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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

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