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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (6): 1715-1725.doi: 10.3724/SP.J.1006.2023.24142

• RESEARCH NOTES • Previous Articles     Next Articles

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 Online:2023-06-12 Published: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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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

Table 1

Primers used in this study"

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

Table 2

PHB gene family in sweet potato"

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

Fig. 1

Phylogenetic tree of PHB gene family proteins in sweet potato and Arabidopsis thaliana"

Fig. 2

Distribution of PHB gene family on chromosomes in sweet potato"

Fig. 3

Phylogenetic tree and gene structure of PHB gene family in sweet potato A: the phylogenetic tree of PHB family genes in sweet potato; B: IbPHB conservative motif; C: the distribution of conservative domains."

Fig. 4

Promoter prediction of PHB gene family in sweet potato"

Fig. 5

Tissue specific expression analysis of IbPHB gene family Different lowercase letters in the figure indicate significant differences between the data at the 0.05 probability level."

Fig. 6

Relative expression levels of IbPHB gene family in response to high salt stress Different lowercase letters in the figure indicate significant differences between the data at the 0.05 probability level."

Fig. 7

Relative expression levels of IbPHB gene family in response to drought stress Different lowercase letters in the figure indicate significant differences between the data at the 0.05 probability level."

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