Comparative analysis of codon usage between Gossypium hirsutum and G. barbadense mitochondrial genomes

Gossypium hirsutum and G. barbadense mitochondrial genomes were analyzed to understand the factors shaping codon usage. While most analyses of codon usage suggest minimal to no bias, nucleotide composition, specifically GC content, was significantly correlated with codon usage. In general, both mito...

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Bibliographic Details
Published in:Mitochondrial DNA. Part B. Resources 2020-07, Vol.5 (3), p.2500-2506
Main Authors: Chen, Zhiwen, Zhao, Jianguo, Qiao, Jun, Li, Weijia, Li, Jingwei, Xu, Ran, Wang, Haiyan, Liu, Zehui, Xing, Baoyan, Wendel, Jonathan F., Grover, Corrinne E.
Format: Article
Language:English
Subjects:
Bias
Codons
Comparative analysis
ENC and GC content
Food chains
Genomes
Gossypium barbadense
Gossypium hirsutum
Gossypium mitochondria
Interferon
Mitochondria
neutral mutation
preferred codons
Rapid Communications
selection
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Summary:Gossypium hirsutum and G. barbadense mitochondrial genomes were analyzed to understand the factors shaping codon usage. While most analyses of codon usage suggest minimal to no bias, nucleotide composition, specifically GC content, was significantly correlated with codon usage. In general, both mitochondrial genomes favor codons that end in A or U, with a secondary preference for pyrimidine rich codons. These observations are similar to previous reports of codon usage in cotton nuclear genomes, possibly suggestive of a general bias spanning genomic compartment. Although evidence for codon usage bias is weak for most genes, we identified six genes (i.e. atp8, atp9, sdh3, sdh4, mttB and rpl2) with significant nonrandom codon usage. In general, we find multiple factors that influence cotton mitochondrial genome codon usage, which may include selection in a subset of genes.
ISSN:2380-2359
2380-2359
DOI:10.1080/23802359.2020.1780969