采用高频密码子分析法,对甜橙C itrus sinensis、温州蜜柑C.unshiu、葡萄柚C.paradisi和柠檬C.lim on等4种柑橘的蛋白质编码基因序列(codon DNA sequence,CDS)进行了分析,计算出了柑橘同义密码子相对使用频率(rela-tive frequency of sy...采用高频密码子分析法,对甜橙C itrus sinensis、温州蜜柑C.unshiu、葡萄柚C.paradisi和柠檬C.lim on等4种柑橘的蛋白质编码基因序列(codon DNA sequence,CDS)进行了分析,计算出了柑橘同义密码子相对使用频率(rela-tive frequency of synonymous codon,RFSC),确定出了4种柑橘的高频率密码子,发现不同种类柑橘偏爱密码子稍有差别.展开更多
Codon usage is the selective and nonrandom use of synonymous codons to encode amino acids in genes for proteins. The analysis of codon usage may improve the understanding of cocion preferences between different specie...Codon usage is the selective and nonrandom use of synonymous codons to encode amino acids in genes for proteins. The analysis of codon usage may improve the understanding of cocion preferences between different species and allow to rebuild the codons of exogenous genes to increase the expression efficiency of exogenous genes, Here, codon DNA sequence (CDS) of four poplar species, including Populus tremuloides Michx., P. tomentosa Carr., P. deltoides Marsh., and P. trichocarpa Torr. & Gray., is used to analyze the relative frequency of synonymous codon (RFSC). High-frequency codons are selected by high-frequency (HF) codon analysis. The results indicate that the codon usage is common for all four poplar species and the codon preference is quite similar among the four poplar species. However, CCT encoding for Pro, and ACT coding for Thr are the preferred codons in P. tremuloides and P. tomentosa, whereas CCA coding for Pro, and ACA coding for Thr are preferred in P. deltoides and P. trichocarpa The codons such as TGC coding for Cys, TTC coding for Phe, and AAG coding for Lys, are preferred in the poplar species except P trichocarpa. GAG coding for Glu is preferred only in P deltoides, while the other three poplar species prefer to use GAA. The commonness of preferred codon allows exogenous gene designed by the preferred cocion of one of the different poplar species to be used in other poplar species.展开更多
为全面了解黄皮(Clausena lansium)表达基因的密码子使用特点,以转录组测序获得的12 696条编码蛋白基因序列为数据来源,利用CodonW 14.4软件对其密码子碱基组成以及有效密码子数(effective number of codon, ENC)、同义密码子相对使用频...为全面了解黄皮(Clausena lansium)表达基因的密码子使用特点,以转录组测序获得的12 696条编码蛋白基因序列为数据来源,利用CodonW 14.4软件对其密码子碱基组成以及有效密码子数(effective number of codon, ENC)、同义密码子相对使用频率(relative frequency of synonymous codon, RFSC)等密码子使用参数进行计算和统计,发现黄皮表达基因密码子的平均GC含量为0.448,同义密码子第3位核苷酸的平均GC含量(GC3S)为0.400。表达基因整体的ENC取值为56.5,其中绝大部分的ENC值大于35,说明黄皮表达基因密码子使用偏好性程度整体水平较低。通过高频密码子分析法确定了GCU、AGA、AAU、GAU、AUU、UUU、UCU、CAU、CUU、UUG和GUU 11个高频密码子。将黄皮的密码子使用频率与人、小鼠、果蝇、酵母、大肠杆菌5种模式生物以及拟南芥、水稻、葡萄、草莓4种不同类型植物进行比较,发现其与果蝇和大肠杆菌存在较大差异,而与拟南芥和葡萄基本一致。以上研究结果对黄皮基因合适表达系统的选择以及外源基因在黄皮中的高效表达具有重要指导意义。展开更多
生物体内密码子使用偏性对外源基因表达存在较大影响。本研究采用CodonW软件和高频密码子分析法,对白梨(Pyrus bretschneideri Rehd)、西洋梨(Pyrus communis Linn)、砂梨(Pyrus pyrifolia Nakai)、秋子梨(Pyrusussuriensis Maxim)4种...生物体内密码子使用偏性对外源基因表达存在较大影响。本研究采用CodonW软件和高频密码子分析法,对白梨(Pyrus bretschneideri Rehd)、西洋梨(Pyrus communis Linn)、砂梨(Pyrus pyrifolia Nakai)、秋子梨(Pyrusussuriensis Maxim)4种梨蛋白质编码基因序列(Codon DNA sequence,CDS)进行了同义密码子相对使用频率(relativefrequency of synonymous,RFSC)分析,确定了梨高频密码子共23个,结果同时显示梨不同种之间在密码子使用上具有较高的一致性。展开更多
