Analysis of codon usage patterns inTaenia pisiformisthrough annotated transcriptome data
Chen L, Liu T, Yang D, Nong X, Xie Y, Fu Y, Wu X, Huang X, Gu X, Wang S, Peng X, Yang G.
Abstract
Taeniapisiformis(Cestoidea; Cyclophyllidea; Taeniidae) tapeworms infect the small intestine of canids and felines, such as dogs and foxes. SynonymouscodonusageinT.pisiformiswas examined through 8118 reconstructed annotationsoftranscriptomesequences. The mean value of GC content for the reconstructed genes was 49.48%. Twenty-four codons were determined as "optimal codons". Approximately all translational optimal codons (except CGU) ended on G or C. The gene positions on the primary axis were strongly positively correlated with GC content at the thirdcodonpositions and GC content of individual genes. At the same time, the gene expression level assessed by the CAI, the hydrophobicity and aromaticity of encoded proteins were correlated with the GC content at the thirdcodonpositions and the effective number of codons (ENC), respectively. We infer that the gene expression level, the hydrophobicity and the aromaticity of the encoded proteins also influencedcodonusageinT.pisiformis. Knowledge of thecodonusagepattern inT.pisiformiscan improve our understanding of the mechanisms of biasedusageof synonymous codons and can help in selecting appropriate host expression systems for potential vaccine genes ofT.pisiformis.
Copyright © 2012 Elsevier Inc. All rights reserved.
Biochem Biophys Res Commun.2013 Jan 25;430(4):1344-8. doi: 10.1016/j.bbrc.2012.12.078. Epub 2012 Dec 23.
Read full text: http://www.sciencedirect.com/science/article/pii/S0006291X12024266
