Scientia Agricultura Sinica ›› 2016, Vol. 49 ›› Issue (12): 2368-2378.doi: 10.3864/j.issn.0578-1752.2016.12.012
• HORTICULTURE • Previous Articles Next Articles
WU Yan-qing, ZHAO Da-qiu, TAO Jun
[1] Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Molecular Biology and Evolution, 1985, 2: 13-34.
[2] Angellotti M C, Bhuiyan S B, Chen G, Wan X F. CodonO: Codon usage bias analysis within and across genomes. Nucleic Acids Research, 2007, 35: 132-136.
[3] LuH,ZhaoW M,ZhengY, Wang H, Qi M, Yu X P.AnalysisofsynonymouscodonusagebiasinChlamydia. Acta Biochimica Biophysica Sinica (Shanghai), 2005,37(1):1-10.
[4] 郭秀丽, 王玉, 杨路成, 丁兆堂. 茶树CBF1基因密码子使用特性分析. 遗传, 2012, 34(12): 1614-1623.
Guo X L, Wang Y, Yang L C, Ding Z T. Analysis of codon use features of CBF gene in Camellia sinensis. Hereditas, 2012, 34(12): 1614-1623. (in Chinese)
[5] 石秀凡, 黄京飞, 柳树群, 刘次全. 人类基因同义密码子偏好的特征以及与基因GC含量的关系. 生物化学与生物物理进展, 2002, 29(3): 411-414.
Shi X F, Huang J F, Liu S Q, Liu C Q. The features of synonymous codon bias and GC-content relationship in human genes. Progress in Biochemistry and Biophysics, 2002, 29(3): 411-414. (in Chinese)
[6] Fedorov A, Saxonov S, Gilbert W. Regular ties of context- dependent codon bias in eukaryotic genes. Nucleic Acids Research, 2002, 30: 1192-1197.
[7] Hiraoka Y, Kawamata K, Haraguchi T, Chikashige Y. Codon usage bias is correlated with gene expression levels in the fission yeast Schizosaccharomyces pombe. Genes to Cells, 2009, 14: 499-509.
[8] Moriyama E, Powell J. Codon usage bias and tRNA abundance in Drosophila. Journal of Molecular Evolution, 1997, 45(5): 514-523.
[9] Oresic M, Dehn M, Korenblum D, Shalloway D. Tracing specific synonymous codon-secondary structure correlations through evolution. Journal of Molecular Evolution, 2003, 56: 473-484.
[10] Sakai H, Washio T, Saito R, Shinagawa A, Itoh M, Shibata K, Carninci P, Konno H, Kawai J, Hayashizaki Y, Tomita M. Correlation between sequENCe conservation of the 5′untranslated region and codon usage bias in Mus musculus genes. Gene, 2001, 276(1/2): 101-105.
[11] Gustafsson C, Govindarajan S, Minshull J. Codon bias and heterologous protein expression. Trends in Biotechnology, 2004, 22(7): 346-353.
[12] 吴正常, 王靖, 赵乔辉, 朱世平, 訾臣, 吴圣龙, 包文斌. 猪脂多糖结合蛋白基因(LBP)的密码子偏好性分析. 农业生物技术学报, 2013, 21(10): 1135-1144.
Wu Z C, Wang J, Zhao Q H, Zhu S P, Zi C, Wu S L, Bao W B. Analysis of codon bias of lipopolysaccharide-binding protein gene (LBP) in pigs (Sus scrofa). Journal of Agricultural Biotechnology, 2013, 21(10): 1135-1144. (in Chinese)
[13] Sharp P M, Bailes E, Grocock R J, Peden J F, Sockett R E. Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Research, 2005, 33: 1141-1153.
[14] Sharp P M, Tuohy T M, Mosurski K R. Codon usage in yeast: Cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Research, 1986, 14: 5125-5143.
[15] Zhou T, Sun X, Lu Z. Synonymous codon usage in environmental chlamydia UWE25 reflects an evolutional divergence from pathogenic chlamydiae. Gene, 2006, 368: 117-125.
[16] Duret L, Mouchiroud D. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 1999, 96: 4482-4487.
[17] Bulmer M. The selection-mutation-drift theory of synonymous codon usage. Genetics, 1991, 129(3): 897-907.
[18] 吴彦庆, 葛金涛, 陶俊. 芍药AP1(APETALA1)基因密码子使用的偏好性分析. 湖南农业大学学报(自然科学版), 2015, 41(6): 610-615.
Wu Y Q, Ge J T, Tao J. Analysis the codon bias of AP1 gene in Paeonia lactiflora. Journal of Hunan Agricultural University (Natural Sciences Edition), 2015, 41(6): 610-615. (in Chinese)
[19] Zhao D Q, Jiang Y, Ning C L, Meng J S, Lin S, Ding W, Tao J. Transcriptome sequencing of a chimaera reveals coordinated expression of anthocyanin biosynthetic genes mediating yellow formation in herbaceous peony (Paeonia lactiflora Pall.). BMC Genomics, 2014, 15(1): 689.