AIIopolyploidy has played an important role in plant evolution and heterosis. Recent studies indicate that the process of wide hybridization and (or) polyploidization may induce rapid and extensive genetic and epige...AIIopolyploidy has played an important role in plant evolution and heterosis. Recent studies indicate that the process of wide hybridization and (or) polyploidization may induce rapid and extensive genetic and epigenetic changes in some plant species. To better understand the allopolyploidy evolutionism and the genetic mechanism of Arachis interspecific hybridization, this study was conducted to monitor the gene expression variation by cDNA start codon targeted polymorphism (cDNA-SCoT) and cDNA high-frequency oligonucleotide-targeting active gene (cDNA-HFO-TAG) techniques, from the hybrids (F1) and newly synthesized allopolyploid generations (S0-$3) between tetraploid cultivated peanut Zhongkaihua 4 with diploid wild one Arachis doigoi. Rapid and considerable gene expression variations began as early as in the FI hybrid or immediately after chromosome doubling. Three types of gene expression changes were observed, including complete silence (gene from progenitors was not expressed in all progenies), incomplete silence (gene expressed only in some progenies) and new genes activation. Those silent genes mainly involved in RNA transcription, metabolism, disease resistance, signal transduction and unknown functions. The activated genes with known function were almost retroelements by cDNA-SCoT technique and all metabolisms by cDNA-HFO-TAG. These findings indicated that interspecific hybridization and ploidy change affected gene expression via genetic and epigenetic alterations immediately upon allopolyploid formation, and some obtained transcripts derived fragments (TDFs) probably could be used in the research of molecular mechanism of Arachis allopolyploidization which contribute to thwe genetic diploidization of newly formed allopolyploids. Our research is valuable for understanding of peanut evolution and improving the utilization of putative and beneficial genes from the wild peanut.展开更多
文摘采用高频密码子分析法,对甜橙C itrus sinensis、温州蜜柑C.unshiu、葡萄柚C.paradisi和柠檬C.lim on等4种柑橘的蛋白质编码基因序列(codon DNA sequence,CDS)进行了分析,计算出了柑橘同义密码子相对使用频率(rela-tive frequency of synonymous codon,RFSC),确定出了4种柑橘的高频率密码子,发现不同种类柑橘偏爱密码子稍有差别.
基金This work was supported by the National Major Basic Research and Development Program(No.TG1999016004)Jiangsu Provincial Natural Science Foundation(No.BK2003213).
文摘Codon usage is the selective and nonrandom use of synonymous codons to encode amino acids in genes for proteins. The analysis of codon usage may improve the understanding of cocion preferences between different species and allow to rebuild the codons of exogenous genes to increase the expression efficiency of exogenous genes, Here, codon DNA sequence (CDS) of four poplar species, including Populus tremuloides Michx., P. tomentosa Carr., P. deltoides Marsh., and P. trichocarpa Torr. & Gray., is used to analyze the relative frequency of synonymous codon (RFSC). High-frequency codons are selected by high-frequency (HF) codon analysis. The results indicate that the codon usage is common for all four poplar species and the codon preference is quite similar among the four poplar species. However, CCT encoding for Pro, and ACT coding for Thr are the preferred codons in P. tremuloides and P. tomentosa, whereas CCA coding for Pro, and ACA coding for Thr are preferred in P. deltoides and P. trichocarpa The codons such as TGC coding for Cys, TTC coding for Phe, and AAG coding for Lys, are preferred in the poplar species except P trichocarpa. GAG coding for Glu is preferred only in P deltoides, while the other three poplar species prefer to use GAA. The commonness of preferred codon allows exogenous gene designed by the preferred cocion of one of the different poplar species to be used in other poplar species.
