Codon usage bias(CUB) is a unique property of genome which refers to non-random usage of synonymous codons in coding sequences. The present study makes an attempt to find out the pattern of CUB in chloroplast(cp) gene...Codon usage bias(CUB) is a unique property of genome which refers to non-random usage of synonymous codons in coding sequences. The present study makes an attempt to find out the pattern of CUB in chloroplast(cp) genes among three tea species, i.e., Camellia sinensis var. assamica(Assam tea), Camellia sinensis var. sinensis(Chinese tea) and Camellia pubicosta(wild tea species) as no work on CUB was reported earlier. To understand the patterns of codon usage among the cp genes of three tea groups, we used bioinformatic tools to investigate the protein coding sequences of cp genes. In our present study, the mean nucleobase T was the highest whereas C was the lowest in all the three tea groups. The overall AT content was more than GC content, i.e., genes were AT rich. The scaled chi-square(SCS) value indicated that the CUB of cp genes was low. The codon CGT(Arg) was over-represented in C. sinensis var. sinensis whereas GGA(Pro) was over-represented in C. pubicosta species. Heatmap study revealed that most of the GC ending codons showed positive correlations between codon usage and GC3 while AT ending codons exhibited negative correlations. From neutrality plot analysis, it was evident that natural selection had played a major role, while mutation pressure exerted a minor effect in the CUB of cp genes in three tea groups. Highly significant(P<0.01) positive correlation was found between SCS and synonymous codon usage order(SCUO) of cp genes which suggested that high expression of cp genes was associated with high degree of CUB.展开更多
对云南地区栽培的大叶茶（Camellia sinensis var. assamica）9个居群和大理茶（C.taliensis）3个居群的遗传多样性和居群遗传结构进行了比较研究。通过对94条叶绿体DNA RPL32-TRNL序列的核苷酸序列变异进行分析,共发现了7个单倍型。研...对云南地区栽培的大叶茶（Camellia sinensis var. assamica）9个居群和大理茶（C.taliensis）3个居群的遗传多样性和居群遗传结构进行了比较研究。通过对94条叶绿体DNA RPL32-TRNL序列的核苷酸序列变异进行分析,共发现了7个单倍型。研究结果表明,大叶茶（h=0.728,π=0.00469）比大理茶（h=0.610,π=0.00225）拥有更为丰富的遗传变异,但其居群遗传分化水平（Gst=0.580,FST=0.612）却低于大理茶（Gst=0.696,FST=0.773）。AMOVA分析进一步证实了它们的遗传变异主要存在于居群间,且大叶茶（61.21%）低于大理茶（77.34%）。相对于大理茶,遗传多样性水平在本研究所取的大叶茶居群间存在着较大的差异,单倍型多态性水平变化范围为0~0.809,核苷酸多态性水平变化范围为0~0.00487。最后,讨论并提出了科学有效地保护我国古茶园茶种资源的建议和对策。展开更多
为揭示大叶茶(Camellia sinensis var.assamica,CSA)研究的热点及前沿,研究采用文献计量学的方法,利用SCI-E和SSCI数据库进行检索,从发文趋势、研究力量布局、研究主题及演变规律、前沿发展态势探测方面进行分析。结果显示:关于大叶茶...为揭示大叶茶(Camellia sinensis var.assamica,CSA)研究的热点及前沿,研究采用文献计量学的方法,利用SCI-E和SSCI数据库进行检索,从发文趋势、研究力量布局、研究主题及演变规律、前沿发展态势探测方面进行分析。结果显示:关于大叶茶的研究总发文量呈上升趋势,分为萌芽期(1976-2004年)、发展期(2005-2014年)和快速增长期(2015年至今)3个阶段;发文单位以安徽农业大学、中国科学院和云南农业大学为主,刊载相关研究论文最多的期刊为《Journal of Agricultural and Food Chemistry》;关键词分析中,Antioxidant(抗氧化)、Theacrine(苦茶碱)和Fermentation(发酵)等具有较高词频,Genome(基因组)和Metabolomics(代谢组学)兼具高频词和新兴词的特征,为研究的热点词汇;引文网络分析显示,全基因组遗传分析、茶树系统发生学研究、靶向/非靶向代谢组分析以及化合物差异化分析为研究前沿。研究结果为学者开展研究以及相关机构制定科技战略规划提供参考。展开更多
