Abstract
Simple SummaryWe evaluated codon usage bias in the FoxP2 gene in fishes, birds, reptiles, and mammals. Fishes use C or G—ending codons, while birds, reptiles, and mammals employ T or A—ending codons. Apart from the nucleotide composition, natural selection and mutation pressure might influence the CUB. The ENC observed/ENC expected ratio demonstrated that mutation pressure influences FoxP2 codon usage patterns. Natural selection may have had a key influence in shaping the CUB, although mutation pressure may have played a minor role. FoxP2 gene codon usage is affected by the base composition under mutation bias.The protein-coding gene FoxP2 (fork head box protein P2) plays a major role in communication and evolutionary changes. The present study carried out a comprehensive codon usage bias analysis in the FoxP2 gene among a diverse group of animals including fishes, birds, reptiles, and mammals. We observed that in the genome of fishes for the FoxP2 gene, codons ending with C or G were most frequently used, while in birds, reptiles, and mammals, codons ending with T or A were most frequently used. A higher ENC value was observed for the FoxP2 gene indicating a lower CUB. Parity role two-bias plots suggested that apart from mutation pressure, other factors such as natural selection might have influenced the CUB. The frequency distribution of the ENC observed and ENC expected ratio revealed that mutation pressure plays a key role in the patterns of codon usage of FoxP2. Besides, correspondence analysis exposed the composition of the nucleobase under mutation bias affects the codon usage of the FoxP2 gene. However, neutrality plots revealed the major role of natural selection over mutation pressure in the CUB of FoxP2. In addition, the codon usage patterns for FoxP2 among the selected genomes suggested that nature has favored nearly all the synonymous codons for encoding the corresponding amino acid. The uniform usage of 12 synonymous codons for FoxP2 was observed among the species of birds. The amino acid usage frequency for FoxP2 revealed that the amino acids Leucine, Glutamine, and Serine were predominant over other amino acids among all the species of fishes, birds, reptiles, and mammals.
Highlights
The standard genetic code makes use of 64 codons to characterize the 20 standard amino acids, including 3 stop codons, during the translation of a protein
The redundancy of the genetic code implies that one amino acid may be encoded by more than one codon leading to the occurrence of synonymous codon usage bias (CUB) in the genome of an organism, which varies among diverse groups [1]
In our study of the FoxP2 gene, we found GC and P3 content was higher than 50% in fishes, while in reptiles, birds, and mammals, GC content was lower than 50%
Summary
The standard genetic code makes use of 64 codons to characterize the 20 standard amino acids, including 3 stop codons, during the translation of a protein. FoxP2 was reported in 1990 as a putative “speech gene” that binds to the fork head box protein P2 and the autosomal dominant trait, causing a severe and specific speech disorder [23]. These findings attracted the scientific community to study the FoxP2 phenotype in diverse taxa including mammals, birds, and insects [24]. The expression patterns of FoxP2 in songbird and human brains are identical, with strong expression in the basal ganglia, thalamus, and cerebellum [31,32]
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