Codon usage bias analysis of the gene encoding NAD
Codon usage bias
DNA ligase
Invertebrate iridescent virus 6
ORF 205R
Journal
Archives of microbiology
ISSN: 1432-072X
Titre abrégé: Arch Microbiol
Pays: Germany
ID NLM: 0410427
Informations de publication
Date de publication:
09 Oct 2023
09 Oct 2023
Historique:
received:
05
08
2023
accepted:
18
09
2023
medline:
2
11
2023
pubmed:
9
10
2023
entrez:
9
10
2023
Statut:
epublish
Résumé
The genome of Invertebrate iridescent virus 6 (IIV6) contains a sequence that shows similarity to eubacterial NAD
Identifiants
pubmed: 37812231
doi: 10.1007/s00203-023-03688-5
pii: 10.1007/s00203-023-03688-5
doi:
Substances chimiques
NAD
0U46U6E8UK
DNA Ligases
EC 6.5.1.-
Codon
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
352Subventions
Organisme : Recep Tayyip Erdogan Üniversitesi
ID : FBA-2016-533
Informations de copyright
© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
Références
Arulmoorthy MP, Vijayan R, Sinduja K et al (2022) Infection with Decapod iridescent virus 1: an emerging disease in shrimp culture. Arch Microbiol 204:685. https://doi.org/10.1007/s00203-022-03289-8
doi: 10.1007/s00203-022-03289-8
pubmed: 36319873
Benarroch D, Shuman S (2006) Characterization of mimivirus NAD
doi: 10.1016/j.virol.2006.04.032
pubmed: 16844179
Bera BC, Virmani N, Kumar N et al (2017) Genetic and codon usage bias analyses of polymerase genes of equine influenza virus and its relation to evolution. BMC Genomics 18(1):652. https://doi.org/10.1186/s12864-017-4063-1
doi: 10.1186/s12864-017-4063-1
pubmed: 28830350
pmcid: 5568313
Borrel G, Harris HMB, Tottey W et al (2012) Genome sequence of “candidatus methanomethylophilus alvus” Mx1201, a methanogenic archaeon from the human gut belonging to a seventh order of methanogens. J Bacteriol 194(24):6944–6945. https://doi.org/10.1128/JB.01867-12
doi: 10.1128/JB.01867-12
pubmed: 23209209
pmcid: 3510639
Burge C, Campbell AM, Karlin S (1992) Over- and under-representation of short oligonucleotides in DNA sequences. Proc Natl Acad Sci USA 89(4):1358–1362. https://doi.org/10.1073/pnas.89.4.1358
doi: 10.1073/pnas.89.4.1358
pubmed: 1741388
pmcid: 48449
Butt AM, Nasrullah I, Tong Y (2014) Genome-wide analysis of codon usage and influencing factors in chikungunya viruses. PLoS ONE 9(3):e90905. https://doi.org/10.1371/journal.pone.0090905
doi: 10.1371/journal.pone.0090905
pubmed: 24595095
pmcid: 3942501
Butt AM, Nasrullah I, Qamar R, Tong Y (2016) Evolution of codon usage in Zika virus genomes is host and vector specific. Emerg Microbes Infect 5(10):e107. https://doi.org/10.1038/emi.2016.106
doi: 10.1038/emi.2016.106
pubmed: 27729643
pmcid: 5117728
Canuti M, Large G, Verhoeven JTP, Dufour SC (2022) A novel iridovirus discovered in deep-sea carnivorous sponges. Viruses 14:8. https://doi.org/10.3390/v14081595
doi: 10.3390/v14081595
Chantawannakul P, Cutler RW (2008) Convergent host-parasite codon usage between honeybee and bee associated viral genomes. J Invertebr Pathol 98(2):206–210. https://doi.org/10.1016/j.jip.2008.02.016
doi: 10.1016/j.jip.2008.02.016
pubmed: 18397791
Chauleau M, Shuman S (2016) Kinetic mechanism and fidelity of nick sealing by Escherichia coli NAD
