[5] Analysis of transcriptome data reveals multifactor constraint on codon usage in Taenia multiceps

Abstract

BACKGROUND:

Codon usage bias (CUB) is an important evolutionary feature in genomes that has been widely observed in many organisms. However, the synonymous codon usage pattern in the genome ofT. multicepsremainsto be clarified. In this study, we analyzed the codon usage ofT. multiceps based on the transcriptomedata to reveal the constraint factors and to gain an improved understanding of the mechanisms that shape synonymous CUB.

RESULTS:

Analysis of a total of 8,620 annotated mRNA sequences fromT. multiceps indicated only a weak codon bias, with mean GC and GC3 content values of 49.29% and 51.43%, respectively. Our analysis indicated that nucleotide composition, mutational pressure, natural selection, gene expression level, amino acids with grand average of hydropathicity (GRAVY) and aromaticity (Aromo) and the effective selection of amino-acids all contributed to the codon usage inT. multiceps. Among these factors, natural selection was implicated as the major factor affecting the codon usage variation inT. multiceps. The codon usage of ribosome genes was affected mainly by mutations, while the essential genes were affected mainly by selection. In addition, 21codons were identified as "optimal codons". Overall, the optimal codons were GC-rich (GC:AU, 41:22), and ended with G or C (except CGU). Furthermore, different degrees of variation in codon usage were found betweenT. multicepsandEscherichia coli, yeast, Homo sapiens. However, little difference was found betweenT. multiceps and Taenia pisiformis.

CONCLUSIONS:

In this study, the codon usage pattern ofT. multiceps was analyzed systematically and factors affected CUB were also identified. This is the first study of codon biology inT. multiceps. Understanding the codon usage pattern inT. multiceps can be helpful for the discovery of new genes, molecular genetic engineering and evolutionary studies.