JIA-2018-09

Journal of Integrative Agriculture 2018, 17(9): 2074–2081 RESEARCH ARTICLE Available online at www.sciencedirect.com ScienceDirect Synonymous codon usage pattern in model legume Medicago truncatula SONG Hui 1, 2 , LIU Jing 1 , CHEN Tao 1 , NAN Zhi-biao 1 1 State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, P.R.China 2 Grassland Agri-husbandry Research Center, Qingdao Agricultural University, Qingdao 266109, P.R.China Abstract Synonymous codon usage pattern presumably reflects gene expression optimization as a result of molecular evolution. Though much attention has been paid to various model organisms ranging from prokaryotes to eukaryotes, codon usage has yet been extensively investigated for model legume Medicago truncatula . In present study, 39 531 available coding sequences (CDSs) from M. truncatula were examined for codon usage bias (CUB). Based on analyses including neutrality plots, effective number of codons plots, and correlations between optimal codons frequency and codon adaptation index, we conclude that natural selection is a major driving force in M. truncatula CUB. We have identified 30 optimal codons encoding 18 amino acids based on relative synonymous codon usage. These optimal codons characteristically end with A or T, except for AGG and TTG encoding arginine and leucine respectively. Optimal codon usage is positively correlated with the GC content at three nucleotide positions of codons and the GC content of CDSs. The abundance of expressed sequence tag is a proxy for gene expression intensity in the legume, but has no relatedness with either CDS length or GC content. Collectively, we unravel the synonymous codon usage pattern in M. truncatula , which may serve as the valuable information on genetic engineering of the model legume and forage crop. Keywords: codon usage, gene expression, Medicago truncatula , natural selection, optimal codon several different codons encode the same amino acid. Bias in synonymous codon usage may arise as a result of evolutionary forces such as natural selection and mutation pressure (Hershberg and Petrov 2008). Studies have shown that selection favours specific codons that promote efficient and accurate translation of genes expressed at high levels (Duret 2000; Hershberg and Petrov 2008). Thus, an effective method to identify codons favoured by selection (i.e., optimal codons) is the comparison of codon usages for each amino acid encoded by both highly and lowly expressed genes (Ingvarsson 2008; Qiu et al . 2011a; Whittle and Extavour 2015). Under mutation pressure, in contrast, preference is given to codons that tend to demonstrate lower equilibrium toward particular nucleotides (i.e., GC vs . AT) at Received 5 September, 2017 Accepted 11 April, 2018 Correspondence SONG Hui, E-mail: biosonghui@outlook.com; NAN Zhi-biao, E-mail: zhibiao@lzu.edu.cn © 2018 CAAS. Publishing services by Elsevier B.V. All rights reserved. doi: 10.1016/S2095-3119(18)61961-6 1. Introduction The central dogma of molecular biology describes 61 codons that encode 20 amino acids in the process of translation. Fifty-nine out of the 61 codons are synonymous, i.e.,