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

BMC Genomics

Research Article

Xuerong Peng¹  Jing Xu²  Yu Wang²  Xiaobin Gu²  Guangyou Yang²  Xing Huang³  Lin Chen⁴ 

[1] College of Science, Sichuan Agricultural University, 625014, Ya’an, China;Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, 611130, Chengdu, China;Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, 611130, Chengdu, China;Chengdu Agricultural College, 611130, Chengdu, China;Meat-processing Application Key Laboratory of Sichuan Province, College of Pharmacy and Biological Engineering, Chengdu University, 610106, Chengdu, China;

关键词: Taenia multiceps;    Codon usage pattern;    Natural selection;    Genome;    Evolution;   

DOI  :  10.1186/s12864-017-3704-8

 received in 2016-09-27, accepted in 2017-04-12,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundCodon 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 of T. multiceps remains to be clarified. In this study, we analyzed the codon usage of T. multiceps based on the transcriptome data to reveal the constraint factors and to gain an improved understanding of the mechanisms that shape synonymous CUB.ResultsAnalysis of a total of 8,620 annotated mRNA sequences from T. 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 in T. multiceps. Among these factors, natural selection was implicated as the major factor affecting the codon usage variation in T. 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 between T. multiceps and Escherichia coli, yeast, Homo sapiens. However, little difference was found between T. multiceps and Taenia pisiformis.ConclusionsIn this study, the codon usage pattern of T. multiceps was analyzed systematically and factors affected CUB were also identified. This is the first study of codon biology in T. multiceps. Understanding the codon usage pattern in T. multiceps can be helpful for the discovery of new genes, molecular genetic engineering and evolutionary studies.

【 授权许可】

CC BY   
© The Author(s). 2017