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作物学报

作物学报 ›› 2023, Vol. 49 ›› Issue (6): 1715-1725.doi: 10.3724/SP.J.1006.2023.24142

• 研究简报 • 上一篇    下一篇

甘薯PHB基因家族的全基因组鉴定和表达分析

梅玉琴1,2,**(), 刘意1,**(), 王崇2,3, 雷剑2, 朱国鹏1,*(), 杨新笋2,*()   

  1. 1海南大学园艺学院/海南省热带园艺作物品质调控重点实验室, 海南海口 570228
    2湖北省农业科学院粮食作物研究所, 湖北武汉 430064
    3长江大学农学院, 湖北荆州 434025
  • 收稿日期:2022-06-16 接受日期:2022-10-11 出版日期:2023-06-12 网络出版日期:2022-10-21
  • 通讯作者: *朱国鹏, E-mail: guopengzhu@163.com;杨新笋, E-mail: yangxins013@163.com
  • 作者简介:梅玉琴, E-mail: 20095131210148@hainanu.edu.cn;
    刘意, E-mail: 15549421602@163.com第一联系人：**同等贡献
  • 基金资助:
    财政部和农业农村部国家现代农业产业技术体系建设专项(CARS-10-C13-2021);国家重点研发计划项目“双子叶杂粮抗性种质创制”(2019YFD1001303-4);湖北省农业科技创新中心湖北省农科院领军人才培养计划项目(L2018005);湖北省重点研发计划项目“中贝鄂薯系列新品种与新技术示范”(2020BHB024)

Genome-wide identification and expression analysis of PHB gene family in sweet potato

MEI Yu-Qin1,2,**(), LIU Yi1,**(), WANG Chong2,3, LEI Jian2, ZHU Guo-Peng1,*(), YANG Xin-Sun2,*()   

  1. 1Horticulture College, Hainan University/Key Laboratory for Quality Regulation of Tropical Horticultural Plants of Hainan Province, Haikou 570228, Hainan, China
    2Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, Hubei, China
    3College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China
  • Received:2022-06-16 Accepted:2022-10-11 Published:2023-06-12 Published online:2022-10-21
  • Contact: *E-mail: guopengzhu@163.com;E-mail: yangxins013@163.com
  • About author:First author contact:**Contributed equally to this work
  • Supported by:
    China Agriculture Research System of MOF and MARA(CARS-10-C13-2021);National Key Research and Development Program of China “Creation of Resistant Germplasm for Dicotyledonous Grains”(2019YFD1001303-4);Leading Talent Training Plan of Hubei Academy of Agricultural Sciences(L2018005);Hubei Province Key Research and Development Program Project “China and Benin Eshu Series New Varieties and New Technology Demonstration”(2020BHB024)

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摘要：

蛋白质抑制素(prohibitin, PHB)是在原核生物到真核生物中发现的含有SPFH结构域的蛋白质。植物PHB基因家族参与多种不同生物过程的重要功能, 包括生长发育以及对生物和非生物胁迫的响应。目前PHB蛋白在拟南芥、水稻、玉米、大豆、番茄和陆地棉等多种植物中被鉴定。但对甘薯中PHB家族的系统分析仍未确定。本研究鉴定出甘薯11个PHB基因, 且对这些保守的蛋白质基序和基因结构的分析显示它们在系统发育亚群中具有高度的保守性。此外, 启动子区域预测出与多种激素调节及胁迫相关的顺式作用元件, 同时研究发现IbPHB基因在植物不同部位及受到不同的非生物胁迫时的表达模式存在差异。本研究系统分析了甘薯中IbPHB基因的一般特性, 为甘薯及其他植物中PHB基因的功能特性研究提供了理论基础。

关键词: 甘薯, PHB基因家族, 系统进化, 生物信息学, 表达分析

Abstract:

The prohibitins (PHB) are SPFH domain-containing proteins found in the prokaryotes to eukaryotes. Plant PHB gene family is involved in many important functions in a variety of different biological processes, including growth and development and responses to biotic and abiotic stresses. At present, PHB proteins have been identified in Arabidopsis, rice, maize, soybean, tomato, upland cotton, and other plants. However, the systematic analysis of PHB family in sweet potato is still uncertain. In this study, 11 PHB genes in sweet potato were identified, and the analysis of these conserved protein motifs and gene structures showed that they were highly conserved in phylogenetic subgroups. In addition, the cis-acting elements related to various hormone regulation and stress were predicted in the promoter region and the relative expression patterns of IbPHB genes were different in different parts of plants and under different abiotic stresses. This study systematically analyzed the general characteristics of IbPHB gene in sweet potato, and provided a theoretical basis for the study of functional characteristics of PHB gene in sweet potato and other plants.

