Phylogeny and codon usage bias of bacterial genomes in Bifidobacterium animalis

Open Access

Issue		BIO Web Conf. Volume 59, 2023 2023 5^th International Conference on Biotechnology and Biomedicine (ICBB 2023)


Article Number		01009
Number of page(s)		9
Section		Biotechnology and Cell Structure Analysis
DOI		https://doi.org/10.1051/bioconf/20235901009
Published online		08 May 2023

Sharp P.M., Emery L.R. and Zeng, K. (2010). Forces that influence the evolution of codon bias. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 365(1544), 1203–1212. https://doi.org/10.1098/rstb.2009.0305 [CrossRef] [PubMed] [Google Scholar]
Grantham, R., Gautier, C., Gouy, M., Mercier, R., & Pavé, A. (1980). Codon catalog usage and the genome hypothesis. Nucleic acids research, 8(1), r49–r62. https://doi.org/10.1093/nar/8.1.197-c [Google Scholar]
Parvathy, S. T., Udayasuriyan, V., & Bhadana, V. (2022). Codon usage bias. Molecular biology reports, 49(1), 539–565. https://doi.org/10.1007/s11033-021-06749-4 [CrossRef] [PubMed] [Google Scholar]
Iriarte, A., Lamolle, G., & Musto, H. (2021). Codon Usage Bias: An Endless Tale. Journal of molecular evolution, 89(9-10), 589–593. https://doi.org/10.1007/s00239-021-10027-z [CrossRef] [PubMed] [Google Scholar]
Yang, J., Ding, H., & Kan, X. (2021). Codon usage patterns and evolution of HSP60 in birds. International journal of biological macromolecules, 183, 1002–1012. https://doi.org/10.1016/j.ijbiomac.2021.05.017 [CrossRef] [Google Scholar]
Bulmer M. (1991). The selection-mutation-drift theory of synonymous codon usage. Genetics, 129(3), 897–907. https://doi.org/10.1093/genetics/129.3.897 [CrossRef] [Google Scholar]
Frank, A. C., & Lobry, J. R. (1999). Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene, 238(1), 65–77. https://doi.org/10.1016/s0378-1119(99)00297-8 [CrossRef] [Google Scholar]
Carbone, A., Zinovyev, A., & Képès, F. (2003). Codon adaptation index as a measure of dominating codon bias. Bioinformatics (Oxford, England), 19(16), 2005–2015. https://doi.org/10.1093/bioinformatics/btg272 [Google Scholar]
Turroni, F., van Sinderen, D., & Ventura, M. (2011). Genomics and ecological overview of the genus Bifidobacterium. International journal of food microbiology, 149(1), 37–44. https://doi.org/10.1016/j.ijfoodmicro.2010.12.010 [CrossRef] [Google Scholar]
Dantas, A., Verruck, S., Canella, M. H. M., Hernandez, E., & Prudencio, E. S. (2021). Encapsulated Bifidobacterium BB-12 addition in a concentrated lactose-free yogurt: Its survival during storage and effects on the product’s properties. Food research international (Ottawa, Ont.), 150(Pt A), 110742. https://doi.org/10.1016/j.foodres.2021.110742 [CrossRef] [Google Scholar]
Engevik, M. A., Danhof, H. A., Hall, A., Engevik, K. A., Horvath, T. D., Haidacher, S. J., Hoch, K. M., Endres, B. T., Bajaj, M., Garey, K. W., Britton, R. A., Spinler, J. K., Haag, A. M., & Versalovic, J. (2021). The metabolic profile of Bifidobacterium dentium reflects its status as a human gut commensal. BMC microbiology, 21 (1), 154. https://doi.org/10.1186/s12866-021-02166-6 [CrossRef] [Google Scholar]
Luo, J., Li, Y., Xie, J., Gao, L., Liu, L., Ou, S., Chen, L., & Peng, X. (2018). The primary biological network of Bifidobacterium in the gut. FEMS microbiology letters, 365(8), doi: 10.1093/femsle/fny057. https://doi.org/10.1093/femsle/fny057 [CrossRef] [Google Scholar]
Xia X. (2018). DAMBE7: New and Improved Tools for Data Analysis in Molecular Biology and Evolution. Molecular biology and evolution, 35(6), 1550–1552. https://doi.org/10.1093/molbev/msy073 [CrossRef] [PubMed] [Google Scholar]
Katoh, K., Rozewicki, J., & Yamada, K. D. (2019). MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Briefings in bioinformatics, 20(4), 1160–1166. https://doi.org/10.1093/bib/bbx108 [CrossRef] [PubMed] [Google Scholar]
