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.
Highlights
Codon usage bias is a common phenomenon in most prokaryotic and eukaryotic species
Analyses reveal unequal nucleotide composition suggestive of codon usage bias Codon usage biases can be revealed by several different measures, including by comparing the GC content of third codon positions to the first two
Differences in GC content were greatest at the third codon position, which is typically considered neutral with respect to mutations
Summary
Biased codon usage can arise as a result of neutral mutations (Osawa et al 1988; Kano et al 1991; Liu et al 2015) or selective constraints (Akashi 1994), and may be different among species or genes within species (Uddin et al 2018; Bhattacharyya et al 2019). Trends in codon usage biases within and among species can provide insight into the different evolutionary pressures that affect genes and species. Studies have shown that mitochondrial, chloroplast, and nuclear genes can exhibit differences in codon usage and evolutionary constraints, as observed in Triticum aestivum (Zhang et al 2007), and natural selection might play a major role in shaping codon usage bias in plant mitochondrial genomes (Zhou and Li 2009)
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