葡萄SKP1基因家族鉴定与表达分析

doi:10.13560/j.cnki.biotech.bull.1985.2025-0210

摘要/Abstract

摘要：

目的研究葡萄（Vitis vinifera）S期激酶相关蛋白1（S-phase kinase-associated-protein 1, SKP1）基因家族（VvSKP1）特征和表达分析，为后续深入研究VvSKP1基因家族的生物学功能提供理论依据。方法基于葡萄基因组数据，利用生物信息学方法对SKP1基因家族成员进行筛选鉴定，对其编码蛋白质的特征、系统进化关系、基因结构、染色体定位、顺式作用元件以及共线性关系等进行分析，并利用实时荧光定量PCR（RT-qPCR）分析其在灰霉菌和霜霉菌侵染下的表达模式。结果从葡萄基因组内共鉴定到11个SKP1家族基因（VvSKP1-1‒VvSKP1-11），分布于7条染色体和1条未知染色体上，编码119个（VvSKP1-3）‒438（VvSKP1-8）个氨基酸。系统发育分析显示，SKP1家族蛋白可分为3个亚家族，葡萄的11个SKP1蛋白只分布在第I和第Ⅱ亚家族，第III亚家族全是小麦SKP1基因家族成员。同亚家族的VvSKP1成员在基因结构和保守基序上表现出一定的相似性。基因的启动子顺式作用元件主要与光响应、激素响应和胁迫应答有关。共线性分析发现VvSKP1有8对同源基因。选择压力分析表明，VvSKP1基因处于纯化选择。RT-qPCR分析表明，分别有11和10个VvSKP1基因积极响应灰霉菌和霜霉菌的侵染。结论从葡萄基因组中鉴定出11个VvSKP1s基因家族成员，该家族成员在灰霉病和霜霉病胁迫下的表达模式存在差异，表明葡萄SKP1基因家族可能参与葡萄灰霉病和霜霉病胁迫响应过程。

关键词: 葡萄, VvSKP1基因家族, 生物信息学分析, 灰霉菌, 霜霉菌, 生物胁迫, 表达分析

Abstract:

Objective The characteristics and expression analysis of the S-phase kinase-associated protein 1 (SKP1) gene family (VvSKP1) in Vitis vinifera were studied, providing a theoretical basis for further research on the biological function of the VvSKP1 gene family. Method Based on the grape genome data, the SKP1 gene family members were screened and identified using bioinformatics methods. The characteristics of the encoded proteins, phylogenetic relationships, gene structure, chromosome localization, cis-acting elements, and collinearity were analyzed. The expression patterns of the SKP1 gene family under Botrytis cinerea and Peronospora variabilis infections were analyzed using real-time quantitative PCR (RT-qPCR). Result A total of 11 SKP1 family genes (VvSKP1-1 to VvSKP1-11) were identified from the grape genome, distributed on 7 chromosomes and 1 unknown chromosome, encoding 119 (VvSKP1-3) to 438 (VvSKP1-8) amino acids. Phylogenetic analysis revealed that the VvSKP1 family proteins could be classified into three subfamilies. The 11 SKP1 proteins of grape were found only in the first and second subfamilies, while the third subfamily consisted of all members of the wheat SKP1 gene family. VvSKP1 members of the same group or subfamily showed some similarity in gene structure and conserved motifs. The cis-acting elements in the gene promoter were mainly associated with light response, hormone response, and stress response. Synteny analysis showed that VvSKP1 had 8 pairs of homologous genes. Selection pressure analysis showed that the VvSKP1 gene was under purifying selection. The RT-qPCR analysis showed that 11 and 10 VvSKP1 genes responded positively to B. cinerea and P. variabilis infection, respectively. Conclusion Eleven members of the VvSKP1 gene family were identified from the grape genome. The expression patterns of the family members under the stress of B. cinerea and P. variabilis were different, indicating that the grape SKP1 gene family may be involved in the stress response processes of B. cinerea and P. variabilis.

Key words: grapevine, VvSKP1 gene family, bioinformatics analysis, Botrytis cinerea, Peronospora variabilis, biotic stress, expression analysis

李珊, 马登辉, 马红义, 姚文孔, 尹晓. 葡萄SKP1基因家族鉴定与表达分析[J]. 生物技术通报, 2025, 41(9): 147-158.

LI Shan, MA Deng-hui, MA Hong-yi, YAO Wen-kong, YIN Xiao. Identification and Expression Analysis of SKP1 Gene Family in Grapevine （Vitis vinifera L.）[J]. Biotechnology Bulletin, 2025, 41(9): 147-158.

