[1]屈亚亚,辛静,冯发玉,等. 香花枇杷质体基因组序列密码子偏性分析[J].西北林学院学报,2021,36(4):138-144.[doi:10.3969/j.issn.1001-7461.2021.04.20]
　QU Ya-ya,XIN Jing,FENG Fa-yu,et al. Codon Usage Bais in Chloroplast Genome of Eriobotrya fragrans Champ.ex Benth.[J].JOURNAL OF NORTHWEST FORESTRY UNIVERSITY,2021,36(4):138-144.[doi:10.3969/j.issn.1001-7461.2021.04.20]
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 香花枇杷质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36卷
期数:
2021年第4期
页码:
138-144
栏目:
出版日期:
2021-07-31

文章信息/Info

Title:
 Codon Usage Bais in Chloroplast Genome of Eriobotrya fragrans Champ.ex Benth.
文章编号:
1001-7461(2021)04-0138-07
作者:
 屈亚亚1; 2; 辛静1; 2; 冯发玉1; 2; 董章宏1; 2; 瞿绍宏1; 2; 王海洋1; 2; 李斌3; 辛培尧1; 2*
 （1.西南林业大学 园林园艺学院 国家林业和草原局西南风景园林工程技术研究中心，云南 昆明 650224；2.西南林业大学 西南山地森林资源保育与利用教育部重点实验室，云南 昆明 650224；3.毕节市林业科学研究所，贵州 毕节 551700）
Author(s):
 QU Ya-ya1; 2; XIN Jing1; 2; FENG Fa-yu1; 2; DONG Zhang-hong1; 2; QU Shao-hong1; 2; WANG Hai-yang1; 2; LI Bin3; XIN Pei-yao1; 2*
 （1.Southwest Research Center for Engineering Technology of Landscape Architecture,State Forestry and Grassland Administration,College of Landscape Architecture and Horticulture Sciences,Southwest Forestry University,Kunming 650224,Yunnan,China)
关键词:
 ; 香花枇杷; 叶绿体基因组; 密码子偏性
Keywords:
Eriobotrya fragrans;  chloroplast genome;  codon usage bias
分类号:
S667.3
DOI:
10.3969/j.issn.1001-7461.2021.04.20
文献标志码:
A
摘要:
 选取香花枇杷质体基因组进行密码子使用偏好性的生物信息学分析，用于理解其密码子使用偏性的主要原因，为今后该属植物基因的进化、起源以及转化体系中载体构建等方面研究提供借鉴。利用Codon W 1.4.2、SPSS statistics 17.0、Excel 2016和cusp等软件对筛选出的37条基因编码序列密码子进行最优密码子分析、中性绘图分析、ENC-plot和PR2-plot绘图分析。结果表明，ENC平均值为47.02；GC3与GC1、GC2的相关性均不显著；GCall为39.08%，GC1（48.79%）>GC2（40.18 %）>GC3（28.44%）；RSCU>1的29个密码子中有28个以A或U结尾；PR2-plot绘图分析显示多数位点偏离中心，落于左下方位置；确定了UUU、UUG、CUU等15个最优密码子。香花枇杷叶绿体基因组中，同义密码子的使用偏性较弱（47.02）；密码子的第1、 2位碱基组成比较相似，但均不同于第3位；整体A、U含量大于C、G，末位碱基以A、U为主，且嘧啶的使用频率高于嘌呤；香花枇杷叶绿体基因组密码子的使用模式主要受到选择、突变的和其他因素的综合作用影响。
Abstract:
 Codon usage pattern of the chloroplast genome of Eriobotrya fragrans was analyzed to provide useful references for the further studies on the genetic evolution,origin and vector construction in the transformation system of the plants of Eriobotrya genus.The selected 37 coding DNA sequences were used to conduct the analyses of optimal codons,neutrality test,ENC-plot and PR2-plot by using Codon W 1.4.2 software,SPSS statistics 17.0 program,and online program CUSP.The average ENC was 47.02.The correlations between GC3&GC1,GC3&GC2were not significant.The GC1,GC2 and GC3 of codons in the plastome of E.fragrans was 48.79%,40.18%,and 28.44%,respectively.Among the 29 coding genes with the RSCU values over 1.0,28 genes ended with U or A.The PR2-plot showed that most of points fell in the lower left region.UUU,UUG,CUU and other 15 codons were determined as optimal codons.The codon usage bias of E.fragrans was relatively weak (47.02).The first and second base compositions of codons were similar but they were both different from that of the third position.The codons were rich in A/U and preferred to end with A/U.Pyridine was used more frequently than purine.The codon usage bias in the plastome of E.fragrans was formed under effects of mutation and selection pressure mainly,as well as other factors.

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备注/Memo

备注/Memo:
 收稿日期：2020-09-16修回日期：2020-12-02
作者简介：屈亚亚。研究方向：林木遗传育种。E-mail:838552880@qq.com
*通信作者：辛培尧，教授。研究方向：林木遗传育种。E-mail:xpytgyx@163.com
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