Analysis of codon usage in the chloroplast genome of Medicago truncatula

doi:10.11686/cyxb2015016

Abstract

Abstract: The complete nucleotide sequence of the chloroplast genome of Medicago truncatula was investigated. Fifty CDS (coding DNA sequences) selected from the chloroplast genome sequence of M. truncatula, were analyzed using CodonW software. The results show that the third codon position was rich in A and U. ENC ranged from 37.1 to 51.9 meaning that the codon bias was weak. There were 23 codons with relative synonymous codon usage greater than 1 and 20 codons ending with A and T. ENC-plot analysis showed that GC₃ was not correlated with GC₁₂; ENC ratio’s of most genes ranged from -0.05 to 0.05. In the correspondence analysis of the first group of four axes, the first axis showed 10.3% variation. The correlation coefficients for axis 1 between ENC and GC₃ were 0.091 and -0.092 respectively (not significant). Synonymous codon usage bias was found, mainly due to the effect of mutation pressure, but there were other factors. In addition, analysis of the high expression codons enabled 23 to be affirmed as the “optimal codons” as UAA, UUG, CCU. The results provide evidence for molecular modification of exogenous genes to increase the expression efficiency in M. truncatula chloroplasts.

YANG Guo-Feng, SU Kun-Long, ZHAO Yi-Ran, SONG Zhi-Bin, SUN Juan. Analysis of codon usage in the chloroplast genome of Medicago truncatula[J]. Acta Prataculturae Sinica, 2015, 24(12): 171-179.

