Codon-pair usage pattern and cluster analysis of the ABC gene family in silkworm, Bombyx mori

Abstract

In this study, gene sequences from the silkworm genome database were screened to analyze codon usage in the silkworm ABC gene family. We also assessed the main factors affecting codon usage pattern in these genes. Our results showed that the average A+T content in Coding sequences (CDS) of the silkworm ABC gene family was comparable to the average G+C content. The base composition was diverse and showed no obvious preference. The number of codons with relative synonymous codon usage (RSCU) scores >1 was 34. We found preferences to use codons ending in A and G, not to use C-terminated codons, and that synonymous codons used in the whole genome were not strongly preferred. We also found differences in codon usage preference between different gene subfamilies. We speculate that the expression of the BGIBMGA010825 gene of the H subgroup is the lowest in the silkworm ABC transporter family, while the expression of BGIBMGA012743, BGIBMGA004187, and BGIBMGA004188 genes of the B subgroup of the A subfamily are the highest in this family. Using neutrality plot and effective number of codons (ENC-plot) analyses, we found that the codon preference of the silkworm ABC gene family was affected by both base mutations and natural selection pressures, but base composition constraint played a more important role in codon usage preference.