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

Abstract

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.

Keywords:

• Gossypium mitochondria
• ENC and GC content
• preferred codons
• neutral mutation
• selection

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The data that support the findings of this study are openly available in the NCBI database under Genbank Accession Numbers JX065074 (https://www.ncbi.nlm.nih.gov/nuccore/JX065074.1/) and KP898249 (https://www.ncbi.nlm.nih.gov/nuccore/KP898249).