Genome-Wide Identification and Stress-Responsive Expression Analysis of the Cucumber SRS Gene Family

doi:10.16420/j.issn.0513-353x.2023-0569

Acta Horticulturae Sinica ›› 2024, Vol. 51 ›› Issue (10): 2281-2296.doi: 10.16420/j.issn.0513-353x.2023-0569

• Genetic & Breeding·Germplasm Resources·Molecular Biology • Previous Articles Next Articles

Genome-Wide Identification and Stress-Responsive Expression Analysis of the Cucumber SRS Gene Family

HAN Shiwen¹, LIU Tao¹, WANG Liping¹^,², LI Nanyang¹^,², WANG Suna¹^,², WANG Xing¹^,²^,³^,^*()

¹ Department of Horticulture，Hebei University of Engineering，Handan，Hebei 056038，China
² Hebei Engineering Research Center for Breeding of Solanaceous Vegetable Seedlings，Handan，Hebei 056038，China
³ Handan Vegetable Improvement and Breeding Technology Innovation Center，Handan，Hebei 056038，China

Received:2023-10-31 Revised:2024-07-22 Online:2024-10-25 Published:2024-10-21
Contact: WANG Xing

Abstract

Abstract:

The SHORT INTERNODES（SHI）-related sequence（SRS）gene family is a crucial group of transcription factors involved in plant growth and development. A genome-wide screening and functional analysis of the SRS gene family in cucumber were conducted. A total of nine members of CsSRS gene family were identified，which unevenly distributed across seven chromosomes in the cucumber genome. Based on phylogenetic relationships，the CsSRS genes were classified into three subfamilies. Gene structure and motif composition analysis revealed that members of the same subfamily contained similar intron/exon patterns and motifs. Sequence analysis indicated that the N-terminal of CsSRS possessed a highly conserved RING domain，while the IGGH domain of C-terminal exhibited signs of loss during evolution. Further analysis of the promoter regions of CsSRS genes uncovered various cis-acting elements related to growth，development，and stress responses. Tissue expression pattern analysis demonstrated significant tissue-specific expression of CsSRS genes. Additionally，transcriptomic expression analysis revealed that CsSRS genes exhibited diverse responses to various biotic and abiotic stresses，indicating functional divergence. Among them，the cucumber CsSRS6 showed high expression in most tissues and displayed differential expression under stress conditions.

Key words: cucumber, SRS gene family, systematic evolution, gene expression, stress responses

HAN Shiwen, LIU Tao, WANG Liping, LI Nanyang, WANG Suna, WANG Xing. Genome-Wide Identification and Stress-Responsive Expression Analysis of the Cucumber SRS Gene Family[J]. Acta Horticulturae Sinica, 2024, 51(10): 2281-2296.

Figures/Tables 13

Fig. 1 Distribution of cucumber SRS gene family on chromosomes

Table 1 The information of SRS proteins in cucumber

基因名称 Gene name	基因ID Gene ID	CDS碱基数/bp CDS size	氨基酸数量/aa Number of amino acids	分子量/kD Molecular weight	等电点 pI
CsSRS1 CsSRS2 CsSRS3 CsSRS4 CsSRS5 CsSRS6 CsSRS7 CsSRS8 CsSRS9	CsaV3_1G043360.1 CsaV3_2G029220.1 CsaV3_3G002100.1 CsaV3_3G045570.1 CsaV3_4G005360.1 CsaV3_5G036780.1 CsaV3_6G039030.1 CsaV3_6G046800.1 CsaV3_7G006060.1	939 646 1 186 1 006 805 927 1 116 1 012 969	307 211 388 329 263 303 365 331 317	31.147 21.978 43.201 37.237 28.683 32.074 37.662 35.897 35.222	8.90 6.87 8.93 9.00 6.24 8.89 7.15 7.00 7.13
基因名称 Gene name	不稳定系数 Instability index	脂肪族氨基酸指数 Aliphatic index	平均亲水性 Grand average of hydropathicity	亚细胞定位 Prediction of subcellular location
CsSRS1 CsSRS2 CsSRS3 CsSRS4 CsSRS5 CsSRS6 CsSRS7 CsSRS8 CsSRS9	41.44 44.57 49.09 48.97 61.27 41.15 37.75 54.07 53.15	58.18 57.63 67.16 60.09 45.59 62.21 61.21 50.45 60.88	1.460 -0.225 -0.865 -0.806 -0.751 -0.493 -0.417 -0.769 -0.736	核内Nuclear 核内、核外Nuclear，extracellular 核内Nuclear 核内Nuclear 核内Nuclear 核内Nuclear 核外、核内Extracellular，nuclear 核内Nuclear 核内Nuclear

Fig. 2 Sequence alignment of CsSRS proteins（black represents high conservatism）

Fig. 3 Evolutionary analysis（A），conserved sequence of SRS proteins（B）and exon-intron structures of SRS genes（C）in cucumber

Fig. 4 Phylogenetic tree of SRS family members in Cucumis sativus（Cs），Arabidopsis thaliana（At），Solanum lycopersicum（Sl），Oryza sativa（Os）and Zea mays（Zm）

Fig. 5 Syntenic analysis of SRS genes among cucumber，rice and Arabidopsis thaliana

Fig. 6 The heatmap of various cis-elements in the promoters of each cucumber SRS gene Colors represent the quantity of cis elements，with deeper red indicating higher quantities and deeper blue indicating lower quantities. The numbers in the image represent the counts of cis-elements.

Fig. 7 The expression heatmap of SRS gene family in different tissues of cucumber

Fig. 8 Expression heatmap of cucumber SRS family genes under high-temperature stress A：The data in the table represents the raw FPKM values；B：The data in the table represents the fold change of raw FPKM values.

Fig. 9 Expression heatmap of cucumber SRS family genes under low-temperature stress A：The data in the table represents the raw FPKM values；B：The data in the table represents the fold change of raw FPKM values.

Fig. 10 Expression heatmap of cucumber SRS family genes under salt and silicon stress treatments A：The data in the table represents the raw FPKM values；B：The data in the table represents the fold change of raw FPKM values.

Fig. 11 Expression patterns of cucumber SRS family genes under downy mildew stress treatment A：The data in the table represents the raw FPKM values；B：The data in the table represents the multiples of the raw FPKM values.

Fig. 12 Expression patterns of cucumber SRS family genes under southern root-knot nematode stress treatment A：The data in the table represents the raw FPKM values；B：The data in the table represents the multiples of the raw FPKM values.

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Genome-Wide Identification and Stress-Responsive Expression Analysis of the Cucumber SRS Gene Family

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