doi: 10.1093/nar/gkw049
pubmed: 26857547
pmcid: 4797296
Cheng X, Virk N, Chen W et al (2013) CpG usage in RNA viruses: data and hypotheses. PLoS ONE 8(9):e74109. https://doi.org/10.1371/journal.pone.0074109
doi: 10.1371/journal.pone.0074109
pubmed: 24086312
pmcid: 3781069
Chinchar VG, Duffus ALJ (2019) Molecular and ecological studies of a virus family (Iridoviridae) infecting invertebrates and ectothermic vertebrates. Viruses 11(6):538. https://doi.org/10.3390/v11060538
doi: 10.3390/v11060538
pubmed: 31181817
pmcid: 6630830
Chinchar VG, Hick P, Ince IA et al (2017) ICTV virus taxonomy profile: iridoviridae. J Gen Virol 98:890–891. https://doi.org/10.1099/jgv.0.000818
doi: 10.1099/jgv.0.000818
pubmed: 28555546
pmcid: 5656800
Clarke RT, Greenacre MJ (1985) Theory and applications of correspondence analysis. J Anim Ecol 54(3):1031. https://doi.org/10.2307/4399
doi: 10.2307/4399
Comeron JM, Aguadé M (1998) An evaluation of measures of synonymous codon usage bias. J Mol Evol 47:268–274. https://doi.org/10.1007/PL00006384
doi: 10.1007/PL00006384
pubmed: 9732453
Cristina J, Moreno P, Moratorio G, Musto H (2015) Genome-wide analysis of codon usage bias in Ebolavirus. Virus Res 196:87–93. https://doi.org/10.1016/j.virusres.2014.11.005
doi: 10.1016/j.virusres.2014.11.005
pubmed: 25445348
D’Costa SM, Yao HJ, Bilimoria SL (2004) Transcriptional mapping in Chilo iridescent virus infections. Arch Virol 149:723–742. https://doi.org/10.1007/s00705-003-0232-4
doi: 10.1007/s00705-003-0232-4
pubmed: 15045560
Das M, Kumar S (2018) Analysis of codon usage pattern of infectious laryngotracheitis virus immunogenic glycoproteins and its biological implications. Infect Genet Evol 62:53–59. https://doi.org/10.1016/j.meegid.2018.04.009
doi: 10.1016/j.meegid.2018.04.009
pubmed: 29654923
Dizman YA, Demirbag Z, Ince IA, Nalcacioglu R (2012) Transcriptomic analysis of Chilo iridescent virus immediate early promoter. Virus Res 167(2):353–357. https://doi.org/10.1016/j.virusres.2012.05.025
doi: 10.1016/j.virusres.2012.05.025
pubmed: 22698875
Dizman YA, Muratoglu H, Sandalli C et al (2016) Chilo iridescent virus (CIV) ORF 012L encodes a protein with both exonuclease and endonuclease functions. Arch Virol 161:3029–3037. https://doi.org/10.1007/s00705-016-3007-4
doi: 10.1007/s00705-016-3007-4
pubmed: 27496102
Doherty AJ, Suh SW (2000) Structural and mechanistic conservation in DNA ligases. Nucleic Acids Res 28(21):4051–4058. https://doi.org/10.1093/nar/28.21.4051
doi: 10.1093/nar/28.21.4051
pubmed: 11058099
pmcid: 113121
Dorn A, Kippenberger S (2008) Clinical application of CpG-, non-CpG-, and antisense oligodeoxynucleotides as immunomodulators. Curr Opin Mol Ther 10(1):10–20 (PMID: 18228177)
pubmed: 18228177
Eaton HE, Metcalf J, Penny E et al (2007) Comparative genomic analysis of the family Iridoviridae: re-annotating and defining the core set of iridovirus genes. Virol J 4:11. https://doi.org/10.1186/1743-422X-4-11
doi: 10.1186/1743-422X-4-11
pubmed: 17239238
pmcid: 1783846
Ellenberger T, Tomkinson AE (2008) Eukaryotic DNA ligases: structural and functional insights. Annu Rev Biochem 77:313–338. https://doi.org/10.1146/annurev.biochem.77.061306.123941