References

[1] Wu X M, Wu S F, Ren D M, et al . The analysis method and progress in the study of codon bias. Hereditas, 2007, 29(4): 420-426.
[2] Grantham R, Gautier C, Gouy M. Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Research, 1980, 8(9): 1893-1912.
[3] Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Molecular Biology and Evolution, 1985, 2(1): 13-34.
[4] Sharp P M, Li W H. The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. Molecular Biology and Evolution, 1987, 4(3): 222-230.
[5] Olejniczak M, Uhlenbeck O C. tRNA residues that have coevolved with their anticodon to ensure uniform and accurate codon recognition. Biochimie, 2006, 88(8): 943-950.
[6] Deschavanne P, Filipski J. Correlation of GC content with replication timing and repair mechanisms in weakly expressed E. coli genes. Nucleic Acids Research, 1995, 23(8): 1350-1353.
[7] Sun Z, Ma L, Murphy R, et al . Analysis of codon usage on Wolbachia pipientis wMel genome. Science in China Series C: Life Sciences, 2009, 39(10): 948-953.
[8] Xia X H. Mutation and selection on the anticodon of tRNA genes in vertebrate mitochondrial genomes. Gene, 2005, 345(1): 13-20.
[9] Zalucki Y M, Power P M, Jennings M P. Selection for efficient translation initiation biases codon usage at second amino acid position in secretory proteins. Nucleic Acids Research, 2007, 35(17): 5748-5754.
[10] Huang Y, Koonin E V, Lipman D J, et al . Selection for minimization of translational frame shifting errors as a factor in the evolution of codon usage. Nucleic Acids Research, 2009, 37(20): 6799-6810.
[11] Hiraoka Y, Kawamata K, Haraguchi T, et al . Codon usage bias is correlated with gene expression levels in the fission yeast Schizosaccharomyces pombe . Genes to Cells, 2009, 14(4): 499-509.
[12] Zhang J, Song L L, Guo D L, et al . Genome-wide identification and investigation of the MADS-box gene family in Medicago truncatula . Acta Prataculturae Sinica, 2014, 23(6): 233-241.
[13] Rosenberg M S, Subramanian S, Kumar S. Patterns of transitional mutation biases within and among mammalian genomes. Molecular Biology and Evolution, 2003, 20(6): 988-993.
[14] Sharp P M, Li W H. The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Research, 1987, 15(3): 1281-1295.
[15] Sueoka N. Directional mutation pressure and neutral molecular evolution. Proceedings of the National Academy of Sciences of the United States of America, 1988, 85(8): 2653-2657.
[16] Wright F. The “effective number of codons” used in a gene. Gene, 1990, 87(1): 23-29.
[17] Sueoka N. Near homogeneity of PR2-Bias fingerprints in the human genome and their implications in phylogenetic analyses. Journal of Molecular Evolution, 2001, 53(4-5): 469-476.
[18] McInerney J O. Replicational and transcriptional selection on codon usage in Borrelia burgdorferi . Proceedings of the National Academy of Sciences of the United States of America, 1998, 95(18): 10698-10703.
[19] Yang H J, Liu G S, Zhang S T, et al . Codon usage bias studies and cluster analysis on chloroplastic gene in tobacco. Acta Tabacaria Sinica, 2012, 18(2): 37-43.
[20] Jiang Y, Deng F, Wang H L. An extensive analysis on the global codon usage pattern of baculoviruses. Archives of Virology, 2008, 153(12): 2273-2282.
[21] Sueoka N, Kawanishi Y. DNA G+C content of the third codon position and codon usage biases of human genes. Gene, 2000, 261(1): 53-62.
[22] Shang M Z, Liu F, Hua J P, et al . Analysis on codon usage of chloroplast genome of Gossypium hirsutum . Scientia Agricultura Sinica, 2011, (2): 245-253.
[23] Zhang W J, Zhou J, Li Z F, et al . Comparative analysis of codon usage patterns among mitochondrion, chloroplast and nuclear genes in Triticum aestivum L. Journal of Integrative Plant Biology, 2007, 49(2): 246-254.
[24] Zhang Y R. Analysis of Codon Usage Patterns of the Chloroplast Genomes in the Poaceae Family and RNA Editing Sites in the Chloroplast Transcripts of Agreartina adenophorum [D]. Yangling: Northwest A&F University, 2013.
[25] Zhou M, Long W, Li X. Patterns of synonymous codon usage bias in chloroplast genomes of seed plants. Forest Study of China, 2008, 11(4): 235-242.
[26] Xu C, Ben A L, Cai X N. Analysis of synonymous codon usage in chloroplast genome of Phalaenopsis aphrodite subsp. Formosana. Molecular Plant Breeding, 2011, 8(5): 945-950.
[27] Liu Q P, Xue Q Z. Codon usage in the chloroplast genome of rice ( Oryza sativa L. ssp. japonica ). Acta Agronomica Sinica, 2004, 30(12): 1220-1224.
[28] Zhou M, Long W, Li X. Analysis of synonymous codon usage in chloroplast genome of Populus alba . Journal of Forestry Research, 2008, 19(4): 293-297.
[29] Zhang X M, Xin W, Wang S F, et al . Optimizing the codon usage of HIV-1 gag gene according to the codon bias of vaccinia virus improves the gag gene expression. Chinese Journal of Virology, 2005, 21(3): 210-216.
[1] 吴宪明, 吴松锋, 任大明. 等. 密码子偏性的分析方法及相关研究进展. 遗传, 2007, 29(4): 420-426.
[7] 孙铮, 马亮, Murphy R, 等. Wolbachia pipientis wMel 基因组水平上的密码子使用分析. 中国科学C辑: 生命科学, 2009, 39(10): 948-953.
[12] 张军, 宋丽莉, 郭东林, 等. MADS-box 基因家族在蒺藜苜蓿的全基因组分析. 草业学报, 2014, 23(6): 233-241.
[19] 杨惠娟, 刘国顺, 张松涛, 等. 烟草叶绿体密码子的偏好性及聚类分析. 中国烟草学报, 2012, 18(2): 37-43.
[22] 尚明照, 刘方, 华金平, 等. 陆地棉叶绿体基因组密码子使用偏性的分析. 中国农业科学, 2011, (2): 245-253.
[24] 张月荣. 禾本科叶绿体基因组密码子使用模式及紫茎泽兰叶绿体RNA编辑分析[D]. 杨凌: 西北农林科技大学, 2013.
[26] 续晨, 贲爱玲, 蔡晓宁. 蝴蝶兰叶绿体基因组密码子使用的相关分析. 分子植物育种, 2010, 8(5): 945-950.
[27] 刘庆坡, 薛庆中. 粳稻叶绿体基因组的密码子用法. 作物学报, 2004, 30(12): 1220-1224.
[29] 张相民, 辛伟, 王世峰, 等. 按痘苗病毒优势密码子改造HIV-1 gag基因提高表达水平的研究. 病毒学报, 2005, 21(3): 210-216.