Codon Usage Bias in Autophagy-Related Gene 13 in Eukaryotes: Uncovering the Genetic Divergence by the Interplay Between Nucleotides and Codon Usages

Synonymous codon usage bias is a universal characteristic of genomes across various organisms. Autophagy-related gene 13 (atg13) is one essential gene for autophagy initiation, yet the evolutionary trends of the atg13 gene at the usages of nucleotide and synonymous codon remains unexplored. Accordin...

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Autores principales:	Yicong Li, Rui Wang, Huihui Wang, Feiyang Pu, Xili Feng, Li Jin, Zhongren Ma, Xiao-xia Ma
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	autophagy-related gene 13 phylogenetic analyses nucleotide usage synonymous codon usage nucleotide composition distribution Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/e0a6fe976cde41cf9136478e156920b1
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spelling	oai:doaj.org-article:e0a6fe976cde41cf9136478e156920b12021-11-05T08:44:23ZCodon Usage Bias in Autophagy-Related Gene 13 in Eukaryotes: Uncovering the Genetic Divergence by the Interplay Between Nucleotides and Codon Usages2235-298810.3389/fcimb.2021.771010https://doaj.org/article/e0a6fe976cde41cf9136478e156920b12021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fcimb.2021.771010/fullhttps://doaj.org/toc/2235-2988Synonymous codon usage bias is a universal characteristic of genomes across various organisms. Autophagy-related gene 13 (atg13) is one essential gene for autophagy initiation, yet the evolutionary trends of the atg13 gene at the usages of nucleotide and synonymous codon remains unexplored. According to phylogenetic analyses for the atg13 gene of 226 eukaryotic organisms at the nucleotide and amino acid levels, it is clear that their nucleotide usages exhibit more genetic information than their amino acid usages. Specifically, the overall nucleotide usage bias quantified by information entropy reflected that the usage biases at the first and second codon positions were stronger than those at the third position of the atg13 genes. Furthermore, the bias level of nucleotide ‘G’ usage is highest, while that of nucleotide ‘C’ usage is lowest in the atg13 genes. On top of that, genetic features represented by synonymous codon usage exhibits a species-specific pattern on the evolution of the atg13 genes to some extent. Interestingly, the codon usages of atg13 genes in the ancestor animals (Latimeria chalumnae, Petromyzon marinus, and Rhinatrema bivittatum) are strongly influenced by mutation pressure from nucleotide composition constraint. However, the distributions of nucleotide composition at different codon positions in the atg13 gene display that natural selection still dominates atg13 codon usages during organisms’ evolution.Yicong LiRui WangHuihui WangFeiyang PuXili FengLi JinZhongren MaXiao-xia MaFrontiers Media S.A.articleautophagy-related gene 13phylogenetic analysesnucleotide usagesynonymous codon usagenucleotide composition distributionMicrobiologyQR1-502ENFrontiers in Cellular and Infection Microbiology, Vol 11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	autophagy-related gene 13 phylogenetic analyses nucleotide usage synonymous codon usage nucleotide composition distribution Microbiology QR1-502
spellingShingle	autophagy-related gene 13 phylogenetic analyses nucleotide usage synonymous codon usage nucleotide composition distribution Microbiology QR1-502 Yicong Li Rui Wang Huihui Wang Feiyang Pu Xili Feng Li Jin Zhongren Ma Xiao-xia Ma Codon Usage Bias in Autophagy-Related Gene 13 in Eukaryotes: Uncovering the Genetic Divergence by the Interplay Between Nucleotides and Codon Usages
description	Synonymous codon usage bias is a universal characteristic of genomes across various organisms. Autophagy-related gene 13 (atg13) is one essential gene for autophagy initiation, yet the evolutionary trends of the atg13 gene at the usages of nucleotide and synonymous codon remains unexplored. According to phylogenetic analyses for the atg13 gene of 226 eukaryotic organisms at the nucleotide and amino acid levels, it is clear that their nucleotide usages exhibit more genetic information than their amino acid usages. Specifically, the overall nucleotide usage bias quantified by information entropy reflected that the usage biases at the first and second codon positions were stronger than those at the third position of the atg13 genes. Furthermore, the bias level of nucleotide ‘G’ usage is highest, while that of nucleotide ‘C’ usage is lowest in the atg13 genes. On top of that, genetic features represented by synonymous codon usage exhibits a species-specific pattern on the evolution of the atg13 genes to some extent. Interestingly, the codon usages of atg13 genes in the ancestor animals (Latimeria chalumnae, Petromyzon marinus, and Rhinatrema bivittatum) are strongly influenced by mutation pressure from nucleotide composition constraint. However, the distributions of nucleotide composition at different codon positions in the atg13 gene display that natural selection still dominates atg13 codon usages during organisms’ evolution.
format	article
author	Yicong Li Rui Wang Huihui Wang Feiyang Pu Xili Feng Li Jin Zhongren Ma Xiao-xia Ma
author_facet	Yicong Li Rui Wang Huihui Wang Feiyang Pu Xili Feng Li Jin Zhongren Ma Xiao-xia Ma
author_sort	Yicong Li
title	Codon Usage Bias in Autophagy-Related Gene 13 in Eukaryotes: Uncovering the Genetic Divergence by the Interplay Between Nucleotides and Codon Usages
title_short	Codon Usage Bias in Autophagy-Related Gene 13 in Eukaryotes: Uncovering the Genetic Divergence by the Interplay Between Nucleotides and Codon Usages
title_full	Codon Usage Bias in Autophagy-Related Gene 13 in Eukaryotes: Uncovering the Genetic Divergence by the Interplay Between Nucleotides and Codon Usages
title_fullStr	Codon Usage Bias in Autophagy-Related Gene 13 in Eukaryotes: Uncovering the Genetic Divergence by the Interplay Between Nucleotides and Codon Usages
title_full_unstemmed	Codon Usage Bias in Autophagy-Related Gene 13 in Eukaryotes: Uncovering the Genetic Divergence by the Interplay Between Nucleotides and Codon Usages
title_sort	codon usage bias in autophagy-related gene 13 in eukaryotes: uncovering the genetic divergence by the interplay between nucleotides and codon usages
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/e0a6fe976cde41cf9136478e156920b1
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Codon Usage Bias in Autophagy-Related Gene 13 in Eukaryotes: Uncovering the Genetic Divergence by the Interplay Between Nucleotides and Codon Usages

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