Key words: sweet potato, PHB gene family, phylogenetic evolution, bioinformatics, the relative expression level

表1

试验所用引物"

引物用途
Primer function		 引物名称
Primer name		 引物序列Primer sequence
正向引物序列
Forward sequence (5°-3°)		 反向引物序列
Reverse sequence (5°-3°)
qRT-PCR 扩增
The qRT-PCR
amplification		 IbPHB1 CACGTGTCTGCTTTGGTTCG TGCTGAGCAACCTGCTTTTG
IbPHB2 CTTTGACATTCGCACCAGGC GCACCCGGAGAGTGAGATTC
IbPHB3 GTGGAGAAATGGGGTCGGTT ACGTCCAGAGAGCAGATCCT
IbPHB4 CCACCGCTTCTTCTCCCATT AGTCATGCCTGGAGCTAGGA
IbPHB5 GTCTTCGACGTTTCTCCGGT TGGCGTACTTCAAGAGGCTG
IbPHB6 TCTGGCGAAGAAGAAGGCTG CTCTGCATCTCTAAGCGCCA
IbPHB7 TGCTGCTGCAAGACTTAGGG TTTGATTCCGCTTCCCCCTC
IbPHB8 AGTATAACGCCAGCCAGCTC GTTGAAGTTAGCCGCCCTCT
IbPHB9 GGTGACTCCTTCGCTGTCAA CCTCCTCTCCAGTAGACCCC
IbPHB10 GGCAAGCTGCGAATGAGAAG CGCGAGGTACTTGGACTCTG
IbPHB11 ATGAAGGAAATTGGCGCTGC GATGGTCAGACTGGGAAGCC
内参基因
Internal reference genes		 β-Actin AGCAGCATGAAGATTAAGGTTGTAGCAC TGGAAAATTAGAAGCACTTCCTGTGAAC

表2

甘薯PHB基因家族"

基因名称 Gene name 基因编号Gene ID 染色体定位
Chromosome
location		 氨基酸
长度
Amino acid length		 等电点Isoelectric
point		 相对分子量Molecular
weight (kD)		 不稳定指数Instability index 脂溶系数 Aliphatic index 亲水性
平均值
Grand average of
hydropathicity		 亚细胞定位
Subcellular
localization
IbPHB1 g1330.t1 LG1(+): 8004568-8006394 277 6.55 30,473.85 40.46 98.59 -0.072 线粒体Mitochondrion
IbPHB2 g1344.t1 LG1 (-): 8093622-8097050 276 8.77 30,402.86 45.33 98.95 -0.106 线粒体Mitochondrion
IbPHB3 g1611.t1 LG1 (+): 10011048-10014530 314 5.38 34,754.86 30.67 91.59 -0.129 线粒体Mitochondrion
基因名称 Gene name 基因编号Gene ID 染色体定位
Chromosome
location		 氨基酸
长度
Amino acid length		 等电点Isoelectric
point		 相对分子量Molecular
weight (kD)		 不稳定指数Instability index 脂溶系数 Aliphatic index 亲水性
平均值
Grand average of
hydropathicity		 亚细胞定位
Subcellular
localization
IbPHB4 g20708.t1 LG5 (+): 29636330-29640330 400 8.89 43,335.23 46.92 90.35 -0.314 线粒体Mitochondrion
细胞核Nucleus
IbPHB5 g22098.t1 LG6 (-): 9204364-9206354 474 5.57 52,238.60 26.20 89.01 -0.343 细胞核Nucleus
IbPHB6 g22144.t1 LG6 (+): 9498264-9500186 446 5.40 49,012.72 27.04 86.95 -0.388 细胞核Nucleus
IbPHB7 g30111.t1 LG7 (+): 34852091-34854904 286 5.30 31,314.79 37.48 93.11 -0.115 线粒体Mitochondrion
IbPHB8 g30789.t1 LG8 (+): 2906392-2910014 283 9.23 31,632.31 36.05 101.38 -0.113 线粒体Mitochondrion
IbPHB9 g47367.t1 LG12 (+): 3383794-3389526 313 6.57 35,302.44 38.84 82.62 -0.401 细胞质Cytoplasm
线粒体Mitochondrion
细胞核Nucleus
IbPHB10 g53565.t1 LG13 (-): 17737704-17740759 287 6.26 31,728.35 23.91 94.81 -0.197 线粒体Mitochondrion
IbPHB11 g59949.t1 LG15 (+): 555231-558804 277 5.84 30,569.89 26.37 93.65 -0.200 线粒体Mitochondrion

图1

甘薯和拟南芥的PHB基因家族蛋白系统发育树"

图2

甘薯PHB基因家族在染色体上的分布"

图3

甘薯PHB基因家族进化树与基因结构 A: 甘薯PHB家族基因系统进化树; B: IbPHB保守基序; C: 保守结构域分布。"

图4

甘薯PHB基因家族启动子预测"

图5

IbPHB基因家族的组织特异性表达分析 图中标以不同字母表示数据间在0.05概率水平差异显著。"

图6

IbPHB基因家族响应高盐胁迫表达分析 图中标以不同字母表示数据间在0.05概率水平差异显著。"

图7

IbPHB基因家族响应干旱胁迫表达分析 图中标以不同字母表示数据间在0.05概率水平差异显著。"

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