doi: 10.1146/annurev.biochem.77.061306.123941
pubmed: 18518823
pmcid: 2933818
Gencer D, Yesilyurt A, Ozsahin E et al (2023) Identification of the potential matrix protein of invertebrate iridescent virus 6 (IIV6). J Invertebr Pathol 197:107885. https://doi.org/10.1016/j.jip.2023.107885
doi: 10.1016/j.jip.2023.107885
pubmed: 36640993
Gregory CR, Latimer KS, Pennick KE et al (2006) Novel iridovirus in a nautilus (Nautilus spp.). J Vet Diagnostic Investig 8(2):208–211. https://doi.org/10.1177/104063870601800213
doi: 10.1177/104063870601800213
Hartl DL, Moriyama EN, Sawyer SA (1994) Selection intensity for codon bias. Genetics 138(1):227–234. https://doi.org/10.1093/genetics/138.1.227
doi: 10.1093/genetics/138.1.227
pubmed: 8001789
pmcid: 1206133
Hernández O, Maldonado G, Williams T (2000) An epizootic of patent iridescent virus disease in multiple species of blackflies in Chiapas, Mexico. Med Vet Entomol 14(4):458–462. https://doi.org/10.1046/j.1365-2915.2000.00258.x
doi: 10.1046/j.1365-2915.2000.00258.x
pubmed: 11129714
Hu C, Chen J, Ye L et al (2014) Codon usage bias in human cytomegalovirus and its biological implication. Gene 545(1):5–14. https://doi.org/10.1016/j.gene.2014.05.018
doi: 10.1016/j.gene.2014.05.018
pubmed: 24814188
Ikemura T (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol 2:13–34. https://doi.org/10.1093/oxfordjournals.molbev.a040335
doi: 10.1093/oxfordjournals.molbev.a040335
pubmed: 3916708
Ince IA, Boeren SA, van Oers MM et al (2010) Proteomic analysis of Chilo iridescent virus. Virology 405(1):253–258. https://doi.org/10.1016/j.virol.2010.05.038
doi: 10.1016/j.virol.2010.05.038
pubmed: 20598335
Ince IA, Özcan K, Vlak JM, van Oers MM (2013) Temporal classification and mapping of non-polyadenylated transcripts of an invertebrate iridovirus. J Gen Virol 94(Pt 1):187–192. https://doi.org/10.1099/vir.0.046359-0
doi: 10.1099/vir.0.046359-0
pubmed: 23052394
İnce İA, Pijlman GP, Vlak JM, van Oers MM (2017) Hairpin structures with conserved sequence motifs determine the 3′ ends of non-polyadenylated invertebrate iridovirus transcripts. Virology 511:344–353. https://doi.org/10.1016/j.virol.2017.06.026
doi: 10.1016/j.virol.2017.06.026
pubmed: 28709684
Jakob NJ, Darai G (2002) Molecular anatomy of Chilo iridescent virus genome and the evolution of viral genes. Virus Genes 25(3):299–316. https://doi.org/10.1023/A:1020984210358
doi: 10.1023/A:1020984210358
pubmed: 12881641
Jakob NJ, Müller K, Bahr U, Darai G (2001) Analysis of the first complete DNA sequence of an invertebrate iridovirus: coding strategy of the genome of Chilo iridescent virus. Virology 286(1):182–196. https://doi.org/10.1006/viro.2001.0963
doi: 10.1006/viro.2001.0963
pubmed: 11448171
Jenkins GM, Holmes EC (2003) The extent of codon usage bias in human RNA viruses and its evolutionary origin. Virus Res 92(1):1–7. https://doi.org/10.1016/S0168-1702(02)00309-X
doi: 10.1016/S0168-1702(02)00309-X
pubmed: 12606071
Jiang L, Zhang Q, Xiao S, Si F (2022) Deep decoding of codon usage strategies and host adaption preferences of soybean mosaic virus. Int J Biol Macromol 222(Pt A):803–817. https://doi.org/10.1016/j.ijbiomac.2022.09.179