图/表 10

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基因 Gene	上游引物 Forward primer （5′‒3′）	下游引物 Reverse primer （5′‒3′）
VvSKP1-1	TGCTCTCCAGTCCAGAACCATCC	AATCGGTGTTGAGATCAATCAAGTGTTTC
VvSKP1-2	TGATGATCCACGGATTCGGCTATTG	ACGCTCCTCTTCAACCTCAACATTC
VvSKP1-3	ACAATCCTGGATATTCTACGAGCTTCTG	ACCAAATAAATCTCTCACCTCTTCTACCG
VvSKP1-4	GAAGGAGGTGGATGAGATGAAGAAGTG	AATCAACCCTGCTATGCTCAAATAATTGG
VvSKP1-5	AGCAAACTATCTGAACATCAAGAGTCTCC	CCGCCGCACCTCCTCCTC
VvSKP1-6	GGTGAATGGTAGAACCCTGGCTAAAG	CACTTCTTCATCTCATCCACCTCCTTC
VvSKP1-7	CAGCGGTATCCTTGCGATGGTG	CATGATGAGGTGGAACAGAGTAGCC
VvSKP1-8	GGGCTGGGCTGCTGATTTCTTC	TTGATATGTAGATAGTCTGCTGCCTTGATG
VvSKP1-9	ATCAAGTAATAGGACGCTCGAACAAGG	TGTCAGCAGCAGATGTCAACTCAC
VvSKP1-10	CCGATTCTTGGCGATGGTGATAGAG	ATGATGAGATGGTAGAGAAGTGATTGGTC
VvSKP1-11	GGTTGATTGATTTGACATGCGGGAAG	CCTTATCTCAGCCTCCTCCTCTACG
Actin	AACCCCAAGGCCAACAGAGAAAA	CACCATCACCAGAATCCAGCACA

基因 Gene	上游引物 Forward primer （5′‒3′）	下游引物 Reverse primer （5′‒3′）
VvSKP1-1	TGCTCTCCAGTCCAGAACCATCC	AATCGGTGTTGAGATCAATCAAGTGTTTC
VvSKP1-2	TGATGATCCACGGATTCGGCTATTG	ACGCTCCTCTTCAACCTCAACATTC
VvSKP1-3	ACAATCCTGGATATTCTACGAGCTTCTG	ACCAAATAAATCTCTCACCTCTTCTACCG
VvSKP1-4	GAAGGAGGTGGATGAGATGAAGAAGTG	AATCAACCCTGCTATGCTCAAATAATTGG
VvSKP1-5	AGCAAACTATCTGAACATCAAGAGTCTCC	CCGCCGCACCTCCTCCTC
VvSKP1-6	GGTGAATGGTAGAACCCTGGCTAAAG	CACTTCTTCATCTCATCCACCTCCTTC
VvSKP1-7	CAGCGGTATCCTTGCGATGGTG	CATGATGAGGTGGAACAGAGTAGCC
VvSKP1-8	GGGCTGGGCTGCTGATTTCTTC	TTGATATGTAGATAGTCTGCTGCCTTGATG
VvSKP1-9	ATCAAGTAATAGGACGCTCGAACAAGG	TGTCAGCAGCAGATGTCAACTCAC
VvSKP1-10	CCGATTCTTGGCGATGGTGATAGAG	ATGATGAGATGGTAGAGAAGTGATTGGTC
VvSKP1-11	GGTTGATTGATTTGACATGCGGGAAG	CCTTATCTCAGCCTCCTCCTCTACG
Actin	AACCCCAAGGCCAACAGAGAAAA	CACCATCACCAGAATCCAGCACA

蛋白 Protein	氨基酸数目 Amino acid number	CDS长度Length of CDS （bp）	分子质量 Molecular weight （Da）	等电点 Isoelectric point	不稳定指数Instability index	脂肪系数Aliphatic index	总平均亲水性GRAVY	亚细胞定位预测Subcellular localization	跨膜结构	信号肽 Signal peptide	结构域 Domain
VvSKP1-1	151	456	17 523.08	4.66	36.05	95.56	-0.227	细胞核 Nucleus	无	无	Skp1、Skp1_POZ
VvSKP1-2	372	1 119	42 659.31	5.77	55.66	76.8	-0.833	细胞核 Nucleus	无	无	Skp1
VvSKP1-3	119	360	13 436.95	4.15	36.44	90.08	-0.569	叶绿体 Chloroplast	无	无	Skp1
VvSKP1-4	152	459	17 258.86	4.77	29.56	87.24	-0.325	细胞质 Cytoplasm	无	无	Skp1、Skp1_POZ
VvSKP1-5	156	471	17 694.94	4.60	48.33	83.78	-0.529	细胞核 Nucleus	无	无	Skp1、Skp1_POZ
VvSKP1-6	152	459	17 286.83	4.77	31.67	85.99	-0.349	细胞质 Cytoplasm	无	无	Skp1、Skp1_POZ
VvSKP1-7	141	426	15 668.21	5.26	39.89	107.87	0.149	细胞质 Cytoplasm	无	无	Skp1_POZ
VvSKP1-8	438	1 317	49 885.82	5.67	38.62	99.77	-0.209	细胞质 Cytoplasm	无	无	Skp1、Skp1_POZ
VvSKP1-9	351	1 056	40 552.66	5.25	51.36	77.75	-0.874	细胞核 Nucleus	无	无	Skp1、Skp1_POZ
VvSKP1-10	162	489	18 903.61	4.77	58.12	93.33	-0.359	细胞质 Cytoplasm	无	无	Skp1、Skp1_POZ
VvSKP1-11	157	474	17 522.99	4.75	29.13	91.91	-0.259	细胞质 Cytoplasm	无	无	Skp1、Skp1_POZ

