
Identifiants
pubmed: 39478059
doi: 10.1038/s42003-024-07098-1
pii: 10.1038/s42003-024-07098-1
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1412Subventions
Organisme : Vetenskapsrådet (Swedish Research Council)
ID : 2015-05307
Organisme : Svenska Forskningsrådet Formas (Swedish Research Council Formas)
ID : 2017/0009
Informations de copyright
© 2024. The Author(s).
Références
Karlin, S. & Burge, C. Dinucleotide relative abundance extremes: a genomic signature. Trends in Genet. 11, 403–409 (1995).
Sandberg, R., Branden, C. I., Ernberg, I. & Coster, J. Quantifying the species-specificity in genomic signatures, synonymous codon choice, amino acid usage and G+C content. Gene 311, 35–42 (2003).
pubmed: 12853136
doi: 10.1016/S0378-1119(03)00581-X
Hooper, S. D. & Berg, O. G. Detection of genes with atypical nucleotide sequence in microbial genomes. J. Mol. Evol. 54, 365–375 (2002).
pubmed: 11847562
doi: 10.1007/s00239-001-0051-8
Coleman, J. R. et al. Virus attenuation by genome-scale changes in codon pair bias. Science 320, 1784–1787 (2008).
pubmed: 18583614
pmcid: 2754401
doi: 10.1126/science.1155761
Deschavanne, P. J., Giron, A., Vilain, J., Fagot, G. & Fertil, B. Genomic signature: characterization and classification of species assessed by chaos game representation of sequences. Mol. Biol. Evol. 16, 1391–1399 (1999).
pubmed: 10563018
doi: 10.1093/oxfordjournals.molbev.a026048
Dalevi, D., Dubhashi, D. & Hermansson, M. Bayesian classifiers for detecting HGT using fixed and variable order Markov models of genomic signatures. Bioinformatics 22, 517–522 (2006).
pubmed: 16403797
doi: 10.1093/bioinformatics/btk029
Norberg, P., Bergstrom, M., Jethava, V., Dubhashi, D. & Hermansson, M. The IncP-1 plasmid backbone adapts to different host bacterial species and evolves through homologous recombination. Nat. Commun. 2, 268 (2011).
pubmed: 21468020
doi: 10.1038/ncomms1267
de la Fuente, R., Díaz-Villanueva, W., Arnau, V. & Moya, A. Genomic signature in evolutionary biology: a review. Biology 12, https://doi.org/10.3390/biology12020322 (2023).
Karlin, S. & Ladunga, I. Comparisons of eukaryotic genomic sequences. Proc. Natl. Acad. Sci. USA 91, 12832–12836 (1994).
pubmed: 7809130
pmcid: 45534
doi: 10.1073/pnas.91.26.12832
Lobo, F. P. et al. Virus-host coevolution: common patterns of nucleotide motif usage in Flaviviridae and their hosts. PLoS ONE 4, e6282 (2009).
pubmed: 19617912
pmcid: 2707012
doi: 10.1371/journal.pone.0006282
Edwards, R. A., McNair, K., Faust, K., Raes, J. & Dutilh, B. E. Computational approaches to predict bacteriophage-host relationships. FEMS Microbiol. Rev. 40, 258–272 (2016).
pubmed: 26657537
doi: 10.1093/femsre/fuv048
Buchan, J. R., Aucott, L. S. & Stansfield, I. tRNA properties help shape codon pair preferences in open reading frames. Nucleic Acids Res. 34, 1015–1027 (2006).
pubmed: 16473853
pmcid: 1363775
doi: 10.1093/nar/gkj488
Le Nouen, C. et al. Attenuation of human respiratory syncytial virus by genome-scale codon-pair deoptimization. Proc. Natl. Acad. Sci. USA 111, 13169–13174 (2014).
pubmed: 25157129
pmcid: 4246931
doi: 10.1073/pnas.1411290111
Mueller, S. et al. Live attenuated influenza virus vaccines by computer-aided rational design. Nat. Biotechnol. 28, 723–726 (2010).
pubmed: 20543832
pmcid: 2902615
doi: 10.1038/nbt.1636
Martrus, G., Nevot, M., Andres, C., Clotet, B. & Martinez, M. A. Changes in codon-pair bias of human immunodeficiency virus type 1 have profound effects on virus replication in cell culture. Retrovirology 10, 78 (2013).
pubmed: 23885919
pmcid: 3726367
doi: 10.1186/1742-4690-10-78
Kunec, D. & Osterrieder, N. Codon pair bias is a direct consequence of dinucleotide bias. Cell Rep. 14, 55–67 (2016).