doi: 10.1016/j.ijbiomac.2022.09.179
pubmed: 36167098
Kaczmarek FS, Zaniewski RP, Gootz TD et al (2001) Cloning and functional characterization of an NAD
doi: 10.1128/JB.183.10.3016-3024.2001
pubmed: 11325928
pmcid: 95200
Kariin S, Burge C (1995) Dinucleotide relative abundance extremes: a genomic signature. Trends Genet 11(7):283–290. https://doi.org/10.1016/S0168-9525(00)89076-9
doi: 10.1016/S0168-9525(00)89076-9
Karniychuk UU (2016) Analysis of the synonymous codon usage bias in recently emerged enterovirus D68 strains. Virus Res 223:73–79. https://doi.org/10.1016/j.virusres.2016.06.015
doi: 10.1016/j.virusres.2016.06.015
pubmed: 27364082
Khandia R, Khan AA, Karuvantevida N et al (2023) Insights into synonymous codon usage bias in hepatitis C virus and its adaptation to hosts. Pathogens 12(2):325. https://doi.org/10.3390/pathogens12020325
doi: 10.3390/pathogens12020325
pubmed: 36839597
pmcid: 9961758
Kleespies RG, Tidona CA, Darai G (1999) Characterization of a new iridovirus isolated from crickets and investigations on the host range. J Invertebr Pathol 73(1):84–90. https://doi.org/10.1006/jipa.1998.4821
doi: 10.1006/jipa.1998.4821
pubmed: 9878293
Lee JY, Chang C, Song HK et al (2000) Crystal structure of NAD
doi: 10.1093/emboj/19.5.1119
pubmed: 10698952
pmcid: 305650
Lehman IR (1974) DNA ligase: structure, mechanism, and function. Science 186(4166):790–797. https://doi.org/10.1126/science.186.4166.790
doi: 10.1126/science.186.4166.790
pubmed: 4377758
Li B, Wu H, Miao Z et al (2022) Codon usage of hepatitis E viruses: a comprehensive analysis. Front Microbiol 13:938651. https://doi.org/10.3389/fmicb.2022.938651
doi: 10.3389/fmicb.2022.938651
pubmed: 35801104
pmcid: 9253588
Lobo FP, Mota BEF, Pena SDJ et al (2009) Virus-host coevolution: common patterns of nucleotide motif usage in Flaviviridae and their hosts. PLoS ONE 4(7):e6282. https://doi.org/10.1371/journal.pone.0006282
doi: 10.1371/journal.pone.0006282
pubmed: 19617912
pmcid: 2707012
Lobry JR, Gautier C (1994) Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes. Nucleic Acids Res 22(15):3174–3180. https://doi.org/10.1093/nar/22.15.3174
doi: 10.1093/nar/22.15.3174
pubmed: 8065933
pmcid: 310293
Lu J, Tong J, Feng H et al (2004) Unique ligation properties of eukaryotic NAD
doi: 10.1016/j.bbapap.2004.06.008
Martin IV, Macneill SA (2002) Protein family review ATP-dependent DNA ligases. Genome Biol 3(4):REVIEWS3005. https://doi.org/10.1186/gb-2002-3-4-reviews3005
Mioduser O, Goz E, Tuller T (2017) Significant differences in terms of codon usage bias between bacteriophage early and late genes: a comparative genomics analysis. BMC Genomics 18(1):866. https://doi.org/10.1186/s12864-017-4248-7
doi: 10.1186/s12864-017-4248-7
pubmed: 29132309
pmcid: 5683454
Montaña-Lozano P, Balaguera-Reina SA, Prada-Quiroga CF (2023) Comparative analysis of codon usage of mitochondrial genomes provides evolutionary insights into reptiles. Gene 851:146999. https://doi.org/10.1016/j.gene.2022.146999
doi: 10.1016/j.gene.2022.146999
pubmed: 36309241
Nair RR, Mohan M, Rudramurthy GR et al (2021) Strategies and patterns of codon bias in molluscum contagiosum virus. Pathogens 10(12):1649. https://doi.org/10.3390/pathogens10121649
