Identification and Expression Analysis of the GRAM Gene Family in Potato

doi:10.13560/j.cnki.biotech.bull.1985.2024-0804

Abstract

Abstract:

Objective GRAM (Glucosyltransferases, Rab-like GTPase activators and Myotubularins) is a domain commonly found in animal and plant proteins and plays an important role in plant growth and development and response to stress. The GRAM gene family members were identified in the whole genome of potato, the expression pattern of potato GRAM family genes under salt stress was analyzed, and the role of GRAM family in potato salt stress was explored. Method Bioinformatics methods were used to identify the GRAM family members in potato (Solanum tuberosum L.), and analyze the physicochemical properties, chromosome localization, subcellular localization, gene structure, motif and collinearity of the protein. The expression patterns of the family members under salt stress were studied by transcriptome sequencing and real-time quantitative PCR (RT-qPCR). Result A total of 26 GRAM family genes were identified in potato, which were unevenly distributed on 7 chromosomes. Physicochemical properties analysis showed that all StGRAM proteins were hydrophilic proteins and most of them were alkaline proteins. Subcellular localization predicted that most of the StGRAM proteins were present in chloroplasts and nuclei. According to the phylogenetic analysis, the StGRAM family was divided into three subfamilies, and the members of the same subfamily had similar gene structure and motif distribution. Through the intra-species collinearity analysis of potato, it was found that StGRAM had only one pair of collinearity genes, and the inter-species collinearity showed that StGRAM had 5 pairs and 3 pairs of homologous genes in rice and Arabidopsis thaliana, respectively. A large number of hormone response elements and stress response elements were found in the promoter region of StGRAM gene. Transcriptome sequencing analysis and RT-qPCR analysis showed that StGRAM gene was induced by salt stress, which may be involved in the response of potato to salt stress. StGRAM25 gene may have different response patterns to neutral salt and alkaline salt. Conclusion The StGRAM gene family plays an important role in potato salt stress response and signal transduction.

Key words: potato, GRAM gene family, bioinformatics, salt stress, expression analysis

LIU Tao, WANG Zhi-qi, WU Wen-bo, SHI Wen-ting, WANG Chao-nan, DU Chong, YANG Zhong-min. Identification and Expression Analysis of the GRAM Gene Family in Potato[J]. Biotechnology Bulletin, 2025, 41(4): 145-155.

Figures/Tables 9

References 30

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基因名称 Gene name	上游引物 Forward primer（5'-3'）	下游引物 Reverse primer（5'-3'）
Actin	GGATCTTGCTGGTCGTGATTTAAC	CATAGGCAAGCTTTTCCTTCATGT
StGRAM25	TCTTTCCACTGCAACTGGTCCTG	ATGGGCGATCACTGCAAAAAGC

基因名称 Gene name	上游引物 Forward primer（5'-3'）	下游引物 Reverse primer（5'-3'）
Actin	GGATCTTGCTGGTCGTGATTTAAC	CATAGGCAAGCTTTTCCTTCATGT
StGRAM25	TCTTTCCACTGCAACTGGTCCTG	ATGGGCGATCACTGCAAAAAGC

基因名称 Gene name	基因ID Gene ID	蛋白长度 Amino acid length/aa	分子量 Molecular mass/Da	等电点 pI	不稳定系数 Instability index	脂肪指数 Aliphatic index	亲水性 Hydropathicity	亚细胞定位 Subcellular location
StGRAM1	Soltu.DM.01G007240	233	26 247.80	9.14	42.35	68.20	-0.485	叶绿体Chloroplast
StGRAM2	Soltu.DM.01G030910	192	21 272.18	6.29	74.01	78.85	-0.188	叶绿体Chloroplast
StGRAM3	Soltu.DM.03G018700	235	26 346.02	9.66	53.78	69.70	-0.503	细胞核Nuclear
StGRAM4	Soltu.DM.03G025920	1 019	115 351.4	5.47	40.11	85.16	-0.298	叶绿体Chloroplast
StGRAM5	Soltu.DM.04G004990	874	98 928.22	9.82	33.16	94.03	-0.288	细胞核Nuclear
StGRAM6	Soltu.DM.04G005060	228	25 742.96	9.70	35.24	89.78	-0.341	叶绿体Chloroplast
StGRAM7	Soltu.DM.04G005070	228	25 687.00	9.6	38.83	85.53	-0.284	叶绿体Chloroplast
StGRAM8	Soltu.DM.04G005080	235	26 935.40	9.73	37.01	82.13	-0.365	叶绿体Chloroplast
StGRAM9	Soltu.DM.04G005090	228	25 837.11	9.71	39.30	87.24	-0.364	叶绿体Chloroplast
StGRAM10	Soltu.DM.04G005100	228	26 217.88	9.72	40.21	88.07	-0.182	叶绿体Chloroplast
StGRAM11	Soltu.DM.04G005110	228	26 217.88	9.72	40.21	88.07	-0.182	细胞核Nuclear
StGRAM12	Soltu.DM.04G005120	251	28 580.60	9.80	41.56	41.56	-0.224	叶绿体Chloroplast
StGRAM13	Soltu.DM.04G005130	228	25 716.98	9.75	33.02	89.78	-0.304	叶绿体Chloroplast
StGRAM14	Soltu.DM.04G005140	228	25 714.98	9.67	35.74	87.63	-0.304	叶绿体Chloroplast
StGRAM15	Soltu.DM.04G005150	228	25 660.87	9.68	31.98	88.07	-0.302	叶绿体Chloroplast
StGRAM16	Soltu.DM.04G005160	208	23 468.61	9.97	41.15	90.43	-0.266	叶绿体Chloroplast
StGRAM17	Soltu.DM.04G005170	261	29 478.80	9.86	36.96	96.74	-0.226	叶绿体Chloroplast
StGRAM18	Soltu.DM.04G005180	261	29 672.17	9.93	35.23	101.61	-0.210	叶绿体Chloroplast
StGRAM19	Soltu.DM.04G005190	261	29 589.97	9.90	37.89	101.95	-0.188	叶绿体Chloroplast
StGRAM20	Soltu.DM.04G008560	300	33 183.95	5.33	49.30	66.30	-0.630	细胞核Nuclear
StGRAM21	Soltu.DM.04G010140	1 052	117 398.65	5.70	43.73	84.20	-0.281	叶绿体Chloroplast
StGRAM22	Soltu.DM.06G014320	621	69 760.28	6.23	54.74	82.40	-0.279	叶绿体Chloroplast
StGRAM23	Soltu.DM.07G009230	216	23 378.40	6.08	39.23	67.31	-0.439	细胞核Nuclear
StGRAM24	Soltu.DM.08G005660	85	9 692.38	5.21	36.43	104.24	0.055	线粒体Mitochondrial
StGRAM25	Soltu.DM.08G024750	327	36 731.69	7.18	55.26	67.13	-0.416	细胞核Nuclear
StGRAM26	Soltu.DM.11G003200	281	31 205.20	5.78	46.09	68.75	-0.458	细胞质Cytoplasmic

