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Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes

INTRODUCTION: Codon usage bias is a prevalent phenomenon observed across various species and genes. However, the specific attributes of codon usage in the mitochondrial genome of Ganoderma species remain unknown. METHODS: In this study, we investigated the codon bias of 12 mitochondrial core protein...

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Autores principales: Wu, Peng, Xiao, Wenqi, Luo, Yingyong, Xiong, Zhuang, Chen, Xiaodie, He, Jing, Sha, Ajia, Gui, Mingying, Li, Qiang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10192751/
https://www.ncbi.nlm.nih.gov/pubmed/37213503
http://dx.doi.org/10.3389/fmicb.2023.1170790
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author Wu, Peng
Xiao, Wenqi
Luo, Yingyong
Xiong, Zhuang
Chen, Xiaodie
He, Jing
Sha, Ajia
Gui, Mingying
Li, Qiang
author_facet Wu, Peng
Xiao, Wenqi
Luo, Yingyong
Xiong, Zhuang
Chen, Xiaodie
He, Jing
Sha, Ajia
Gui, Mingying
Li, Qiang
author_sort Wu, Peng
collection PubMed
description INTRODUCTION: Codon usage bias is a prevalent phenomenon observed across various species and genes. However, the specific attributes of codon usage in the mitochondrial genome of Ganoderma species remain unknown. METHODS: In this study, we investigated the codon bias of 12 mitochondrial core protein-coding genes (PCGs) in 9 Ganoderma species, including 13 Ganoderma strains. RESULTS: The codons of all Ganoderma strains showed a preference for ending in A/T. Additionally, correlations between codon base composition and the codon adaptation index (CAI), codon bias index (CBI) and frequency of optimal codons (FOP) were identified, demonstrating the impact of base composition on codon bias. Various base bias indicators were found to vary between or within Ganoderma strains, including GC3s, the CAI, the CBI, and the FOP. The results also revealed that the mitochondrial core PCGs of Ganoderma have an average effective number of codons (ENC) lower than 35, indicating strong bias toward certain codons. Evidence from neutrality plot and PR2-bias plot analysis indicates that natural selection is a major factor affecting codon bias in Ganoderma. Additionally, 11 to 22 optimal codons (ΔRSCU>0.08 and RSCU>1) were identified in 13 Ganoderma strains, with GCA, AUC, and UUC being the most widely used optimal codons in Ganoderma. By analyzing the combined mitochondrial sequences and relative synonymous codon usage (RSCU) values, the genetic relationships between or within Ganoderma strains were determined, indicating variations between them. Nevertheless, RSCU-based analysis illustrated the intra- and interspecies relationships of certain Ganoderma species. DISCUSSION: This study deepens our insight into the synonymous codon usage characteristics, genetics, and evolution of this important fungal group.
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spelling pubmed-101927512023-05-19 Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes Wu, Peng Xiao, Wenqi Luo, Yingyong Xiong, Zhuang Chen, Xiaodie He, Jing Sha, Ajia Gui, Mingying Li, Qiang Front Microbiol Microbiology INTRODUCTION: Codon usage bias is a prevalent phenomenon observed across various species and genes. However, the specific attributes of codon usage in the mitochondrial genome of Ganoderma species remain unknown. METHODS: In this study, we investigated the codon bias of 12 mitochondrial core protein-coding genes (PCGs) in 9 Ganoderma species, including 13 Ganoderma strains. RESULTS: The codons of all Ganoderma strains showed a preference for ending in A/T. Additionally, correlations between codon base composition and the codon adaptation index (CAI), codon bias index (CBI) and frequency of optimal codons (FOP) were identified, demonstrating the impact of base composition on codon bias. Various base bias indicators were found to vary between or within Ganoderma strains, including GC3s, the CAI, the CBI, and the FOP. The results also revealed that the mitochondrial core PCGs of Ganoderma have an average effective number of codons (ENC) lower than 35, indicating strong bias toward certain codons. Evidence from neutrality plot and PR2-bias plot analysis indicates that natural selection is a major factor affecting codon bias in Ganoderma. Additionally, 11 to 22 optimal codons (ΔRSCU>0.08 and RSCU>1) were identified in 13 Ganoderma strains, with GCA, AUC, and UUC being the most widely used optimal codons in Ganoderma. By analyzing the combined mitochondrial sequences and relative synonymous codon usage (RSCU) values, the genetic relationships between or within Ganoderma strains were determined, indicating variations between them. Nevertheless, RSCU-based analysis illustrated the intra- and interspecies relationships of certain Ganoderma species. DISCUSSION: This study deepens our insight into the synonymous codon usage characteristics, genetics, and evolution of this important fungal group. Frontiers Media S.A. 2023-05-04 /pmc/articles/PMC10192751/ /pubmed/37213503 http://dx.doi.org/10.3389/fmicb.2023.1170790 Text en Copyright © 2023 Wu, Xiao, Luo, Xiong, Chen, He, Sha, Gui and Li. 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 Microbiology
Wu, Peng
Xiao, Wenqi
Luo, Yingyong
Xiong, Zhuang
Chen, Xiaodie
He, Jing
Sha, Ajia
Gui, Mingying
Li, Qiang
Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes
title Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes
title_full Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes
title_fullStr Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes
title_full_unstemmed Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes
title_short Comprehensive analysis of codon bias in 13 Ganoderma mitochondrial genomes
title_sort comprehensive analysis of codon bias in 13 ganoderma mitochondrial genomes
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10192751/
https://www.ncbi.nlm.nih.gov/pubmed/37213503
http://dx.doi.org/10.3389/fmicb.2023.1170790
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