doi: 10.3390/pathogens10121649
pubmed: 34959603
pmcid: 8703355
Nasrullah I, Butt AM, Tahir S et al (2015) Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Marburg virus evolution. BMC Evol Biol 15:1–15. https://doi.org/10.1186/s12862-015-0456-4
doi: 10.1186/s12862-015-0456-4
Nguyen TH, Wang D, Rahman SU et al (2021) Analysis of codon usage patterns and influencing factors in rice tungro bacilliform virus. Infect Genet Evol 90:104750. https://doi.org/10.1016/j.meegid.2021.104750
doi: 10.1016/j.meegid.2021.104750
pubmed: 33548490
O’Brien EP, Ciryam P, Vendruscolo M, Dobson CM (2014) Understanding the influence of codon translation rates on cotranslational protein folding. Acc Chem Res 47:1536–1544. https://doi.org/10.1021/ar5000117
doi: 10.1021/ar5000117
pubmed: 24784899
Parvathy ST, Udayasuriyan V, Bhadana V (2022) Codon usage bias. Mol Biol Rep 49:539–565. https://doi.org/10.1007/s11033-021-06749-4
doi: 10.1007/s11033-021-06749-4
pubmed: 34822069
Patil SS, Indrabalan UB, Suresh KP, Shome BR (2021) Analysis of codon usage bias of classical swine fever virus. Vet World 14(6):1450–1458. https://doi.org/10.14202/vetworld.2021.1450-1458
Pechmann S, Frydman J (2013) Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding. Nat Struct Mol Biol 20:237–243. https://doi.org/10.1038/nsmb.2466
doi: 10.1038/nsmb.2466
pubmed: 23262490
Poidevin L, MacNeill SA (2006) Biochemical characterisation of LigN, an NAD
doi: 10.1186/1471-2199-7-44
pubmed: 17132163
pmcid: 1684257
Pu F, Wang R, Yang X et al (2023) Nucleotide and codon usage biases involved in the evolution of African swine fever virus: a comparative genomics analysis. J Basic Microbiol 63(5):499–518. https://doi.org/10.1002/jobm.202200624
doi: 10.1002/jobm.202200624
pubmed: 36782108
Puigbò P, Bravo IG, Garcia-Vallve S (2008) CAIcal: a combined set of tools to assess codon usage adaptation. Biol Direct 3:38. https://doi.org/10.1186/1745-6150-3-38
doi: 10.1186/1745-6150-3-38
pubmed: 18796141
pmcid: 2553769
Qi X, Wei C, Li Y et al (2020) The characteristic of the synonymous codon usage and phylogenetic analysis of hepatitis B virus. Genes Genomics 42(7):805–815. https://doi.org/10.1007/s13258-020-00932-w
doi: 10.1007/s13258-020-00932-w
pubmed: 32462516
pmcid: 7311504
Rahman SU, Yao X, Li X et al (2018) Analysis of codon usage bias of Crimean-Congo hemorrhagic fever virus and its adaptation to hosts. Infect Genet Evol 58:1–16. https://doi.org/10.1016/j.meegid.2017.11.027
doi: 10.1016/j.meegid.2017.11.027
pubmed: 29198972
Rahman SU, Abdullah M, Khan AW et al (2022) A detailed comparative analysis of codon usage bias in Alongshan virus. Virus Res 308:198646. https://doi.org/10.1016/j.virusres.2021.198646
doi: 10.1016/j.virusres.2021.198646
pubmed: 34822954
Rosa GM, Ayala Botto G, Mitra AT et al (2022) Invasive fish disrupt host-pathogen dynamics leading to amphibian declines. Biol Conserv 276:109785. https://doi.org/10.1016/j.biocon.2022.109785
doi: 10.1016/j.biocon.2022.109785
Sexton NR, Ebel GD (2019) Effects of arbovirus multi-host life cycles on dinucleotide and codon usage patterns. Viruses 11(7):643. https://doi.org/10.3390/v11070643
