[1]段祥光,于涛,曹萌,等. 樟叶槭叶绿体基因组序列密码子偏性分析[J].西北林学院学报,2023,38(1):102-107.[doi:10.3969/j.issn.1001-7461.2023.01.14]
　DUAN Xiang-guang,YU Tao,CAO Meng,et al. Codon Usage Bias of Acer cinnamomifolium Chloroplast Genome[J].JOURNAL OF NORTHWEST FORESTRY UNIVERSITY,2023,38(1):102-107.[doi:10.3969/j.issn.1001-7461.2023.01.14]
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 樟叶槭叶绿体基因组序列密码子偏性分析()
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《西北林学院学报》[ISSN:1001-7461/CN:61-1202/S]

卷:
第38卷
期数:
2023年第1期
页码:
102-107
栏目:
出版日期:
2023-01-31

文章信息/Info

Title:
 Codon Usage Bias of Acer cinnamomifolium Chloroplast Genome
文章编号:
1001-7461(2023)01-0102-06
作者:
 段祥光1; 于涛2; 曹萌3; 马文宝4*
 （1.信阳师范学院 旅游学院，河南 信阳 464000；2.中节能生态产品发展研究中心，北京 100089；3.中国消防救援学院，北京 102202；4.四川省林业科学研究院 森林和湿地生态恢复与保育四川重点实验室，四川 成都 610081）
Author(s):
 DUAN Xiang-guang1; YU Tao2; CAO Meng3; MA Wen-bao4*
 (1.Tourism College,Xinyang Normal University,Xinyang 464000,Henan,China; 2.CECEP Eco-Product Development Research Center,Beijing 100089,China; 3.China Academy of Fire Protection and Rescue,Beijing 102202,China; 4.Sichuan Key Laboratory of Forest and Wetland Ecological Restoration and Conservation,Sichuan Academy of Forestry,Chengdu 610081,Sichuan,China)
关键词:
 ; 樟叶槭; 叶绿体基因组; 密码子; 偏好性; 最优密码子
Keywords:
Acer cinnamomifolium;  chloroplast genome;  codon;  usage bias;  optimal codon
分类号:
S792.35
DOI:
10.3969/j.issn.1001-7461.2023.01.14
文献标志码:
A
摘要:
 为确定槭属樟叶槭叶绿体基因组密码子使用模式和原因，通过对樟叶槭叶绿体基因组中筛选的53条基因序列进行中性绘图、ENC-plot与PR2-plot等分析，确定樟叶槭叶绿体基因组密码子偏好性基本特征与其最佳密码子的构成，分析过程中主要使用Codon W 1.4.2、CUSP、R等软件。结果表明，共有28个密码子，且均以A或U结尾，说明樟叶槭叶绿体基因组密码子对A/U结尾偏好。密码子第1、2和3位上的GC平均含量分别为47.04%、39.56%与29.66%，GC平均含量为38.75%，ENC范围在 37.60～57.16，其中ENC小于45的只有11个，表明樟叶槭叶绿体基因组密码子存在较弱的偏性。PR2-plot绘图分析显示多数位点偏离中心，落于右下方位置；最优密码子确定为UGU、CAA、GUU等15个最优密码子。该结果为槭属植物叶绿体基因组进化与转化体系中载体构建研究提供参考依据。
Abstract:
 To determine the codon usage pattern of chloroplast genome in Acer cinnamomifolium,Codon W 1.4.2,cusp and R software were used to analyze 53 selected protein coding sequences,and codons were analyzed by neutral plotting,ENC-plot,PR2-plot and optimal codon.The results showed that there were 28 codons with RSCU>1,all ending in A/U,indicating that the synonymous codons in the chloroplast genome and A/U ending bias of A.cinnamomifolium.The average content of GC at the first,second and third positions of codon were 47.04%,39.56% and 29.66%,respectively,and the average content of all GC was 38.75%.The range of ENC (effective number of codon) value ranged from 37.60 to 57.16,and 42 genes ENC were greater than 45,indicating weak bias in A.cinnamomifolium chloroplast genome.PR2-plot analysis showed that the number of genes located in the lower right corner of PR2-plot ichnography was the largest.The optimal codons were determined as UGU,CAA,GUU and other 12 optimal codons.The results will take some bases for future studies on vector construction in chloroplast genome evolution and transformation system of Acer genus.

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备注/Memo

备注/Memo:
 收稿日期：2021-12-06修回日期：2022-04-06
基金项目：极小种群野生动植物资源拯救项目；四川省科技支撑项目（2020YJ470）。
第一作者：段祥光，博士。研究方向：植物功能性状和分子生态学。E-mail:m18238802921@163.com
*通信作者：马文宝，博士，副研究员。研究方向：珍稀濒危植物、高山景观植物种子生态学，繁殖生态学。E-mail:mawenbao_2021@163.com
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