黄瓜SRS基因家族鉴定及胁迫响应表达分析

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

摘要/Abstract

摘要：

短节间基因家族[SHORT INTERNODES（SHI）-related sequence，SRS]是植物生长和发育重要的转录因子家族。对黄瓜SRS基因家族进行了全基因组筛选和功能特征分析，鉴定到9个SRS成员，不均匀地分布于7条染色体上。根据系统发生关系，CsSRS被分为3个亚族。基因结构和基序组成表明，同一亚族中的CsSRS成员具有类似的内含子/外显子和基序。序列分析发现CsSRS氨基酸N-末端具有高度保守的RING结构域，C-末端IGGH结构域在进化中有丢失现象。CsSRS的启动子区域存在多种与生长、发育和逆境应答相关的顺式作用元件。组织表达模式分析发现CsSRS表现出显著组织特异性。此外，转录组表达分析表明CsSRS对多种生物和非生物胁迫表现出不同的响应，表明它们在功能上发生了分化。其中，CsSRS6在大部分组织中都有表达，且在逆境胁迫下均发生差异表达。

关键词: 黄瓜, SRS家族, 系统进化, 基因表达, 胁迫响应

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

韩世文, 刘涛, 王丽萍, 李楠洋, 王素娜, 王星. 黄瓜SRS基因家族鉴定及胁迫响应表达分析[J]. 园艺学报, 2024, 51(10): 2281-2296.

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.

图/表 13

图1 黄瓜SRS家族基因在染色体上的分布

Fig. 1 Distribution of cucumber SRS gene family on chromosomes

表1 黄瓜SRS基因家族成员蛋白信息

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

图2 黄瓜CsSRS家族成员蛋白序列比对（黑色代表高度保守）

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

图3 黄瓜SRS家族进化分析（A）、保守序列（B）与基因结构（C）示意图

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

图4 黄瓜（Cs）、拟南芥（At）、番茄（Sl）、水稻（Os）和玉米（Zm）SRS家族成员系统发育树

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）

图5 黄瓜、水稻、拟南芥SRS家族基因的共线性关系

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

图6 黄瓜SRS基因启动子顺式作用元件热图颜色代表顺式作用元件数量，红色越深表示数量越多，蓝色越深表示数量越少，图中数字表示元件数。

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.

图7 黄瓜SRS家族基因在不同组织器官中的表达热图

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

图8 黄瓜SRS家族基因在高温胁迫下的表达热图 A：表格中的数据是原始的FPKM值。B：表格中的数据是原始的FPKM值的差异倍数。

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.

图9 黄瓜SRS家族基因在低温胁迫下的表达热图 A：表格中的数据是原始的FPKM值。B：表格中的数据是原始的FPKM值的差异倍数。

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.

图10 黄瓜SRS家族基因在盐和硅处理下的表达热图 A：表格中的数据是原始的FPKM值。B：表格中的数据是原始的FPKM值的差异倍数。

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.

图11 黄瓜SRS家族基因在霜霉病胁迫下的表达模式 A：表格中的数据是原始的FPKM值。B：表格中的数据是原始的FPKM值的差异倍数。

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.

图12 黄瓜SRS家族基因在南方根结线虫病胁迫下的表达模式 A：表格中的数据是原始的FPKM值。B：表格中的数据是原始的FPKM值的差异倍数。

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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