Version 1
: Received: 2 October 2019 / Approved: 8 October 2019 / Online: 8 October 2019 (10:43:24 CEST)
How to cite:
Miller, J.B.; Whiting, M.F.; Kauwe, J.S.; Ridge, P.G. How Codon Usage Bias Affects Our Ability to Recover the Tree of Life. Preprints2019, 2019100086. https://doi.org/10.20944/preprints201910.0086.v1
Miller, J.B.; Whiting, M.F.; Kauwe, J.S.; Ridge, P.G. How Codon Usage Bias Affects Our Ability to Recover the Tree of Life. Preprints 2019, 2019100086. https://doi.org/10.20944/preprints201910.0086.v1
Miller, J.B.; Whiting, M.F.; Kauwe, J.S.; Ridge, P.G. How Codon Usage Bias Affects Our Ability to Recover the Tree of Life. Preprints2019, 2019100086. https://doi.org/10.20944/preprints201910.0086.v1
APA Style
Miller, J.B., Whiting, M.F., Kauwe, J.S., & Ridge, P.G. (2019). How Codon Usage Bias Affects Our Ability to Recover the Tree of Life. Preprints. https://doi.org/10.20944/preprints201910.0086.v1
Chicago/Turabian Style
Miller, J.B., John S.K. Kauwe and Perry G. Ridge. 2019 "How Codon Usage Bias Affects Our Ability to Recover the Tree of Life" Preprints. https://doi.org/10.20944/preprints201910.0086.v1
Abstract
Phylogenies depict shared evolutionary patterns and structures on a tree topology, enabling the identification of hierarchical and historical relationships. Recent analyses indicate that phylogenetic signals extend beyond the primary structure of protein or DNA, and various aspects of codon usage biases are phylogenetically conserved. Several functional biases exist within genes, including the number of codons that are used, the position of the codons, and the overall nucleotide composition of the genome. Codon usage biases can significantly affect transcription and translational efficiencies, leading to differential gene expression. Although systematic codon usage biases originate from the overall GC content of a species, ramp sequences, codon aversion, codon pairing, and tRNA competition also significantly affect gene expression and are phylogenetically conserved. We review recent advances in analyzing codon usage biases and their implications in phylogenomics. We first outline common phylogenomic techniques. Next, we identify several codon usage biases and their effects on secondary structure, gene expression, and implications in phylogenetics. Finally, we suggest how codon usage biases can be included in phylogenomics. By incorporating various codon usage biases in common phylogenomic algorithms, we propose that we can significantly improve tree inference. Since codon usage biases have significant biological implications, they should be considered in conjunction with other phylogenetic algorithms.
Keywords
phylogenomics; phylogenetics; codon usage bias; Tree of Life
Subject
Biology and Life Sciences, Life Sciences
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