文摘Codon usage bias(CUB) is a unique property of genome which refers to non-random usage of synonymous codons in coding sequences. The present study makes an attempt to find out the pattern of CUB in chloroplast(cp) genes among three tea species, i.e., Camellia sinensis var. assamica(Assam tea), Camellia sinensis var. sinensis(Chinese tea) and Camellia pubicosta(wild tea species) as no work on CUB was reported earlier. To understand the patterns of codon usage among the cp genes of three tea groups, we used bioinformatic tools to investigate the protein coding sequences of cp genes. In our present study, the mean nucleobase T was the highest whereas C was the lowest in all the three tea groups. The overall AT content was more than GC content, i.e., genes were AT rich. The scaled chi-square(SCS) value indicated that the CUB of cp genes was low. The codon CGT(Arg) was over-represented in C. sinensis var. sinensis whereas GGA(Pro) was over-represented in C. pubicosta species. Heatmap study revealed that most of the GC ending codons showed positive correlations between codon usage and GC3 while AT ending codons exhibited negative correlations. From neutrality plot analysis, it was evident that natural selection had played a major role, while mutation pressure exerted a minor effect in the CUB of cp genes in three tea groups. Highly significant(P<0.01) positive correlation was found between SCS and synonymous codon usage order(SCUO) of cp genes which suggested that high expression of cp genes was associated with high degree of CUB.
文摘对云南地区栽培的大叶茶（Camellia sinensis var. assamica）9个居群和大理茶（C.taliensis）3个居群的遗传多样性和居群遗传结构进行了比较研究。通过对94条叶绿体DNA RPL32-TRNL序列的核苷酸序列变异进行分析,共发现了7个单倍型。研究结果表明,大叶茶（h=0.728,π=0.00469）比大理茶（h=0.610,π=0.00225）拥有更为丰富的遗传变异,但其居群遗传分化水平（Gst=0.580,FST=0.612）却低于大理茶（Gst=0.696,FST=0.773）。AMOVA分析进一步证实了它们的遗传变异主要存在于居群间,且大叶茶（61.21%）低于大理茶（77.34%）。相对于大理茶,遗传多样性水平在本研究所取的大叶茶居群间存在着较大的差异,单倍型多态性水平变化范围为0~0.809,核苷酸多态性水平变化范围为0~0.00487。最后,讨论并提出了科学有效地保护我国古茶园茶种资源的建议和对策。
文摘为揭示大叶茶(Camellia sinensis var.assamica,CSA)研究的热点及前沿,研究采用文献计量学的方法,利用SCI-E和SSCI数据库进行检索,从发文趋势、研究力量布局、研究主题及演变规律、前沿发展态势探测方面进行分析。结果显示:关于大叶茶的研究总发文量呈上升趋势,分为萌芽期(1976-2004年)、发展期(2005-2014年)和快速增长期(2015年至今)3个阶段;发文单位以安徽农业大学、中国科学院和云南农业大学为主,刊载相关研究论文最多的期刊为《Journal of Agricultural and Food Chemistry》;关键词分析中,Antioxidant(抗氧化)、Theacrine(苦茶碱)和Fermentation(发酵)等具有较高词频,Genome(基因组)和Metabolomics(代谢组学)兼具高频词和新兴词的特征,为研究的热点词汇;引文网络分析显示,全基因组遗传分析、茶树系统发生学研究、靶向/非靶向代谢组分析以及化合物差异化分析为研究前沿。研究结果为学者开展研究以及相关机构制定科技战略规划提供参考。
