[1]李亚麒,黄家雄,娄予强,等. 小粒咖啡铁皮卡叶绿体基因组密码子偏好性分析[J].西北林学院学报,2023,38(2):92-99.[doi:10.3969/j.issn.1001-7461.2023.02.12]
　LI Ya-qi,HUANG Jia-xiong,LOU Yu-qiang,et al. Codon Usage Bias of the Chloroplast Genome in Coffea arabica ’Typica’[J].JOURNAL OF NORTHWEST FORESTRY UNIVERSITY,2023,38(2):92-99.[doi:10.3969/j.issn.1001-7461.2023.02.12]
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 小粒咖啡铁皮卡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38卷
期数:
2023年第2期
页码:
92-99
栏目:
出版日期:
2023-03-31

文章信息/Info

Title:
 Codon Usage Bias of the Chloroplast Genome in Coffea arabica ’Typica’
文章编号:
1001-7461(2023)02-0092-08
作者:
 李亚麒1; 黄家雄1; 娄予强1; 付兴飞1; 王健敏2; 李亚男1; 吕玉兰1; 李贵平1; 程金焕1*
 （1.云南省农业科学院 热带亚热带经济作物研究所，云南 保山 678000；2.云南省农村科技服务中心，云南 昆明 650021）
Author(s):
 LI Ya-qi1; HUANG Jia-xiong1; LOU Yu-qiang1; FU Xing-fei1; WANG Jian-min2; LI Ya-nan1; LV Yu-lan1; LI Gui-ping1; CHENG Jin-huan1*
 (1.Institute of Tropical and Subtropical Cash Crops,Yunnan Academy of Agricultural Sciences,Baoshan 678000,Yunnan,China;2.Yunnan Rural Science and Technology Service Center,Kunming 650021,Yunnan,China)
关键词:
 ; 小粒咖啡; 铁皮卡; 叶绿体基因组; 密码子偏好性; 最优密码子
Keywords:
Coffea arabica;  "Typica";  chloroplast genome;  codon bias;  optimal codon
分类号:
S571.2
DOI:
10.3969/j.issn.1001-7461.2023.02.12
文献标志码:
A
摘要:
 为了解铁皮卡叶绿体基因组密码子的使用特征及其成因，以筛选的52条蛋白编码序列为研究对象，利用CodonW和CUSP在线软件对其密码子使用特征进行系统分析。结果表明，基因组各位置的GC含量GC1、GC2、GC3分别为47.47%、39.52%、27.92%，30个高频密码子中，以U结尾占比53.33%，以A结尾占比43.33%，以G结尾占比3.33%，说明铁皮卡叶绿体基因偏好使用NNA 和NNU 型密码子，尤其偏好使用NNU型密码子。有效密码子数（ENC）、密码子适应指数（CAI）、最优密码子频率（Fop）分别为46.85、0.167、0.352，均揭示该基因组的密码子偏性较弱。中性绘图、ENC-plot、PR2-plot以及对应分析揭示密码子的偏好性受到选择及其他因素共同作用，最终确定了AUU、GUU和UCU等20个最优密码子。表明铁皮卡叶绿体基因组密码子的偏性较弱，偏好AU结尾的密码子。密码子的使用偏好性受到突变及选择等多种作用共同影响。
Abstract:
 To dissect the codon usage bias of the chloroplast genome codons and contributing factors,52 protein coding gene sequences from the chloroplast genome of Coffea arabica ’Typica’ were studied.CodonW and CUSP online software were used to analyze the characteristics of its codon usage.It was found out that the GC1,GC2 and GC3 contents were 47.47%,39.52% and 27.92%,respectively,among the 30 high-frequency codons,53.33% ended with U,43.33% ended with A,and 3.33% ended with G,indicating that the chloroplast genes of C.arabica ’Typica’ preferred to NNA and NNU codons,especially NNU codons.The effective codon number (ECN),codon adaptation index (CAI) and optimal codon frequency (Fop) were 46.85,0.167 and 0.352,respectively,suggesting that the codon bias of the genome was weak.The Neutral plot analysis,ENC-plot analysis,PR2-plot analysis and correspondence analysis showed that codon usage bias was influenced by selection and other factors.Finally,20 codons,including AUU,GUU and UCU,were identified as the optimal codons.In summary,the codon usage bias of C.arabica ’Typica’ is weak,and prefers to the AU ending codons.Multiple factors contribute to the codon usage bias,such as selection and mutation.

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备注/Memo

备注/Memo:
 收稿日期：2022-03-11修回日期：2022-09-20
基金项目：国家重点研发计划课题（2020YFD1001202-2）；云南省科技厅创新引导与科技型企业培养计划（202104BI090015）；国家咖啡标准化区域服务与推广平台（NBFW-17-2021）；云南省重点研发计划课题（2018ZG015）。
第一作者：李亚麒。研究方向：咖啡栽培与利用。E-mail:1640949082@qq.com
*通信作者：程金焕，副研究员。研究方向：咖啡加工。E-mail:jinhuancheng-2006@163.com
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