JIA-2018-09

2081 SONG Hui et al. Journal of Integrative Agriculture 2018, 17(9): 2074–2081 Rao Y, Wu G, Wang Z, Chai X, Nie Q, Zhang X. 2011. Mutation bias is the driving force of codon usage in the Gallus gallus genome. DNA Research , 18 , 499–512. Shah P, Gilchrist M A. 2010. Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias. PLoS Genetics , 6 , e1001128. Sharp P M, Li W H. 1987. The codon adaption index - A measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Research , 15 , 1281–1295. Song H, Gao H, Liu J, Tian P, Nan Z. 2017a. Comprehensive analysis of correlations among codon usage bias, gene expression, and substitution rate in Arachis duranensis and Arachis ipaënsis orthologs. Scientific Reports , 7 , 14853. Song H, Liu J, Song Q, Zhang Q, Tian P, Nan Z. 2017b. Comprehensive analysis of codon usage bias in seven Epichloë species and their peramine-coding genes. Frontiers in Microbiology , 8 , 1419. Song H, Nan Z. 2014. Genome-wide analysis of nucleotide- binding site disease resistance genes in Medicago truncatula . Chinese Science Bulletin , 59 , 1129–1138. Song H, Wang P F, Li T T, Xia H, Zhao S Z, Hou L, Zhao C Z. 2015. Genome-wide identification and evolutionary analysis of nucleotide-binding site-encoding resistance genes in Lotus japonicus (Fabaceae). Genetics and Molecular Research , 14 , 16024–16040. Song H, Zhang Q, Tian P, Nan Z. 2017c. Differential evolutionary patterns and expression levels between sex-specific and somatic tissue-specific genes in peanut. Scientific Reports , 7 , 9016. Sueoka N. 1988. Directional mutation pressure and neutral molecular evolution. Proceedings of the National Academy of Sciences of the United States of America , 85 , 2653–2657. De La Torre A R, Lin Y C, Van de Peer Y, Ingvarsson P K. 2015. Genome-wide analysis reveals diverged pattern of codon bias, gene expression, and rates of sequence evolution in Picea gene families. Genome Biology and Evolution , 7 , 1002–1015. Wang B, Shao Z Q, Xu Y, Liu J, Liu Y, Hang Y Y, Chen J Q. 2011. Optimal codon identities in bacteria: Implications from the conflicting results of two different method. PLoS ONE , 6 , e22714. Wang H C, Hickey D A. 2007. Rapid divergence of codon usage patterns within the rice genome. BMC Evolutionary Biology , 7 , S6. Whittle C A, Extavour C G. 2015. Codon and amino acid usage are shaped by selection across divergent model organisms of the Pancrustacea. G3: Genes Genomes Genetics , 5 , 2307–2321. Whittle C A, Malik M R, Krochko J E. 2007. Gender-specific selection on codon usage in plant genomes. BMC Genomics , 8 , 169. Whittle C A, Sun Y, Johannesson H. 2011. Evolution of synonymous codon usage in Neurospora tetrasperma and Neurospora discreta . Genome Biology and Evolution , 3 , 332–343. Williford A, Demuth J P. 2012. Gene expression levels are correlated with synonymous codon usage, amino acid composition, and gene architecture in the red flour beetle, Tribolium castaneum . Molecular Biology and Evolution , 29 , 3755–3766. Wright F. 1990. The ‘effective number of codons’ used in a gene. Gene , 87 , 23–29. Wright S I, Yan C B, Looseley M, Meyers B C. 2004. Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata . Molecular Biology and Evolution , 21 , 1719–1726. Yang H. 2009. In plants, expression breadth and expression level distinctly and non-linearly correlate with gene structure. Biology Direct , 4 , 45. Young N D, Debellé F, Oldroyd G E, Geurts R, Cannon S B, Udvardi M K, Benedito V A, Mayer K F, Gouzy J, Schoof H, Van de Peer Y, Proost S, Cook D R, Meyers B C, Spannagl M, Cheung F, De Mita S, Krishnakumar V, Gundlach H, Zhou S, et al . 2011. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature , 480 , 520–524. Zhang W J, Zhou J, Li Z F, Wang L, Gu X, Zhong Y. 2007. Comparative analysis of codon usage patterns among mitochondrion, chloroplast and nuclear genes in Triticum aestivum L. Journal of Integrative Plant Biology , 49 , 246–254. Zhou M, Guo J, Cha J, Chae M, Chen S, Barral J M, Sachs M S, Liu Y. 2013. Non-optimal codon usage affects expression, structure and function of clock protein FRQ. Nature , 495 , 111–115. Section editor LUO Xu-gang Managing editor ZHANG Juan