[1]雷佳欣,张丽娟,高丹丹,等. 文冠果基因组密码子偏好性分析[J].西北林学院学报,2023,38(4):104-110.[doi:10.3969/j.issn.1001-7461.2023.04.13]
　LEI Jia-xin,ZHANG Li-juan,GAO Dan-dan,et al. Codon Usage Bias of Xanthoceras sorbifolium Genome[J].JOURNAL OF NORTHWEST FORESTRY UNIVERSITY,2023,38(4):104-110.[doi:10.3969/j.issn.1001-7461.2023.04.13]
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 文冠果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4期
页码:
104-110
栏目:
出版日期:
2023-07-31

文章信息/Info

Title:
 Codon Usage Bias of Xanthoceras sorbifolium Genome
文章编号:
1001-7461(2023)04-0104-07
作者:
 雷佳欣; 张丽娟; 高丹丹; 田晓静; 刘珊珊*
 （西北民族大学 生命科学与工程学院，甘肃 兰州 730030）
Author(s):
 LEI Jia-xin; ZHANG Li-juan; GAO Dan-dan; TIAN Xiao-jing; LIU Shan-shan*
 (College of Life Sciences and Engineering,Northwest Minzu University,Lanzhou 730030,Gansu,China)
关键词:
 ; 文冠果; 基因组; 密码子偏好性; 最优密码子
Keywords:
Xanthoceras sorbifolium;  genome;  codon usage bias;  optimal codons
分类号:
S759.33
DOI:
10.3969/j.issn.1001-7461.2023.04.13
文献标志码:
A
摘要:
 为解析文冠果基因组密码子的偏好性使用模式，提高基因异源表达效率，利用CodonW1.4.4和Python程序对文冠果基因组21,294条编码序列的密码子进行中性绘图、ENC-plot、PR2-plot和对应性分析。结果表明，文冠果基因组密码子不同位置上的GC含量表现为GC1（50.13%）>GC3（40.22%）>GC2（42.86%），RSCU>1的29个密码子中以A或U结尾的有25个，通过RSCU确定了22个最优密码子，全部以A/U结尾，说明文冠果基因组密码子末位碱基较偏好使用A/U；文冠果基因组密码子使用偏好性主要受到自然选择和突变压力因素的影响。通过比较发现文冠果密码子偏好性与拟南芥、小麦、烟草、杨树、小立碗藓、大肠杆菌及酿酒酵母等物种存在不同程度的差异，其中与拟南芥和烟草差异最小。研究结果不仅可为文冠果基因组学的研究提供理论基础，还为实现文冠果的异源基因表达提供了指导。
Abstract:
 To explore the pattern of codon usage bias in Xanthoceras sorbifolium genome and to improve heterologous expression efficiency of the genes,we adopted CodonW1.4.4 and Python to conduct neutral plot,ENC-plot,PR2-plot,and correspondence analysis for codons of 21 294 coding sequences in X.sorbifolium genome.The results showed that the GC content at different positions of the codons in the X.sorbifolium genome was GC1(50.13%)>GC3(40.22%)>GC2(42.86%).Among the 30 codons with RSCU>1,25 ended with A or U,and 22 optimal codons were determined by RSCU,all of which ended with A/U,indicating that the codon terminal bases of X.sorbifolium genome preferred to A/U.The codon usage bias of X.sorbifolium genome was mainly affected by natural selection and mutation pressure.The codon usage bias of X.sorbifolium genome had differences in various degree with Arabidopsis thaliana,Triticum aestivum,Nicotiana tabacum,Populus trichocarpa,Escherichia coli,and Saccharomyces cerevisiae,the differences with A.thaliana and N.tabacum were the smallest.Our results not only lay a theoretical basis for the follow-up research on X.sorbifolium genome,but also provide guidance for the realization of heterologous gene expression in X.sorbifolium.

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备注/Memo

备注/Memo:
 收稿日期：2022-10-09 修回日期：2022-11-23
基金项目：西北民族大学引进人才项目（xbmuyjrc202222,xbmuyjrc202223）；中央高校基本科研业务费项目（31920210055）。
第一作者：雷佳欣。研究方向:油料作物遗传育种。E-mail:1979053584@qq.com
*通信作者：刘珊珊，博士，讲师。研究方向：遗传育种与分子生物学。E-mail:liushsh@xbmu.edu.cn
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