doi: 10.3390/v11070643
pubmed: 31336898
pmcid: 6669465
Sharp PM, Li WH (1986) Codon usage in regulatory genes in Escherichia coli does not reflect selection for “rare” codons. Nucleic Acids Res 14(19):7737–7749. https://doi.org/10.1093/nar/14.19.7737
doi: 10.1093/nar/14.19.7737
pubmed: 3534792
pmcid: 311793
Shuman S (1995) Vaccinia virus DNA ligase: specificity, fidelity, and inhibition. Biochemistry 34(49):16138–16147. https://doi.org/10.1021/bi00049a029
doi: 10.1021/bi00049a029
pubmed: 8519771
Shuman S, Lima CD (2004) The polynucleotide ligase and RNA capping enzyme superfamily of covalent nucleotidyltransferases. Curr Opin Struct Biol 14(6):757–764. https://doi.org/10.1016/j.sbi.2004.10.006
doi: 10.1016/j.sbi.2004.10.006
pubmed: 15582400
Simón D, Cristina J, Musto H (2022) An overview of dinucleotide and codon usage in all viruses. Arch Virol 167(6):1443–1448. https://doi.org/10.1007/s00705-022-05454-2
doi: 10.1007/s00705-022-05454-2
pubmed: 35467158
Spang A, Saw JH, Jørgensen SL et al (2015) Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521(7551):173–179. https://doi.org/10.1038/nature14447
doi: 10.1038/nature14447
pubmed: 25945739
pmcid: 4444528
Sriskanda V, Shuman S (2002) Conserved residues in domain Ia are required for the reaction of Escherichia coli DNA ligase with NAD
doi: 10.1074/jbc.M111164200
pubmed: 11781321
Sriskanda V, Moyer RW, Shuman S (2001) NAD
doi: 10.1074/jbc.M105643200
pubmed: 11459847
Sueoka N (1988) Directional mutation pressure and neutral molecular evolution. Proc Natl Acad Sci USA 85(8):2653–2657. https://doi.org/10.1073/pnas.85.8.2653
doi: 10.1073/pnas.85.8.2653
pubmed: 3357886
pmcid: 280056
Sueoka N (1992) Directional mutation pressure, selective constraints, and genetic equilibria. J Mol Evol 34(2):95–114. https://doi.org/10.1007/BF00182387
doi: 10.1007/BF00182387
pubmed: 1556753
Sueoka N (1995) Intrastrand parity rules of DNA base composition and usage biases of synonymous codons. J Mol Evol 40(3):318–325. https://doi.org/10.1007/BF00163236
doi: 10.1007/BF00163236
pubmed: 7723058
Sueoka N (1999) Two aspects of DNA base composition: G+C content and translation- coupled deviation from intra-strand rule of A = T and G = C. J Mol Evol 49(1):49–62. https://doi.org/10.1007/PL00006534
doi: 10.1007/PL00006534
pubmed: 10368434
Sun J, Zhao W, Wang R et al (2020) Analysis of the codon usage pattern of HA and NA genes of H7N9 influenza A virus. Int J Mol Sci 21(19):7129. https://doi.org/10.3390/ijms21197129
doi: 10.3390/ijms21197129
pubmed: 32992529
pmcid: 7583936
Suresh KP, Indrabalan UB, Shreevatsa B et al (2023) Evaluation of codon usage patterns and molecular evolution dynamics in Japanese encephalitis virus: an integrated bioinformatics approach. Infect Genet Evol 109:105410. https://doi.org/10.1016/j.meegid.2023.105410
doi: 10.1016/j.meegid.2023.105410
pubmed: 36791944
Tamura K, Stecher G, Kumar S (2021) MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol 38:3022–3027. https://doi.org/10.1093/molbev/msab120
doi: 10.1093/molbev/msab120
pubmed: 33892491
pmcid: 8233496
