尖孢镰刀菌全基因组密码子偏好性及特征分析

doi:10.12190/j.issn.2096-1197.2022.04.02

北方农业学报 ›› 2022, Vol. 50 ›› Issue (4): 11-17.doi: 10.12190/j.issn.2096-1197.2022.04.02

• 分子生物学 · 生理生化 • 上一篇下一篇

尖孢镰刀菌全基因组密码子偏好性及特征分析

路景诗¹, 赵远征², 王东¹, 李晓杰¹, 彭静文², 张龙梅³, 张晓明¹

1.内蒙古农业大学,内蒙古呼和浩特 010018
2.内蒙古自治区农牧业科学院,内蒙古呼和浩特 010031
3.内蒙古自治区农牧业技术推广中心,内蒙古呼和浩特 010011

收稿日期:2022-06-15 出版日期:2022-08-20 发布日期:2022-09-30
通讯作者: 张晓明
作者简介:张晓明(1980—),男,讲师,博士,主要从事植物与微生物互作的研究工作。
路景诗(2001—),男,本科生,专业为植物与微生物互作。
基金资助:
国家自然科学基金专项项目(M2042002);内蒙古科技重大专项(zdzx2018049);内蒙古大学生创新创业训练计划项目(202010129016);内蒙古自治区自然科学基金项目(2021BS03008)

Analysis of genome-wide codon preference and characterization of Fusarium oxysporum

LU Jingshi¹, ZHAO Yuanzheng², WANG Dong¹, LI Xiaojie¹, PENG Jingwen², ZHANG Longmei³, ZHANG Xiaoming¹

1. Inner Mongolia Agricultural University,Hohhot 010018,China
2. Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences,Hohhot 010031,China
3. Inner Mongolia Agricultural and Animal Husbandry Technology Extension Center, Hohhot 010011,China

Received:2022-06-15 Online:2022-08-20 Published:2022-09-30
Contact: ZHANG Xiaoming

摘要/Abstract

摘要：

【目的】探究尖孢镰刀菌(Fusarium oxysporum)全基因组的密码子使用模式,分析影响其密码子组成和编码特性的因素。【方法】以F. oxysporum全基因组数据为试验材料,利用CodonW、R等软件分析密码子偏好性及其影响因素。【结果】共得到18 125条符合分析要求的序列;F. oxysporum的平均GC含量为51.46%,ENC值为24.31~61.00,且共有94.41%的ENC值大于45。亮氨酸和丙氨酸占比较高,分别为8.86%和8.29%;色氨酸和半胱氨酸占比较低,分别仅为1.61%和1.34%。F. oxysporum拥有33个高频密码子、19个最优密码子、密码子主要以G/C结尾;密码子基本参数相关性分析表明,GC1和GC2相关性极显著(P<0.01),GC3与ENC的相关性最强(P<0.01)。【结论】尖孢镰刀菌(Fusarium oxysporum)全基因组密码子偏好性主要受自然选择作用影响,同时GC3与ENC相关性最强;33个高频密码子和19个最优密码子主要以G/C结尾。

关键词: 尖孢镰刀菌, 密码子偏好性, 最优密码子, 有效密码子

Abstract:

【Objective】To explore the codon usage pattern of Fusarium oxysporum genome-wide and to assess the factors influencing the codon composition and coding characteristics.【Methods】Using software CodonW and R to analyze the codon preference and its influencing factors on genome-wide data from F. oxysporum.【Results】A total of 18 125 sequences was obtained. The average GC content of F. oxysporum was 51.46%. The ENC value ranged from 24.31 to 61.00,and 94.41% of the ENC values were more than 45. Leucine and Alanine were the major amino acids,and accounted for 8.86% and 8.29% respectively. While Tryptophan and Cysteine accounted for only 1.61% and 1.34% respectively. F. oxysporum had 33 high-frequency codons and 19 optimal codons,with the majority of the codons ending in G/C. The correlation study of basic codon parameters revealed that the correlation between GC1 and GC2 was extreme significant(P<0.01),while the correlation between GC3 and ENC was the strongest(P<0.01).【Conclusion】Natural selection is the primary factor influencing the codon preference of Fusarium oxysporum. The correlation between GC3 and ENC was the strongest. 33 high-frequency codons and 19 optimal codons primarily ending in G/C.

Key words: Fusarium oxysporum, Codon usage preference, Optimal codon, Effective codon

中图分类号:

Q939.11

路景诗, 赵远征, 王东, 李晓杰, 彭静文, 张龙梅, 张晓明. 尖孢镰刀菌全基因组密码子偏好性及特征分析[J]. 北方农业学报, 2022, 50(4): 11-17.

LU Jingshi, ZHAO Yuanzheng, WANG Dong, LI Xiaojie, PENG Jingwen, ZHANG Longmei, ZHANG Xiaoming. Analysis of genome-wide codon preference and characterization of Fusarium oxysporum[J]. Journal of Northern Agriculture, 2022, 50(4): 11-17.

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尖孢镰刀菌全基因组密码子偏好性及特征分析

Analysis of genome-wide codon preference and characterization of Fusarium oxysporum

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