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Acta Agron Sin ›› 2011, Vol. 37 ›› Issue (06): 965-974.doi: 10.3724/SP.J.1006.2011.00965

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

Analysis of Nuclear Gene Codon Bias on Soybean Genome and Transcriptome

ZHANG Le1,JIN Long-Guo1,LUO Ling1,WANG Yue-Ping1,DONG Zhi-Min1,SUN Shou-Hong2,QIU Li-Juan1,*   

  1. 1 National Key Facility for Crop Gene Resources and Genetic Improvement / Key Laboratory of Germplasm Utilization, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; 2 Chinese Academy of Sciences, Beijing 100101, China
  • Received:2010-12-23 Revised:2011-03-28 Online:2011-06-12 Published:2011-04-12
  • Contact: 邱丽娟, E-mail: qiu_lijuan@263.net

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Abstract: Research of soybean nuclear gene codon composition, usage pattern and influencing factors can provide theoretical basis for applying genetic engineering techonology to improve soybean varieties. A total of 46 430 high confidence coding sequences predicted from soybean genome and 2 071 full-length transcripts were used to analyze the composition and characteristics of soybean nuclear gene codons. CodonW software was applied to calculate the nucleotide composition, relative synonymous codon usage and other parameters of soybean genome and transcriptome. The result indicted that gene expression level was significantly and positively correlated with G+C and GC3s contents, and genes with high G+C and GC3s contents had high codon preference. UCC and GCC were identified as optimal codons in soybean. Analysis of coding sequences with different length showed that codon preference reduced as the coding sequence (CDS) length increased, and longer CDS tend to select codons randomly. CDS length between 400 to 600 bp had the highest expression level among the transcriptome data. The preference and expression level were almost the same between leaf-specific and seed-specific genes. But seed-specific genes had significantly higher G+C and GC3s contents than leaf-specific genes, and the contents of aromatic amino acids encoded by seed-specific genes were highly significantly lower than these by leaf-specific genes.