Tang KFJ, Redman RM, Pantoja CR et al (2007) Identification of an iridovirus in Acetes erythraeus (Sergestidae) and the development of in situ hybridization and PCR method for its detection. J Invertebr Pathol 96(3):255–260. https://doi.org/10.1016/j.jip.2007.05.006
doi: 10.1016/j.jip.2007.05.006
pubmed: 17585932
Tao J, Yao H (2020) Comprehensive analysis of the codon usage patterns of polyprotein of Zika virus. Prog Biophys Mol Biol 150:43–49. https://doi.org/10.1016/j.pbiomolbio.2019.05.001
doi: 10.1016/j.pbiomolbio.2019.05.001
pubmed: 31054849
Tian HF, Hu QM, Xiao HB et al (2020) Genetic and codon usage bias analyses of major capsid protein gene in Ranavirus. Infect Genet Evol 84:104379. https://doi.org/10.1016/j.meegid.2020.104379
doi: 10.1016/j.meegid.2020.104379
pubmed: 32497680
Timson DJ, Singleton MR, Wigley DB (2000) DNA ligases in the repair and replication of DNA. Mutat Res—DNA Repair 460(3–4):301–318. https://doi.org/10.1016/S0921-8777(00)00033-1
doi: 10.1016/S0921-8777(00)00033-1
pubmed: 10946235
Tsai CT, Lin CH, Chang CY (2007) Analysis of codon usage bias and base compositional constraints in iridovirus genomes. Virus Res 126(1–2):196–206. https://doi.org/10.1016/j.virusres.2007.03.001
doi: 10.1016/j.virusres.2007.03.001
pubmed: 17434639
Tyagi A, Nagar V (2022) Genome dynamics, codon usage patterns and influencing factors in Aeromonas hydrophila phages. Virus Res 320:198900. https://doi.org/10.1016/j.virusres.2022.198900
doi: 10.1016/j.virusres.2022.198900
pubmed: 36029927
Tyagi A, Singh NK, Gurtler V, Karunasagar I (2016) Bioinformatics analysis of codon usage patterns and influencing factors in Penaeus monodon nudivirus. Arch Virol 161(2):459–464. https://doi.org/10.1007/s00705-015-2689-3
doi: 10.1007/s00705-015-2689-3
pubmed: 26586333
Wang H, Liu S, Zhang B, Wei W (2016) Analysis of synonymous codon usage bias of zika virus and its adaption to the hosts. PLoS ONE 11(11):e0166260. https://doi.org/10.1371/journal.pone.0166260
doi: 10.1371/journal.pone.0166260
pubmed: 27893824
pmcid: 5125587
Wang H, Meng T, Wei W (2018) Analysis of synonymous codon usage bias in helicase gene from Autographa californica multiple nucleopolyhedrovirus. Genes Genomics 40(7):767–780. https://doi.org/10.1007/s13258-018-0689-x
doi: 10.1007/s13258-018-0689-x
pubmed: 29934813
Wang X, Xu W, Fan K et al (2020) Codon usage bias in the H gene of canine distemper virus. Microb Pathog 149:104511. https://doi.org/10.1016/j.micpath.2020.104511
doi: 10.1016/j.micpath.2020.104511
pubmed: 32961282
Wang H, Liu S, Lv Y, Wei W (2023) Codon usage bias of Venezuelan equine encephalitis virus and its host adaption. Virus Res 328:199081. https://doi.org/10.1016/j.virusres.2023.199081
doi: 10.1016/j.virusres.2023.199081
pubmed: 36854361
pmcid: 10194294
Wilkinson A, Day J, Bowater R (2001) Bacterial DNA ligases. Mol Microbiol 40:1241–1248. https://doi.org/10.1046/j.1365-2958.2001.02479.x
doi: 10.1046/j.1365-2958.2001.02479.x
pubmed: 11442824
Williams T (2008) Natural invertebrate hosts of iridoviruses (Iridoviridae). Neotrop Entomol 37:615–632. https://doi.org/10.1590/S1519-566X2008000600001
doi: 10.1590/S1519-566X2008000600001
pubmed: 19169548
Williamson A, Hjerde E, Kahlke T (2016) Analysis of the distribution and evolution of the ATP-dependent DNA ligases of bacteria delineates a distinct phylogenetic group “Lig E.” Mol Microbiol 99(2):274–290. https://doi.org/10.1111/mmi.13229