Sun, X., Yang, Q., & Xia, X. (2013). An improved implementation of effective number of codons (nc). Molecular biology and evolution, 30(1), 191–196. https://doi.org/10.1093/molbev/mss201 [CrossRef] [PubMed] [Google Scholar]
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 [CrossRef] [Google Scholar]
Komar A. A. (2019). Molekuliarnaia biologiia, 53(6), 883–898. https://doi.org/10.1134/S0026898419060090 [Google Scholar]
Shen, W., Wang, D., Ye, B., Shi, M., Ma, L., Zhang, Y., & Zhao, Z. (2015). GC3-biased gene domains in mammalian genomes. Bioinformatics (Oxford, England), 31 (19), 3081–3084. https://doi.org/10.1093/bioinformatics/btv329 [Google Scholar]
Tatarinova, T., Elhaik, E., & Pellegrini, M. (2013). Cross-species analysis of genic GC3 content and DNA methylation patterns. Genome biology and evolution, 5(8), 1443–1456. https://doi.org/10.1093/gbe/evt103 [CrossRef] [Google Scholar]
Ito, K., & Murphy, D. (2013). Application of ggplot2 to Pharmacometric Graphics. CPT: pharmacometrics & systems pharmacology, 2 (10), e79. https://doi.org/10.1038/psp.2013.56 [CrossRef] [Google Scholar]
Morrison D. A. (1996). Phylogenetic tree-building. International journal for parasitology, 26(6), 589–617. https://doi.org/10.1016/0020-7519(96)00044-6 [CrossRef] [Google Scholar]
Yu G. (2020). Using ggtree to Visualize Data on Tree-Like Structures. Current protocols in bioinformatics, 69 (1), e96. https://doi.org/10.1002/cpbi.96 [Google Scholar]
Sueoka N. (1988). Directional mutation pressure and neutral molecular evolution. Proceedings of the National Academy of Sciences of the United States of America, 85(8), 2653–2657. https://doi.org/10.1073/pnas.85.8.2653 [CrossRef] [PubMed] [Google Scholar]
Sun, X., Yang, Q., & Xia, X. (2013). An improved implementation of effective number of codons (nc). Molecular biology and evolution, 30(1), 191–196. https://doi.org/10.1093/molbev/mss201 [Google Scholar]
Forsdyke, D. R., & Mortimer, J. R. (2000). Chargaffs legacy. Gene, 261 (1), 127–137. https://doi.org/10.1016/s0378-1119(00)00472-8 [CrossRef] [Google Scholar]
Forsdyke D. R. (2021). Neutralism versus selectionism: Chargaffs second parity rule, revisited. Genetica, 149(2), 81–88. https://doi.org/10.1007/s10709-021-00119-5 [CrossRef] [PubMed] [Google Scholar]
Sueoka N. (1999). Translation-coupled violation of Parity Rule 2 in human genes is not the cause of heterogeneity of the DNA G+C content of the third codon position. Gene, 238(1), 53–58. https://doi.org/10.1016/s0378-1119(99)00320-0 [CrossRef] [Google Scholar]
Seemann T. (2014). Prokka: rapid prokaryotic genome annotation. Bioinformatics (Oxford, England), 30(14), 2068–2069. https://doi.org/10.1093/bioinformatics/btu153 [PubMed] [Google Scholar]
Sanger-pathogens.github.io. (n.d.). Roary: The pan genome pipeline. https://sanger-pathogens.github.io/Roary/. [Google Scholar]
Rambaut. (n.d.). Release figtree V1.4.4 Rambaut/Figtree. https://github.com/rambaut/figtree/releases/tag/v1.4.4. [Google Scholar]
Hildebrand, F., Meyer, A., & Eyre-Walker, A. (2010). Evidence of selection upon genomic GC-content in bacteria. PLoS genetics, 6 (9), e1001107. https://doi.org/10.1371/journal.pgen.1001107 [CrossRef] [Google Scholar]
Zhou, Z., Dang, Y., Zhou, M., Li, L., Yu, C. H., Fu, J., Chen, S. & Liu, Y. (2016). Codon usage is an important determinant of gene expression levels largely through its effects on transcription. Proceedings of the National Academy of Sciences, 113 (41), E6117–E6125. https://doi.org/10.1073/pnas.1606724113. [Google Scholar]

Current usage metrics show cumulative count of Article Views (full-text article views including HTML views, PDF and ePub downloads, according to the available data) and Abstracts Views on Vision4Press platform.

Data correspond to usage on the plateform after 2015. The current usage metrics is available 48-96 hours after online publication and is updated daily on week days.

Initial download of the metrics may take a while.