A study on the codon usage bias of arenavirus common genes
IntroductionThe Arenaviridae family consists of the genera Mammarenavirus, Reptarenavirus, Hartmanivirus, Antennavirus and Innmovirus. The codon usage bias between the different genera has not yet been studied comparatively.MethodsWe retrieved the arenavirus genome sequences from public databases an...
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Frontiers Media S.A.
2025-01-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2024.1490076/full |
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| author | Pablo Daniel Thomas María Florencia Ferrer Mauricio J. Lozano Ricardo Martín Gómez |
| author_facet | Pablo Daniel Thomas María Florencia Ferrer Mauricio J. Lozano Ricardo Martín Gómez |
| author_sort | Pablo Daniel Thomas |
| collection | DOAJ |
| description | IntroductionThe Arenaviridae family consists of the genera Mammarenavirus, Reptarenavirus, Hartmanivirus, Antennavirus and Innmovirus. The codon usage bias between the different genera has not yet been studied comparatively.MethodsWe retrieved the arenavirus genome sequences from public databases and used bioinformatics tools to compare the codon usage bias between the different genera for the GPC, NP and L proteins, common to all arenaviruses.Results and discussionHartmaniviruses show a larger codon usage bias, which can be partially explained by mutational bias. Patterns of relative use of synonymous codons were maintained within genera, with individual genera differing in their preference for the third nucleotide position in synonymous codons. Of the three proteins examined, the ARN polymerase L protein exhibited a slightly stronger codon usage bias, but overall, the patterns were repeated between genera for the three proteins examined. Our results suggest that codon usage pattern bias in arenaviruses is influenced by selection pressure and to a lesser extent by mutational selection. |
| format | Article |
| id | doaj-art-f79287ec3fd24d95a67eaa4e7d6854e1 |
| institution | Kabale University |
| issn | 1664-302X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj-art-f79287ec3fd24d95a67eaa4e7d6854e12025-01-23T06:56:39ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2025-01-011510.3389/fmicb.2024.14900761490076A study on the codon usage bias of arenavirus common genesPablo Daniel Thomas0María Florencia Ferrer1Mauricio J. Lozano2Ricardo Martín Gómez3Laboratorio de Patogénesis Viral, Instituto de Biotecnología y Biología Molecular, CONICET-UNLP, La Plata, ArgentinaLaboratorio de Patogénesis Viral, Instituto de Biotecnología y Biología Molecular, CONICET-UNLP, La Plata, ArgentinaLaboratorio de Genómica y Ecología Molecular de Microorganismos del Suelo Asociados con Plantas, Instituto de Biotecnología y Biología Molecular, CONICET-UNLP, La Plata, ArgentinaLaboratorio de Patogénesis Viral, Instituto de Biotecnología y Biología Molecular, CONICET-UNLP, La Plata, ArgentinaIntroductionThe Arenaviridae family consists of the genera Mammarenavirus, Reptarenavirus, Hartmanivirus, Antennavirus and Innmovirus. The codon usage bias between the different genera has not yet been studied comparatively.MethodsWe retrieved the arenavirus genome sequences from public databases and used bioinformatics tools to compare the codon usage bias between the different genera for the GPC, NP and L proteins, common to all arenaviruses.Results and discussionHartmaniviruses show a larger codon usage bias, which can be partially explained by mutational bias. Patterns of relative use of synonymous codons were maintained within genera, with individual genera differing in their preference for the third nucleotide position in synonymous codons. Of the three proteins examined, the ARN polymerase L protein exhibited a slightly stronger codon usage bias, but overall, the patterns were repeated between genera for the three proteins examined. Our results suggest that codon usage pattern bias in arenaviruses is influenced by selection pressure and to a lesser extent by mutational selection.https://www.frontiersin.org/articles/10.3389/fmicb.2024.1490076/fullArenaviridaecodon usagephylogenyMammarenavirusevolution |
| spellingShingle | Pablo Daniel Thomas María Florencia Ferrer Mauricio J. Lozano Ricardo Martín Gómez A study on the codon usage bias of arenavirus common genes Frontiers in Microbiology Arenaviridae codon usage phylogeny Mammarenavirus evolution |
| title | A study on the codon usage bias of arenavirus common genes |
| title_full | A study on the codon usage bias of arenavirus common genes |
| title_fullStr | A study on the codon usage bias of arenavirus common genes |
| title_full_unstemmed | A study on the codon usage bias of arenavirus common genes |
| title_short | A study on the codon usage bias of arenavirus common genes |
| title_sort | study on the codon usage bias of arenavirus common genes |
| topic | Arenaviridae codon usage phylogeny Mammarenavirus evolution |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2024.1490076/full |
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