[20] Liu H M, He R, Zhang H Y, Huang Y B, Tian M L, Zhang J J. Analysis of synonymous codon usage in Zea mays. Molecular Biology Reports, 2010, 37(2): 677-684.
[21] Peden J F. CodonW. University of Nottingham, 1999.
[22] Sueoka N. Directional mutation pressure and neutral molecular evolution. Proceedings of the National Academy of Sciences, 1988, 85(8): 2653-2657.
[23] Wright F. The ‘effective number of codons’ used in a gene. Gene, 1990, 87: 23-29.
[24] Comeron J M, Aguade M. An evaluation of measures of synonymous codon usage bias. Journal of Molecular Evolution, 1998, 47: 268-274.
[25] 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: 1281-1295.
[26] SharpPM,LiWH.Anevolutionaryperspectiveonsynonymouscodonusageinunicellularorganisms. Journal of Molecular Evolution,1986, 24(1/2):28-38.
[27] Greenacre M J. Theory and applications of correspondence analysis. London: Academic Press 1984.
[28] Noboru S. Near homogeneity of PR2-bias fingerrints in the human genome and their implications in phylogenetic analyses. Journal of Molecular Evolution, 2001, 53: 469-476.
[29] Yang X, Luo X N, Cai X P. Analysis of codon usage pattern in Taenia saginata based on a transcriptome dataset. Parasites & Vectors, 2014, 7: 527.
[30] Zhou J H, Ding Y Z, He Y, Chu Y F, Zhao P, Zhao P, Ma L Y, Wang X J, Li X R, Liu Y S. The effect of multiple evolutionary selections on synonymous codon usage of genes in the Mycoplasma bovis Genome. Plos One, 2014, 9: e108949.
[31] Naya H, Romero H, Carels N, Zavala A, Musto H. Translational selection shapes codon usage in the GC-rich genome of Chlamydomonas reinhardtii. Febs Letters, 2001,501: 127-130.
[32] Gupta S, Bhattacharyya T, Ghosh T C. Synonymous codon usage in Lactococcus lactis: mutational bias versus translational selection. Journal of Biomolecular Structure & Dynamics, 2004, 21: 527-535.
[33] Bellgard M, Schibeci D, Trifonov E, Gojobori T. Early detection of G+C differences in bacterial species inferred from the comparative analysis of the two completely sequenced Helicobacter pylori strains. Journal of Molecular Evolution, 2001, 53(4/5): 465-468.
[34] Kawabe A, Miyashita N T. Patterns of codon usage bias in three dicot and four monocot plant species. Genes & Genetic Systems, 2003, 78: 343-352.
[35] Saul A, Battistutta D. Codon usage in Plasmodium falciparum. Molecular and Biochemical Parasitology, 1988, 27: 35-42.
[36] Muto A, Yamao F, Osawa S. The genome of Mycoplasma capricolum. Progress in Nucleic Acid Research and Molecular Biology, 1987, 34: 29-58.
[37] Dybvig K, Voelker L L. Molecular biology of mycoplasmas. Annual Reviews in Microbiology, 1996, 50(1): 25-57.
[38] 续晨, 蔡小宁, 钱保俐, 贲爱玲. 葡萄基因组密码子使用偏好模式研究. 西北植物学报, 2012, 32(2): 409-415.
Xu C, Cai X N, Qian B L, Ben A L. Codon usage bias in Vitis vinifera. Acta Botanica Boreali-Occidentalia Sinica, 2012, 32(2): 409-415. (in Chinese)
[39] 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.
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. (in Chinese)
[40] 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.
Xu C, Ben A L, Cai X L. Analysis of synonymous codon usage in chloroplast genome of Phalaenopsis aphrodite subsp. Formosana. Molecular Plant Breeding, 2010, 8(5): 945-950. (in Chinese)
[41] 尚明照, 刘方, 华金平, 王坤波. 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, 44(2): 245-253.
Shang M Z, Liu F, Hua J P, Wang K B. Analysis on codon usage of chloroplast genome of Gossypium hirsutum. Scientia Agricultura Sinica, 2011, 44(2): 245-253. (in Chinese)
[42] 李秀璋, 宋辉, 李春杰. 茄腐镰孢(Fusarium solani)线粒体基因组密码子偏好性分析. 基因组学与应用生物学, 2015, 34(11): 2465-2472.
Li X Z, Song H, Li C J. Analysis of codon usage bias in mitochondria genome of Fusarium solani. Genomics and Applied Biology, 2015, 34(11): 2465-2472. (in Chinese)
[43] Liu Q P, Feng Y, Zhao X A, Dong H, Xue Q Z. Synonymous codon usage bias in Oryza sativa. Plant Science, 2004, 167(1): 101-105.
[44] Zhang W J, Zhou J, Li Z F, Wang L, Gu X, Zhong Y. 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.
[45] Wang L J, Roossinck M J. Comparative analysis of expressed sequences reveals a conserved pattern of optimal codon usage in plants. Plant Molecular Biology, 2006, 61(4): 699-710. |
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