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Next-generation development and application of codon model in evolution

To date, numerous nucleotide, amino acid, and codon substitution models have been developed to estimate the evolutionary history of any sequence/organism in a more comprehensive way. Out of these three, the codon substitution model is the most powerful. These models have been utilized extensively to...

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Autores principales: Gupta, Manoj Kumar, Vadde, Ramakrishna
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9911445/
https://www.ncbi.nlm.nih.gov/pubmed/36777719
http://dx.doi.org/10.3389/fgene.2023.1091575
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author Gupta, Manoj Kumar
Vadde, Ramakrishna
author_facet Gupta, Manoj Kumar
Vadde, Ramakrishna
author_sort Gupta, Manoj Kumar
collection PubMed
description To date, numerous nucleotide, amino acid, and codon substitution models have been developed to estimate the evolutionary history of any sequence/organism in a more comprehensive way. Out of these three, the codon substitution model is the most powerful. These models have been utilized extensively to detect selective pressure on a protein, codon usage bias, ancestral reconstruction and phylogenetic reconstruction. However, due to more computational demanding, in comparison to nucleotide and amino acid substitution models, only a few studies have employed the codon substitution model to understand the heterogeneity of the evolutionary process in a genome-scale analysis. Hence, there is always a question of how to develop more robust but less computationally demanding codon substitution models to get more accurate results. In this review article, the authors attempted to understand the basis of the development of different types of codon-substitution models and how this information can be utilized to develop more robust but less computationally demanding codon substitution models. The codon substitution model enables to detect selection regime under which any gene or gene region is evolving, codon usage bias in any organism or tissue-specific region and phylogenetic relationship between different lineages more accurately than nucleotide and amino acid substitution models. Thus, in the near future, these codon models can be utilized in the field of conservation, breeding and medicine.
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spelling pubmed-99114452023-02-11 Next-generation development and application of codon model in evolution Gupta, Manoj Kumar Vadde, Ramakrishna Front Genet Genetics To date, numerous nucleotide, amino acid, and codon substitution models have been developed to estimate the evolutionary history of any sequence/organism in a more comprehensive way. Out of these three, the codon substitution model is the most powerful. These models have been utilized extensively to detect selective pressure on a protein, codon usage bias, ancestral reconstruction and phylogenetic reconstruction. However, due to more computational demanding, in comparison to nucleotide and amino acid substitution models, only a few studies have employed the codon substitution model to understand the heterogeneity of the evolutionary process in a genome-scale analysis. Hence, there is always a question of how to develop more robust but less computationally demanding codon substitution models to get more accurate results. In this review article, the authors attempted to understand the basis of the development of different types of codon-substitution models and how this information can be utilized to develop more robust but less computationally demanding codon substitution models. The codon substitution model enables to detect selection regime under which any gene or gene region is evolving, codon usage bias in any organism or tissue-specific region and phylogenetic relationship between different lineages more accurately than nucleotide and amino acid substitution models. Thus, in the near future, these codon models can be utilized in the field of conservation, breeding and medicine. Frontiers Media S.A. 2023-01-27 /pmc/articles/PMC9911445/ /pubmed/36777719 http://dx.doi.org/10.3389/fgene.2023.1091575 Text en Copyright © 2023 Gupta and Vadde. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Gupta, Manoj Kumar
Vadde, Ramakrishna
Next-generation development and application of codon model in evolution
title Next-generation development and application of codon model in evolution
title_full Next-generation development and application of codon model in evolution
title_fullStr Next-generation development and application of codon model in evolution
title_full_unstemmed Next-generation development and application of codon model in evolution
title_short Next-generation development and application of codon model in evolution
title_sort next-generation development and application of codon model in evolution
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9911445/
https://www.ncbi.nlm.nih.gov/pubmed/36777719
http://dx.doi.org/10.3389/fgene.2023.1091575
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