Key words: Soybean, Genome, Transcriptome, Codon

[1]Carlini D B, Stephan W. In vivo introduction of unpreferred synonymous codons into the Drosophila Adh gene results in reduced levels of ADH protein. Genetics, 2003, 163: 239–243
[2]Sharp P M, Matassi G. Codon usage and genome evolution. Curr Opin Genet Dev, 1994, 4: 851–860
[3]Stenico M, Lloyd A T, Sharp P M. Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases. Nucl Acid Res, 1994, 22: 2437–2446
[4]Olejniczak M, Uhlenbeck O C. tRNA residues that have coevolved with their anticodon to ensure uniform and accurate codon recognition. Biochinmie, 2006, 88: 943–950
[5]Holmouist G P, Flipske J. Organization of mutations along the genome: a prime determinant of genome evolution. Trends Ecol Evol, 1994, 9: 65–69
[6]Bernard I G. The human genome: Organization and evolutionary history. Annu Rev Genet, 1995, 29: 445–476
[7]Shi X-F(石秀凡), Huang J-F(黄京飞), Liu S-Q(柳树群), Liu C-Q(刘次全). The feature of synonymous codon bias and GC-content relationship in human genes. Prog Biochem Biophys (生物化学与生物物理进展), 2002, 29(3): 411–414 (in Chinese with English abstract)
[8]Xia X. Mutation and selection on the anticodon of tRNA genes in vertebrate mitochondrial genomes. Gene, 2005, 345: 13–20
[9]Chen S L, Lee W, Hottes A K, Shapiro L, McAdams H H. Codon usage between genomes is constrained by genome-wide mutational processes. Pro Natl Acad Sci, 2004, 101: 3480–3485
[10]Romero H, Zavala A, Musto H, Bernaerdi G. The influence of translational selection on codon usage in fishes from the family Cyprinidae. Gene, 2003, 317: 141–147
[11]Moriyama E N, Powell J R. Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cervisiae and Escherichia coli. Nucl Acids Res, 1998, 26: 3188–3193
[12]Knight R D, Freeland S J, Landweber L F. A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes. Genome Biol, 2001, 2: RESERCH0010
[13]Gupta S K, Majumdar S K, Bhattacharya T, Ghosh T C. Studies on the relationships between the synonymous codon usage and protein secondary structural units. Biochem Biophys Res Commun, 2000, 269: 692–696
[14]Goldman N, Yang Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Molr Biol Evol, 1994, 11: 725–736
[15]Schmidt W. Phylogeny reconstruction for protein sequences based on amino acid properties. J Mol Evol, 1995, 41: 522–530
[16]Arumuganathan K, Earle E D. Nuclear DNA content of some important plant species. Plant Mol Rep, 1991, 9: 208–218
[17]Jeremy S, Steven B C, Jessica S, Ma J X, Mitros T, Nelson W, Hyten D L, Song Q J, Thelen J J, Cheng J L, Xu D, Hellsten U, May G D, Yu Y, Sakarai T, Umezawa T, Bhattacharyya M K, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S Q, Abernathy B, Du J C, Tian Z X, Zhu L C, Gill N, Joshi T, Libault M, Sethuraman A, Zhang X C, Shinozak K, Nguyen H T, Wing R A, Cregan P, Specht J, Crimwood J, Rokhsar D, Stavey G, Shoemaker R C, Jackson S A. Genome sequence of the palaeopolyploid soybean. Nature, 2010, 463: 178–183
[18]Cao H-Y(曹慧颖), Zhang R(张锐), Guo S-D(郭三堆). High level expression of human thymosin α1 concatemer in transgenic tomato plants. Sci Agric Sin (中国农业科学), 2009, 42(7): 2291–2296 (in Chinese with English abstract)
[19]Zou Y-M(邹永梅), Shi J-S(施季森), Zhu-Ge Q(诸葛强), Huang M-R(黄敏仁). Reacting the silencing genes in the transgenic plants. Mol Plant Breed (分子植物育种), 2006, 4(1): 95–102 (in Chinese with English abstract)
[20]Dong Z-M(董志敏), Li Y-H(李英慧), Zhang B-S(张宝石), Guan R-X(关荣霞), Chang R-Z(常汝镇), Qiu L-J(邱丽娟). An improved SMART method to construction full-length cDNA library for large clones. Soybean Sci (大豆科学), 2006, (5): 1-4 (in Chinese with English abstract)
[21]Wang Y-P(王跃平), Li Y-H(李英慧), Chen X-T(陈雄庭), Chang R-Z(常汝镇), Qiu L-J(邱丽娟). Construction and characterization of the filling stage’s seed cDNA library from Suinong14 (Glycine max). Chin J Oil Crop Sci (中国油料作物学报), 2008, 30(1): 40–45 (in Chinese with English abstract)
[22]Sharp P M, Haney T M F, Mosurski K R. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucl Acids Res, 1986, 14: 5125–5143
[23]Liu Q, Feng Y, Xue Q. Analysis of factors shaping codon usage in the mitochondrion genome of Oryza sativa. Mitochondrion, 2004, 4: 313–320
[24]Sau K, Gupta S K, Sau S, Mandal S C, Ghosh T C. Factors influencing synonymous codon and amino acid usage biases in Mimivirus. Biosystems, 2006, 85: 107–113
[25]Wright F. The effective number of codons used in a gene. Gene, 1990, 87: 23–29
[26]Gupta S K, Bhattacharyya T K, Ghosh T C. Synonymous codon usage in lactococcus lactis: mutational bias versus translational selection. Biomol Struct Dyn, 2004, 21: 1–9
[27]Peixoto L, Zavala A, Romero H, Musto H. The strength of translational selection for codon usage varies in three relicons of Sinorhizobium melioti. Gene, 2003, 320: 109–116
[28]Romero H, Zavala A, Musto H. Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces. Nucl Acids Res, 2000, 28: 2084–2090
[29]Duret L, Mouchiroud D. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabdits, Drosophila, and Arabidopsis. Proc Natl Acad Sci, 1999, 96: 4482–4487
[30]Sharp P M, Li W H. The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications. Nucl Acids Res, 1987, 15: 1281–1295
[31]Wei C, Brent M R. Using ESTs to improve the accuracy of de novo gene prediction. BMC Bioinformatics, 2006, 7: 327-337
[32]Kwan A L, Li L, Kulp D C, Dutcher S K, Stormo G D. Improving gene-finding in Chlamydomonas reinhardtii Green Genie2. BMC Genomics, 2009, 10: 210–220
[33]Sharp P M, Cowe E, Higgins D G, Shield D C, Wolfe K H, Wright F. Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity. Nucl Acids Res, 1988, 16: 8207–8211
[34]Stoletzki N, Eyre-Walker A. Synonymous codon usage in Escherichia coli: selection for translational accuracy. Mol Biol Evol, 2007, 24: 374–381
[35]Morton B R, Wright S I. Selective constraints on codon usage of nuclear genes from Arabidopsis thaliana. Mol Biol Evol, 2007, 24: 122–129
[36]Cutter A D, Wasmath J D, Blaxter M L. The evolution of biased codon and amino acid usage in nematode genomes. Mol Biol Evol, 2006, 23: 2303–2315
[37]Duret L, Mouchiroud D. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. PNAS, 1999, 96: 4482–4487
[38]Vicario S, Mason C E, White K P, Powell J R. Developmental stage and level of codon usage bias in drosophila. Mol Biol Evol, 2008, 25: 2269–2277
[39]D’Onofrio G, Mouchiroud D, Aissani B, Gautier C, Bernardi G. Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteins. J Mol Evol, 1991, 32: 504–510
[40]Moriyama E N, Powell J R. Codon usage bias and tRNA abundance in Drosophila. J Mol Evol, 1997, 45: 514–523
[41]Holmquist G P, Filipski J. Organization of mutations along the genome: a prime determinant of genome evolution. Trends Ecol Evol, 1994, 9: 65–69
[42]Perlak F J, Deaton R W, Armstrong T A, Fuchs R L, Sims S R, Greenplate J T, Fischhoff D A. Insect resistant cotton plants. Biol Technol, 1990, 8: 939–943
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