[1]梁湘兰,郭松*. 苦马豆叶绿体基因组密码子偏好性分析[J].西北林学院学报,2022,37(2):121-126.[doi:10.3969/j.issn.1001-7461.2022.02.16]
　LIANG Xiang-lan,GUO Song*. Codon Usage Bias in the Chloroplast Genome of Sphaerophysa salsula[J].JOURNAL OF NORTHWEST FORESTRY UNIVERSITY,2022,37(2):121-126.[doi:10.3969/j.issn.1001-7461.2022.02.16]
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 苦马豆叶绿体基因组密码子偏好性分析()
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《西北林学院学报》[ISSN:1001-7461/CN:61-1202/S]

卷:
第37卷
期数:
2022年第2期
页码:
121-126
栏目:
出版日期:
2022-03-31

文章信息/Info

Title:
 Codon Usage Bias in the Chloroplast Genome of Sphaerophysa salsula
文章编号:
1001-7461(2022)02-0121-06
作者:
 梁湘兰1; 郭松1; 2*
 （1.广西科技师范学院 食品与生化工程学院，广西 来宾 546199；2.广西科技师范学院 特色瑶药资源研究与开发重点实验室，广西 来宾 546199）
Author(s):
 LIANG Xiang-lan1; GUO Song1; 2*
 (1.College of Food and Biochemical Engineering,Guangxi Science &Technology Normal University,Laibin 546199,Guangxi,China; 2.Key Laboratory for Research and Development of Characteristic Yao Medicine Resources,Guangxi Science & Technology Normal University,Laibin 546199,Guangxi,China)
关键词:
 ; 叶绿体基因组; 苦马豆; 密码子偏好性; 最优密码子
Keywords:
Sphaerophysa salsula;  chloroplast genome;  codon usage bias;  optimal codon
分类号:
Q943.2
DOI:
10.3969/j.issn.1001-7461.2022.02.16
文献标志码:
A
摘要:
 为确定苦马豆叶绿体基因组密码子的使用模式，利用Codon W 1.4.2、CUSP、Chips等软件，对苦马豆叶绿体基因组中可编码蛋白质基因的密码子偏好性进行分析。结果表明，密码子第3位GC含量最低，为27.14％，29个RSCU＞1的密码子中28个以A、U结尾，苦马豆叶绿体基因组密码子偏好以A、U结尾。有效密码子数ENC平均值为47.110，密码子偏好性较弱。GC1、GC2与GC3无相关性，ENC与GC3相关性显著，GC3对密码子的偏好性存在影响。中性绘图分析和PR2-plot图分析表明，密码子偏好性主要受到选择因素的影响，而ENC-plot绘图分析发现，密码子偏好性还受到突变因素的影响。最终通过构建高低基因表达库，得到GAA、CGA、UUG、GUU、AUU、UCA、CAU、CAA、CCA、ACU、GCU、UUA、UAU、AAA、GAU、GGU 16个最优密码子。研究结果对苦马豆资源的开发和利用具有重要意义。
Abstract:
 To determine the codon usage pattern of chloroplast genome of Sphaerophysa salsula,the codon usage bias of these sequences was analyzed by using software Codon W 1.4.2 and online software CUSP,Chips.The results showed that the GC content at the third codon was the lowest,which was 27.14%.Among the 29 codons with RSCU>1,28 ended with A/U,indicating that synonymous codons in chloroplast genome tended to end with A/U.The average number of effective codons ENC was 47.110,and the codon preference was weak.GC1,GC2 had no correlation with GC3,while ENC had significant correlation with GC3,and GC3 had influence on codon usage bias.ENC-plot analysis and PR2-plot analysis showed that codon usage bias was mainly affected by natural selection,while ENC-plot analysis showed that codon usage bias was also affected by mutation factors.Through the constructed high and low gene expression libraries,16 optimal codons were finally determined,which were GAA,CGA,UUA,UUG,AUU,GUU,AUU,UCA,CAU,CAA,CCA,ACU,GCU,UUA,UAU,CAU,CAA,AAA,GAU,GAA,CGA,GGU.This research might benefit the research and application in S.salsula gene engineering.

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备注/Memo

备注/Memo:
 收稿日期：2021-04-02修回日期：2021-08-09
基金项目：广西科技师范学院高层次人才启动经费(GXKS2020GKY009)；广西高校中青年教师科研基础能力提升项目(2021KY0862)；广西科技师范学院特色瑶药资源研究与开发校级重点实验室经费(KJ5CSH000005)。
第一作者：梁湘兰。研究方向：遗传育种与分子生物学。E-mail：3143437545@qq.com
*通信作者：郭松，博士，助理研究员。研究方向：遗传育种与分子生物学。E-mail：guosong0804@163.com
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