pubmed: 26725119
doi: 10.1016/j.celrep.2015.12.011
Gustafsson, J., Norberg, P., Qvick-Wester, J. R. & Schliep, A. Fast parallel construction of variable-length Markov chains. BMC Bioinform. 22, 1–23 (2021).
doi: 10.1186/s12859-021-04387-y
Bühlmann, P. & Wyner, A. J. Variable length Markov chains. Ann. Stat. 27, 480–513 (1999).
doi: 10.1214/aos/1018031204
Alsop, E. B. & Raymond, J. Resolving prokaryotic taxonomy without rRNA: longer oligonucleotide word lengths improve genome and metagenome taxonomic classification. PLoS ONE 8, e67337 (2013).
pubmed: 23840870
pmcid: 3698125
doi: 10.1371/journal.pone.0067337
Deschavanne, P., Giron, A., Vilain, J., Dufraigne, C., & Fertil, B. Genomic signature is preserved in short DNA fragments. In Proc. IEEE International Symposium on Bio-Informatics and Biomedical Engineering 161–167. https://doi.org/10.1109/BIBE.2000.889603 (2000).
Chapus, C. et al. Exploration of phylogenetic data using a global sequence analysis method. BMC Evol. Biol. 5, 63 (2005).
pubmed: 16280081
pmcid: 1310607
doi: 10.1186/1471-2148-5-63
Yakovchuk, P., Protozanova, E., & Frank-Kamenetskii, M. D. Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res. 34, 564–574 (2006).
pubmed: 16449200
pmcid: 1360284
doi: 10.1093/nar/gkj454
Sharp, P. M. & Li, W. H. The codon Adaptation Index—a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15, 1281–1295 (1987).
pubmed: 3547335
pmcid: 340524
doi: 10.1093/nar/15.3.1281
Plotkin, J. B. & Kudla, G. Synonymous but not the same: the causes and consequences of codon bias. Nat. Rev. 12, 32–42 (2011).
doi: 10.1038/nrg2899
Sharp, P. M. et al. Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity. Nucleic Acids Res. 16, 8207–8211 (1988).
pubmed: 3138659
pmcid: 338553
doi: 10.1093/nar/16.17.8207
Vieira, V. C. & Soares, M. A. The role of cytidine deaminases on innate immune responses against human viral infections. Biomed. Res. Int. 2013, 683095 (2013).
pubmed: 23865062
pmcid: 3707226
doi: 10.1155/2013/683095
Takata, M. A. et al. CG dinucleotide suppression enables antiviral defence targeting non-self RNA. Nature 550, 124–127 (2017).
pubmed: 28953888
pmcid: 6592701
doi: 10.1038/nature24039
Ringlander, J. et al. Impact of ADAR-induced editing of minor viral RNA populations on replication and transmission of SARS-CoV-2. Proc. Natl. Acad. Sci. USA 119, https://doi.org/10.1073/pnas.2112663119 (2022).
Samuel, C. E. Adenosine deaminases acting on RNA (ADARs) are both antiviral and proviral. Virology 411, 180–193 (2011).
pubmed: 21211811
doi: 10.1016/j.virol.2010.12.004
Powdrill, M. H. et al. Contribution of a mutational bias in hepatitis C virus replication to the genetic barrier in the development of drug resistance. Proc. Natl. Acad. Sci. USA 108, 20509–20513 (2011).
pubmed: 22135458
pmcid: 3251051
doi: 10.1073/pnas.1105797108
Hayman, D. T. S. & Knox, M. A. Estimating the age of the subfamily Orthocoronavirinae using host divergence times as calibration ages at two internal nodes. Virology 563, 20–27 (2021).
pubmed: 34411808
doi: 10.1016/j.virol.2021.08.004
Wertheim, J. O., Chu, D. K., Peiris, J. S., Kosakovsky Pond, S. L. & Poon, L. L. A case for the ancient origin of coronaviruses. J. Virol. 87, 7039–7045 (2013).
pubmed: 23596293
pmcid: 3676139
doi: 10.1128/JVI.03273-12
Zhou, Z., Qiu, Y. & Ge, X. The taxonomy, host range and pathogenicity of coronaviruses and other viruses in the Nidovirales order. Anim. Dis. 1, 5 (2021).
pubmed: 34778878
pmcid: 8062217
doi: 10.1186/s44149-021-00005-9
Mavrich, T. N. & Hatfull, G. F. Bacteriophage evolution differs by host, lifestyle and genome. Nat. Microbiol. 2, 17112 (2017).
pubmed: 28692019
pmcid: 5540316
doi: 10.1038/nmicrobiol.2017.112
Strand, M. R. & Burke, G. R. Polydnaviruses: from discovery to current insights. Virology 479, 393–402 (2015).