基因名称 Gene name	基因ID Gene ID	蛋白长度 Amino acid length/aa	分子量 Molecular mass/Da	等电点 pI	不稳定系数 Instability index	脂肪指数 Aliphatic index	亲水性 Hydropathicity	亚细胞定位 Subcellular location
StGRAM1	Soltu.DM.01G007240	233	26 247.80	9.14	42.35	68.20	-0.485	叶绿体Chloroplast
StGRAM2	Soltu.DM.01G030910	192	21 272.18	6.29	74.01	78.85	-0.188	叶绿体Chloroplast
StGRAM3	Soltu.DM.03G018700	235	26 346.02	9.66	53.78	69.70	-0.503	细胞核Nuclear
StGRAM4	Soltu.DM.03G025920	1 019	115 351.4	5.47	40.11	85.16	-0.298	叶绿体Chloroplast
StGRAM5	Soltu.DM.04G004990	874	98 928.22	9.82	33.16	94.03	-0.288	细胞核Nuclear
StGRAM6	Soltu.DM.04G005060	228	25 742.96	9.70	35.24	89.78	-0.341	叶绿体Chloroplast
StGRAM7	Soltu.DM.04G005070	228	25 687.00	9.6	38.83	85.53	-0.284	叶绿体Chloroplast
StGRAM8	Soltu.DM.04G005080	235	26 935.40	9.73	37.01	82.13	-0.365	叶绿体Chloroplast
StGRAM9	Soltu.DM.04G005090	228	25 837.11	9.71	39.30	87.24	-0.364	叶绿体Chloroplast
StGRAM10	Soltu.DM.04G005100	228	26 217.88	9.72	40.21	88.07	-0.182	叶绿体Chloroplast
StGRAM11	Soltu.DM.04G005110	228	26 217.88	9.72	40.21	88.07	-0.182	细胞核Nuclear
StGRAM12	Soltu.DM.04G005120	251	28 580.60	9.80	41.56	41.56	-0.224	叶绿体Chloroplast
StGRAM13	Soltu.DM.04G005130	228	25 716.98	9.75	33.02	89.78	-0.304	叶绿体Chloroplast
StGRAM14	Soltu.DM.04G005140	228	25 714.98	9.67	35.74	87.63	-0.304	叶绿体Chloroplast
StGRAM15	Soltu.DM.04G005150	228	25 660.87	9.68	31.98	88.07	-0.302	叶绿体Chloroplast
StGRAM16	Soltu.DM.04G005160	208	23 468.61	9.97	41.15	90.43	-0.266	叶绿体Chloroplast
StGRAM17	Soltu.DM.04G005170	261	29 478.80	9.86	36.96	96.74	-0.226	叶绿体Chloroplast
StGRAM18	Soltu.DM.04G005180	261	29 672.17	9.93	35.23	101.61	-0.210	叶绿体Chloroplast
StGRAM19	Soltu.DM.04G005190	261	29 589.97	9.90	37.89	101.95	-0.188	叶绿体Chloroplast
StGRAM20	Soltu.DM.04G008560	300	33 183.95	5.33	49.30	66.30	-0.630	细胞核Nuclear
StGRAM21	Soltu.DM.04G010140	1 052	117 398.65	5.70	43.73	84.20	-0.281	叶绿体Chloroplast
StGRAM22	Soltu.DM.06G014320	621	69 760.28	6.23	54.74	82.40	-0.279	叶绿体Chloroplast
StGRAM23	Soltu.DM.07G009230	216	23 378.40	6.08	39.23	67.31	-0.439	细胞核Nuclear
StGRAM24	Soltu.DM.08G005660	85	9 692.38	5.21	36.43	104.24	0.055	线粒体Mitochondrial
StGRAM25	Soltu.DM.08G024750	327	36 731.69	7.18	55.26	67.13	-0.416	细胞核Nuclear
StGRAM26	Soltu.DM.11G003200	281	31 205.20	5.78	46.09	68.75	-0.458	细胞质Cytoplasmic

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