LIU Huimin,WUYUN Tana,DU Hongyan.Analysis of Characteristic of Codon Usage of Eucommia ulmoides Transcriptome[J].Northern Horticulture,2016,40(13):85-89.[doi:10.11937/bfyy.201613023]
杜仲转录组基因密码子使用偏好性分析
- Title:
- Analysis of Characteristic of Codon Usage of Eucommia ulmoides Transcriptome
- Keywords:
- Eucommia ulmoides; transcriptome; codon; bias
- 文献标志码:
- A
- 摘要:
- 以杜仲转录组数据为试材，采用CodonW和SPSS软件相结合的方法，研究了杜仲基因密码子组成和长度对基因表达量的影响，以期为将来改造外源基因及利用基因工程技术改良杜仲提供理论基础。结果表明：杜仲转录组中基因的表达量与G3s、C3s、G+C和GC3s含量均呈极显著正相关(P<0.01)，与A3s含量、T3s含量、单条基因总密码子数(L_aa)和有效密码子数ENC均呈极显著负相关(P<0.01)，与Aro含量呈显著负相关(P<0.05)，表明高表达基因的密码子使用偏好性较强，且偏好于使用以G/C结尾的密码子；ENC与C3s、G3s、G+C和GC3含量均呈极显著负相关(P<0.01)，与A3s、T3s、Aro含量呈极显著正相关(P<0.01)；确定了15个杜仲最优密码子，分别为AAC、AAG、ACC、AGG、AUC、CAC、CAG、CCG、CUC、CUG、GCC、GGC、GUC、UAC和UCC。果实和叶片特异表达基因在氨基酸Leu、Ile、Ser、Pro、Thr、Asn、Glu和Cys密码子的使用上存在差异。
- Abstract:
- Eucommia ulmoides was used as test materials,the correlation between codon composition and gene expression was analyzed based on the transcriptome data by using CodonW and SPSS software,in order to offer a theoretical foundation for transforming exogenous gene and Eucommia genetic engineering.The results showed that the gene expression had a significant and positive correlation to G3s,C3s,G+C and GC3s(P<0.01)content and a negative correlation to A3s content,T3s content,gene coding sequence length and effective codon number(ENC)(P<0.01)and Aro content(P<0.05).These results indicated that genes with a high expression had a stronger codon usage bias and likely end with G/C.ENC had a significant positive correlation to A3s,T3s and Aro content(P<0.01)and a significant negative correlation to C3s,G3s,G+C,and GC3s content(P<0.01).Fifteen optimal codons were identified,namely,AAC,AAG,ACC,AGG,AUC,CAC,CAG,CCG,CUC,CUG,GCC,GGC,GUC,UAC,and UCC.Fruit and leaf special genes had difference on the codon usage of Leu,Ile,Ser,Pro,Thr,Asn,Glu and Cys.
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备注/Memo
第一作者简介：刘慧敏（1989-），女，河南辉县人，博士研究生，研究方向为林木遗传育种。E-mail：313324495@qq.com.责任作者：乌云塔娜（1975-），女，内蒙古通辽人，博士，教授，现主要从事经济林育种与栽培等研究工作。E-mail：tanatana@163.com.基金项目：国家“十二五”科技支撑计划资助项目（2012BAD21B0502）。