Identification and Expression Analysis of SKP1 Gene Family in Grapevine （Vitis vinifera L.）

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

Abstract

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

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.

Figures/Tables 10

References 50

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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