蛋白 Protein	氨基酸数目 Amino acid number	CDS长度Length of CDS （bp）	分子质量 Molecular weight （Da）	等电点 Isoelectric point	不稳定指数Instability index	脂肪系数Aliphatic index	总平均亲水性GRAVY	亚细胞定位预测Subcellular localization	跨膜结构	信号肽 Signal peptide	结构域 Domain
VvSKP1-1	151	456	17 523.08	4.66	36.05	95.56	-0.227	细胞核 Nucleus	无	无	Skp1、Skp1_POZ
VvSKP1-2	372	1 119	42 659.31	5.77	55.66	76.8	-0.833	细胞核 Nucleus	无	无	Skp1
VvSKP1-3	119	360	13 436.95	4.15	36.44	90.08	-0.569	叶绿体 Chloroplast	无	无	Skp1
VvSKP1-4	152	459	17 258.86	4.77	29.56	87.24	-0.325	细胞质 Cytoplasm	无	无	Skp1、Skp1_POZ
VvSKP1-5	156	471	17 694.94	4.60	48.33	83.78	-0.529	细胞核 Nucleus	无	无	Skp1、Skp1_POZ
VvSKP1-6	152	459	17 286.83	4.77	31.67	85.99	-0.349	细胞质 Cytoplasm	无	无	Skp1、Skp1_POZ
VvSKP1-7	141	426	15 668.21	5.26	39.89	107.87	0.149	细胞质 Cytoplasm	无	无	Skp1_POZ
VvSKP1-8	438	1 317	49 885.82	5.67	38.62	99.77	-0.209	细胞质 Cytoplasm	无	无	Skp1、Skp1_POZ
VvSKP1-9	351	1 056	40 552.66	5.25	51.36	77.75	-0.874	细胞核 Nucleus	无	无	Skp1、Skp1_POZ
VvSKP1-10	162	489	18 903.61	4.77	58.12	93.33	-0.359	细胞质 Cytoplasm	无	无	Skp1、Skp1_POZ
VvSKP1-11	157	474	17 522.99	4.75	29.13	91.91	-0.259	细胞质 Cytoplasm	无	无	Skp1、Skp1_POZ

共线性序列1 Collinearity sequence 1	共线性序列2 Collinearity sequence 2	Ka	Ks	Ka/Ks	共线性序列1 Collinearity sequence 1	共线性序列2 Collinearity sequence 2	Ka	Ks	Ka/Ks
VvSKP1-1	VvSKP1-10	0.484 186	2.676 18	0.180 925	VvSKP1-11	VvSKP1-4	0.318 353	0.978 672	0.325 291
VvSKP1-1	VvSKP1-11	0.439 432	2.748 94	0.159 855	VvSKP1-11	VvSKP1-5	0.394 356	3.214 360	0.122 685
VvSKP1-1	VvSKP1-3	0.744 929	1.804 00	0.412 931	VvSKP1-11	VvSKP1-6	0.312 299	0.961 286	0.324 876
VvSKP1-1	VvSKP1-4	0.374 420	3.230 87	0.115 888	VvSKP1-11	VvSKP1-7	0.559 368	2.658 880	0.210 377
VvSKP1-1	VvSKP1-5	0.401 063	3.083 55	0.130 065	VvSKP1-3	VvSKP1-4	0.657 090	2.075 610	0.316 577
VvSKP1-1	VvSKP1-6	0.378 107	3.186 02	0.118 677	VvSKP1-3	VvSKP1-5	0.526 860	2.452 040	0.214 866
VvSKP1-1	VvSKP1-7	0.551 033	2.400 07	0.229 591	VvSKP1-3	VvSKP1-6	0.674 153	2.036 490	0.331 038
VvSKP1-10	VvSKP1-11	0.473 489	2.443 63	0.193 765	VvSKP1-3	VvSKP1-7	0.810 727	1.581 060	0.512 774
VvSKP1-10	VvSKP1-3	0.639 464	2.206 82	0.289 767	VvSKP1-4	VvSKP1-5	0.364 465	3.387 940	0.107 577
VvSKP1-10	VvSKP1-4	0.402 901	2.944 32	0.136 840	VvSKP1-4	VvSKP1-6	0.010 264 2	0.014 291 7	0.718 192
VvSKP1-10	VvSKP1-5	0.384 626	3.164 50	0.121 544	VvSKP1-4	VvSKP1-7	0.511 442	2.655 830	0.192 573
VvSKP1-10	VvSKP1-6	0.403 211	2.906 73	0.138 717	VvSKP1-5	VvSKP1-6	0.380 355	3.273 070	0.116 207
VvSKP1-10	VvSKP1-7	0.545 177	2.499 55	0.218 110	VvSKP1-5	VvSKP1-7	0.273 146	3.618 320	0.075 489 9
VvSKP1-11	VvSKP1-3	0.718 013	1.848 36	0.388 460	VvSKP1-6	VvSKP1-7	0.516 509	2.610 210	0.197 880