甘蓝型油菜BnFAD2基因的生物信息学分析

doi:10.14088/j.cnki.issn0439-8114.2021.11.029

湖北农业科学 ›› 2021, Vol. 60 ›› Issue (11): 134-140.doi: 10.14088/j.cnki.issn0439-8114.2021.11.029

甘蓝型油菜BnFAD2基因的生物信息学分析

陈镇^1,2, 何晓莹¹, 王敬乔¹, 李根泽¹, 束正齐¹, 赵凯琴¹, 程小毛², 俎峰¹

1. 云南省农业科学院经济作物研究所,昆明 650225;
2.西南林业大学园林园艺学院/国家林业与草原局西南风景园林工程技术研究中心,昆明 650224

收稿日期:2020-09-10 出版日期:2021-06-10 发布日期:2021-07-15
通讯作者: 程小毛（1979-）,女,安徽安庆人,副教授,博士,主要从事植物分子育种研究,（电话）15198729165（电子信箱）30375713@qq.com;俎峰（1984-）,男,河南许昌人,副研究员,主要从事油菜分子育种研究,（电话）15398406665（电子信箱）zufeng1984@163.com。
作者简介:陈镇（1995-）,男,湖北孝感人,在读硕士研究生,研究方向为蔬菜分子标记辅助育种,（电话）15629866987（电子信箱）982509585@qq.com。
基金资助:
云南省农业基础研究联合专项（2018FG001-021）; 云南省教育厅科学研究基金项目（2020Y0406）

Bioinformatics analysis of BnFAD2 gene in Brassica napus L.

CHEN Zhen^1,2, HE Xiao-ying¹, WANG Jing-qiao¹, LI Gen-ze¹, SHU Zheng-qi¹, ZHAO Kai-qin¹, CHENG Xiao-mao², ZU Feng¹

1. Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650225,China;
2. College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University/Southwest Landscape Architecture Engineering Research Center of State Forestry and Grassland Administration, Kunming 650224,China

Received:2020-09-10 Online:2021-06-10 Published:2021-07-15

摘要/Abstract

摘要： 以拟南芥（Arabidopsis thaliana）AtFAD2为参考序列,通过BLAST进行同源序列比对,获得FAD2基因在甘蓝（Brassica oleracea）、白菜（Brassica rapa）和甘蓝型油菜（Brassica napus）基因组中的同源拷贝。运用生物信息学方法分析其氨基酸序列的组成、蛋白质基本理化性质、亚细胞定位、亲水性和疏水性、蛋白质二三级结构、保守结构域,并对FAD2基因编辑靶点进行预测及sgRNA设计。在白菜、甘蓝与甘蓝型油菜获得2条FAD2基因同源蛋白质序列;亚细胞定位显示这些AtFAD2同源蛋白质均位于内质网,肽链表现为疏水性、比较稳定;蛋白质序列二三级结构预测表明,主要以α-螺旋和无规则卷曲为组成成分;蛋白质序列保守结构域分析显示,FAD2具有高度的序列保守性,属于Membrane-FADS-like超家族,且含PLN02505保守结构域;系统进化树构建分析显示,甘蓝型油菜和白菜、甘蓝以及芥菜型油菜具有紧密的亲缘关系;CRISPR-Cas9基因编辑靶点分析发现,甘蓝型油菜FAD2基因中存在10段高度保守性序列可作为候选靶点,并设计出相应的sgRNA。

关键词: 甘蓝型油菜, FAD2, 生物信息学, sgRNA, 油酸

Abstract: The gene AtFAD2 was taken as reference sequence, homologous sequence comparison was conducted by BLAST to obtain the homologous copies of FAD2 gene in the genomes of Brassica oleracea, Brassica rapa and Brassica napus. Bioinformatics methods were used to analyze the components of the amino acid sequence, the basic physical and chemical properties of the protein, subcellular localization, hydrophilicity and hydrophobicity, the secondary and tertiary structure of the protein, and the conserved domain of the FAD2 gene editing targets and sgRNA design. Two FAD2 homologus protein sequence were obtained from B. rapa, B. deracea, B.napus. Both subcells were localized in the endoplasmic reticulum, and the peptide chain showed hydrophobness and stability. The predicted secondary and tertiary structure of the protein showed that it was mainly composed of -helix and irregular curl. The conserved structural domain of the protein showed that FAD2 gene was highly sequence conserved, belonging to the Membrane-FADs-like superfamily, and contained PLN02505 conserved structural domain. Phylogenetic tree analysis showed that Brassica napus L was closely related to B. oleracea, B. rapa and B. juncea. The CRISPR-Cas9 gene-editing target analysis revealed that there were 10 highly conserved target sites in the FAD2 gene of Brassica napus L., and the corresponding sgRNA was designed.

Key words: Brassica napus L., FAD2, bioinformatics, sgRNA, oleic acid

中图分类号:

S565.4
Q789

陈镇, 何晓莹, 王敬乔, 李根泽, 束正齐, 赵凯琴, 程小毛, 俎峰. 甘蓝型油菜BnFAD2基因的生物信息学分析[J]. 湖北农业科学, 2021, 60(11): 134-140.

CHEN Zhen, HE Xiao-ying, WANG Jing-qiao, LI Gen-ze, SHU Zheng-qi, ZHAO Kai-qin, CHENG Xiao-mao, ZU Feng. Bioinformatics analysis of BnFAD2 gene in Brassica napus L.[J]. HUBEI AGRICULTURAL SCIENCES, 2021, 60(11): 134-140.

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甘蓝型油菜BnFAD2基因的生物信息学分析

Bioinformatics analysis of BnFAD2 gene in Brassica napus L.

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