pubmed: 25670535
doi: 10.1016/j.virol.2015.01.018
Herniou, E. A. et al. When parasitic wasps hijacked viruses: genomic and functional evolution of polydnaviruses. Philos. Trans. R. Soc. Lond. B Biol. Sci. 368, 20130051 (2013).
pubmed: 23938758
pmcid: 3758193
doi: 10.1098/rstb.2013.0051
Fan, R. L. et al. Generation of live attenuated influenza virus by using codon usage bias. J. Virol. 89, 10762–10773 (2015).
pubmed: 26269186
pmcid: 4621104
doi: 10.1128/JVI.01443-15
Kypr, J. & Mrazek, J. Unusual codon usage of HIV. Nature 327, 20 (1987).
pubmed: 3646480
doi: 10.1038/327020a0
van Hemert, F., van der Kuyl, A. C. & Berkhout, B. Impact of the biased nucleotide composition of viral RNA genomes on RNA structure and codon usage. J. Gen. Virol. 97, 2608–2619 (2016).
pubmed: 27519195
doi: 10.1099/jgv.0.000579
Zhou, T., Gu, W., Ma, J., Sun, X. & Lu, Z. Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses. Biosystems 81, 77–86 (2005).
pubmed: 15917130
doi: 10.1016/j.biosystems.2005.03.002
Simon, D., Cristina, J. & Musto, H. Nucleotide composition and codon usage across viruses and their respective hosts. Front. Microbiol. 12, 646300 (2021).
pubmed: 34262534
pmcid: 8274242
doi: 10.3389/fmicb.2021.646300
Fraser, C. et al. Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective. Science 343, 1243727 (2014).
pubmed: 24653038
pmcid: 5034889
doi: 10.1126/science.1243727
McGeoch, D. J., Dolan, A. & Ralph, A. C. Toward a comprehensive phylogeny for mammalian and avian herpesviruses. J. Virol. 74, 10401–10406 (2000).
pubmed: 11044084
pmcid: 110914
doi: 10.1128/JVI.74.22.10401-10406.2000
He, T. et al. Host shutoff activity of VHS and SOX-like proteins: role in viral survival and immune evasion. Virol. J. 17, 68 (2020).
pubmed: 32430029
pmcid: 7235440
doi: 10.1186/s12985-020-01336-8
Hennig, T., Djakovic, L., Dölken, L. & Whisnant, A. W. A review of the multipronged attack of herpes simplex virus 1 on the host transcriptional machinery. Viruses 13, https://doi.org/10.3390/v13091836 (2021).
Dolan, P. T., Whitfield, Z. J. & Andino, R. Mapping the evolutionary potential of RNA viruses. Cell Host Microbe 23, 435–446 (2018).
pubmed: 29649440
pmcid: 5908228
doi: 10.1016/j.chom.2018.03.012
Wood, D. E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol. 20, 257 (2019).
pubmed: 31779668
pmcid: 6883579
doi: 10.1186/s13059-019-1891-0
Kim, D., Song, L., Breitwieser, F. P. & Salzberg, S. L. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res. 26, 1721–1729 (2016).
pubmed: 27852649
pmcid: 5131823
doi: 10.1101/gr.210641.116
Morgulis, A., Gertz, E. M., Schaffer, A. A. & Agarwala, R. A fast and symmetric DUST implementation to mask low-complexity DNA sequences. J. Comput. Biol. 13, 1028–1040 (2006).
pubmed: 16796549
doi: 10.1089/cmb.2006.13.1028
Mihara, T. et al. Linking virus genomes with host taxonomy. Viruses 8, 66 (2016).
pubmed: 26938550
pmcid: 4810256
doi: 10.3390/v8030066
Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
pubmed: 29750242
pmcid: 6137996
doi: 10.1093/bioinformatics/bty191
Ron, D., Singer, Y. & Tishby, N. The power of amnesia: learning probabilistic automata with variable memory length. Mach. Learn. 25, 117–149 (1997).
doi: 10.1007/BF00114008
Schwarz, G. Estimating the dimension of a model. Ann. Stat. 6, 461–464 (1978).
doi: 10.1214/aos/1176344136
Saitou, N. & Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425 (1987).
pubmed: 3447015
Talevich, E., Invergo, B. M., Cock, P. J. & Chapman, B. A. Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. BMC Bioinform. 13, 209 (2012).
doi: 10.1186/1471-2105-13-209
Huerta-Cepas, J., Serra, F. & Bork, P. ETE 3: reconstruction, analysis, and visualization of phylogenomic data. Mol. Biol. Evol. 33, 1635–1638 (2016).
pubmed: 26921390
pmcid: 4868116
doi: 10.1093/molbev/msw046