文摘为全面了解黄皮(Clausena lansium)表达基因的密码子使用特点,以转录组测序获得的12 696条编码蛋白基因序列为数据来源,利用CodonW 14.4软件对其密码子碱基组成以及有效密码子数(effective number of codon, ENC)、同义密码子相对使用频率(relative frequency of synonymous codon, RFSC)等密码子使用参数进行计算和统计,发现黄皮表达基因密码子的平均GC含量为0.448,同义密码子第3位核苷酸的平均GC含量(GC3S)为0.400。表达基因整体的ENC取值为56.5,其中绝大部分的ENC值大于35,说明黄皮表达基因密码子使用偏好性程度整体水平较低。通过高频密码子分析法确定了GCU、AGA、AAU、GAU、AUU、UUU、UCU、CAU、CUU、UUG和GUU 11个高频密码子。将黄皮的密码子使用频率与人、小鼠、果蝇、酵母、大肠杆菌5种模式生物以及拟南芥、水稻、葡萄、草莓4种不同类型植物进行比较,发现其与果蝇和大肠杆菌存在较大差异,而与拟南芥和葡萄基本一致。以上研究结果对黄皮基因合适表达系统的选择以及外源基因在黄皮中的高效表达具有重要指导意义。
文摘生物体内密码子使用偏性对外源基因表达存在较大影响。本研究采用CodonW软件和高频密码子分析法,对白梨(Pyrus bretschneideri Rehd)、西洋梨(Pyrus communis Linn)、砂梨(Pyrus pyrifolia Nakai)、秋子梨(Pyrusussuriensis Maxim)4种梨蛋白质编码基因序列(Codon DNA sequence,CDS)进行了同义密码子相对使用频率(relativefrequency of synonymous,RFSC)分析,确定了梨高频密码子共23个,结果同时显示梨不同种之间在密码子使用上具有较高的一致性。
基金supported by the Guangxi Academy of Agricultural Sciences Foundation,China(2015JZ08 and 2015YT57)the Guangxi Sciences Foundation,China(2011GXNSFA018079)+1 种基金the Modern Agro-industry Technology Research System,China(CARS-14-19)the National Natural Science Foundation of China(31160294 and 31240059)
文摘AIIopolyploidy has played an important role in plant evolution and heterosis. Recent studies indicate that the process of wide hybridization and (or) polyploidization may induce rapid and extensive genetic and epigenetic changes in some plant species. To better understand the allopolyploidy evolutionism and the genetic mechanism of Arachis interspecific hybridization, this study was conducted to monitor the gene expression variation by cDNA start codon targeted polymorphism (cDNA-SCoT) and cDNA high-frequency oligonucleotide-targeting active gene (cDNA-HFO-TAG) techniques, from the hybrids (F1) and newly synthesized allopolyploid generations (S0-$3) between tetraploid cultivated peanut Zhongkaihua 4 with diploid wild one Arachis doigoi. Rapid and considerable gene expression variations began as early as in the FI hybrid or immediately after chromosome doubling. Three types of gene expression changes were observed, including complete silence (gene from progenitors was not expressed in all progenies), incomplete silence (gene expressed only in some progenies) and new genes activation. Those silent genes mainly involved in RNA transcription, metabolism, disease resistance, signal transduction and unknown functions. The activated genes with known function were almost retroelements by cDNA-SCoT technique and all metabolisms by cDNA-HFO-TAG. These findings indicated that interspecific hybridization and ploidy change affected gene expression via genetic and epigenetic alterations immediately upon allopolyploid formation, and some obtained transcripts derived fragments (TDFs) probably could be used in the research of molecular mechanism of Arachis allopolyploidization which contribute to thwe genetic diploidization of newly formed allopolyploids. Our research is valuable for understanding of peanut evolution and improving the utilization of putative and beneficial genes from the wild peanut.