doi: 10.1111/mmi.13229
pubmed: 26412580
Wong EHM, Smith DK, Rabadan R et al (2010) Codon usage bias and the evolution of influenza A viruses. Codon usage biases of ınfluenza virus. BMC Evol Biol 10:253. https://doi.org/10.1186/1471-2148-10-253
Wright F (1990) The “effective number of codons” used in a gene. Gene 87(1):23–29. https://doi.org/10.1016/0378-1119(90)90491-9
doi: 10.1016/0378-1119(90)90491-9
pubmed: 2110097
Yao X, Fan Q, Yao B et al (2020) Codon usage bias analysis of bluetongue virus causing livestock infection. Front Microbiol 11:655. https://doi.org/10.3389/fmicb.2020.00655
doi: 10.3389/fmicb.2020.00655
pubmed: 32508755
pmcid: 7248248
Yesilyurt A, Demirbag Z, van Oers MM, Nalcacioglu R (2020) Conserved motifs in the invertebrate iridescent virus 6 (IIV6) genome regulate virus transcription. J Invertebr Pathol 177:107496. https://doi.org/10.1016/j.jip.2020.107496
doi: 10.1016/j.jip.2020.107496
pubmed: 33127354
Yu X, Gao K, Pi M et al (2021) Phylogenetic and codon usage analysis for replicase and capsid genes of porcine circovirus 3. Vet Res Commun 45(4):353–361. https://doi.org/10.1007/s11259-021-09816-0
doi: 10.1007/s11259-021-09816-0
pubmed: 34357481
Zang M, He W, Du F et al (2017) Analysis of the codon usage of the ORF2 gene of feline calicivirus. Infect Genet Evol 54:54–59. https://doi.org/10.1016/j.meegid.2017.06.013
doi: 10.1016/j.meegid.2017.06.013
pubmed: 28625542
pmcid: 7106028
Zhang J, Wang M, Liu WQ et al (2011) Analysis of codon usage and nucleotide composition bias in polioviruses. Virol J 8:146. https://doi.org/10.1186/1743-422X-8-146
doi: 10.1186/1743-422X-8-146
pubmed: 21450075
pmcid: 3079669
Zhang X, Cai Y, Zhai X et al (2018) Comprehensive analysis of codon usage on rabies virus and other lyssaviruses. Int J Mol Sci 19(8):2397. https://doi.org/10.3390/ijms19082397
doi: 10.3390/ijms19082397
pubmed: 30110957
pmcid: 6121662
Zhao A, Gray FC, MacNeill SA (2006) ATP- and NAD
doi: 10.1111/j.1365-2958.2005.04975.x
pubmed: 16420348
Zhao R, Gu C, Zou X et al (2022) Comparative genomic analysis reveals new evidence of genus boundary for family Iridoviridae and explores qualified hallmark genes. Comput Struct Biotechnol J 20:3493–3502. https://doi.org/10.1016/j.csbj.2022.06.049
doi: 10.1016/j.csbj.2022.06.049
pubmed: 35860404
pmcid: 9284377
Zhou Y, Chen X, Ushijima H, Frey TK (2012) Analysis of base and codon usage by rubella virus. Arch Virol 157(5):889–899. https://doi.org/10.1007/s00705-012-1243-9
doi: 10.1007/s00705-012-1243-9
pubmed: 22322905
Zhou J, Xing Y, Zhou Z, Wang S (2023) A comprehensive analysis of Usutu virus (USUV) genomes revealed lineage-specific codon usage patterns and host adaptations. Front Microbiol 13:967999. https://doi.org/10.3389/fmicb.2022.967999
doi: 10.3389/fmicb.2022.967999
pubmed: 36713228
pmcid: 9878346
Zu Z, Lin H, Hu Y et al (2022) The genetic evolution and codon usage pattern of severe fever with thrombocytopenia syndrome virus. Infect Genet Evol 99:105238. https://doi.org/10.1016/j.meegid.2022.105238
doi: 10.1016/j.meegid.2022.105238
pubmed: 35144005