Genome-wide Identification and Expression Profiles of DIR Gene Family in Potato

doi:10.13560/j.cnki.biotech.bull.1985.2024-0825

Abstract

Abstract:

Objective All members of the DIR gene family in potato (Solanum tuberosum) were identified by the latest potato genome information. Bioinformatic techniques and transcriptome data were used to predict and analyze the phylogenetic relationship, gene structures, promoter elements and expression profiles of DIR gene family members. These results will lay a foundation for further study on the function of DIR genes in potate growth and development as well as their responses to stresses. Method Based on the protein sequences of Arabidopsis DIR gene and the model file of Dirigent domain, the whole genome identification of potato DIR family members was carried out. The physicochemical characteristic, chromosome localization, collinearity analysis, conserved motif, gene structure and cis-acting elements of potato DIR genes were analyzed by bioinformatics tools such as ExPASy, MEME, MCScanX, GSDS, PlantCARE, and TBtools, respectively. Transcriptome data and RT-qPCR were based to understand the expression patterns of DIR genes in different tissues and under stress treatment, and to explore the candidate DIR genes related to growth and development and stress responses. Result A total of 34 DIR genes were identified from the potato genome and unevenly distributed on 11 chromosomes. Phylogenetic analysis showed that 34 StDIR genes were divided into three subgroups. The conserved motifs and gene structures of StDIR members in the same subgroup were relatively consistent. Most of the StDIR genes contained only one exon. Analysis of cis-acting elements indicated that the StDIR genes had diverse hormone-related elements and abiotic stress response elements. Synteny analysis revealed that 5, 13 and 18 DIR genes in potato were collinear with 3, 15 and 16 DIR genes in rice, Arabidopsis and eggplant, respectively. The expression analysis of StDIR gene showed that the StDIR genes had relatively high expressions in the leaves, roots, stolons, and callus. However, the transcript abundance of the StDIR genes was lower in sepals, carpels, stamens, and petals. Furthermore, StDIR genes had different expressions under salt, drought, heat, and cold stresses, indicating that StDIR genes play important roles in abiotic stress responses. Conclusion A total of 34 DIR genes are identified in potato and divided into three subgroups. The conserved motif and gene structure in the same subgroup are basically consistent. The expression pattern of StDIR genes vary in different tissues and significantly respond to drought and high temperature stresses.

Key words: potato, DIR protein, gene family, bioinformatics, abiotic stress, expression profile

ZHANG Yi-xuan, MA Yu, WANG Tong-tong, SHENG Su-ao, SONG Jia-feng, LYU Zhao-yan, ZHU Xiao-biao, HOU Hua-lan. Genome-wide Identification and Expression Profiles of DIR Gene Family in Potato[J]. Biotechnology Bulletin, 2025, 41(3): 123-136.

Figures/Tables 10

References 47

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基因名Gene name	基因ID Gene ID	蛋白长度Length of protein/aa	分子量Molecular weight/kD	等电点pI	不稳定系数Instability index	脂肪系数Aliphatic index	亲水性平均值Grand average of hydropathicity	信号肽Signal peptide/aa	N-糖基化位点N-Glyc position	亚细胞定位Subcellular location
StDIR1	Soltu.DM.01G001610.1	192	21.26	9.76	31.2	100.47	0.167	1-24	41	Chloroplast
StDIR2	Soltu.DM.01G012660.1	189	21.17	9.57	28	86.19	0.155	1-24	-	Cell membrane. Chloroplast
StDIR3	Soltu.DM.01G012790.1	191	21.29	9.37	24.95	77.12	-0.019	1-24	-	Cell wall. Chloroplast Mitochondrion
StDIR4	Soltu.DM.01G019610.1	174	19.40	6.5	10.61	99.71	0.21	-	-	Cell membrane
StDIR5	Soltu.DM.01G050810.1	127	13.56	5.6	9.14	92.13	0.231	1-20	-	Cell wall
StDIR6	Soltu.DM.01G050820.1	188	20.76	9.1	31.15	90.27	0.062	1-22	-	Cell membrane. Cell wall
StDIR7	Soltu.DM.02G003630.1	190	21.10	8.76	27.85	92.37	-0.015	1-22	-	Cell membrane
StDIR8	Soltu.DM.02G003640.1	185	20.57	9.1	25.39	91.19	0.001	1-17	-	Cell membrane
StDIR9	Soltu.DM.02G022680.1	318	34.60	9.56	27.65	91.01	0.041	-	289 315	Endoplasmic reticulum
StDIR10	Soltu.DM.04G003460.1	185	20.66	9.58	32.65	101.84	0.038	-	25	Cell membrane
StDIR11	Soltu.DM.04G007230.1	335	35.58	5.17	35.6	83.52	-0.05	1-30	-	Cell membrane
StDIR12	Soltu.DM.05G023520.1	137	14.84	9.45	29.19	95.33	0.299	1-28	-	Chloroplast. Peroxisome
StDIR13	Soltu.DM.05G025340.1	400	41.21	4.29	41.77	88.55	0.023	1-30	-	Cell membrane
StDIR14	Soltu.DM.05G025350.1	240	26.46	6.34	34.48	78.38	-0.238	1-25	-	Nucleus
StDIR15	Soltu.DM.06G015540.1	188	20.75	6.13	46.29	78.4	0.116	1-25	-	Cell membrane
StDIR16	Soltu.DM.06G031100.1	329	33.10	4.66	24.04	86.69	0.235	1-30	-	Cell membrane
StDIR17	Soltu.DM.07G013170.1	187	20.55	9.49	22.41	93.8	0.195	1-22	-	Chloroplast
StDIR18	Soltu.DM.07G017590.1	177	19.60	6.36	19.62	103.05	0.193	1-22	127	Cell membrane Mitochondrion
StDIR19	Soltu.DM.08G028530.1	189	21.53	6.35	25.21	70.69	-0.086	1-24	-	Cell membrane
StDIR20	Soltu.DM.08G028540.1	189	21.16	6.9	20.34	91.9	0.1	1-26	-	Cell membrane. Cell wall. Chloroplast
StDIR21	Soltu.DM.09G028090.1	246	25.71	5.02	31.88	87.24	0.178	1-17	145 222	Cell membrane
StDIR22	Soltu.DM.10G004800.1	190	21.33	9.73	33.17	87.74	0.017	1-22	26	Cell membrane
StDIR23	Soltu.DM.10G017030.1	184	20.24	9.21	23.79	96.9	0.188	1-20	59	Cell membrane. Cell wall. Chloroplast. Mitochondrion
StDIR24	Soltu.DM.10G017040.1	194	20.93	9.27	20.18	101.6	0.176	1-26	-	Cell membrane. Cell wall. Chloroplast
StDIR25	Soltu.DM.10G017050.1	128	14.03	9.7	14.52	75.47	0.008	1-22	128	Cell membrane
StDIR26	Soltu.DM.10G017060.1	173	19.23	5.45	22.87	77.23	-0.086	-	-	Cell wall
StDIR27	Soltu.DM.10G017070.1	194	20.90	9.3	17.68	105.62	0.213	1-26	-	Cell membrane
StDIR28	Soltu.DM.10G017090.1	193	21.18	9.52	16.09	82.28	0.069	1-23	75	Cell membrane
StDIR29	Soltu.DM.10G017100.1	174	19.35	5.81	20.61	79.02	-0.113	-	-	Cell wall
StDIR30	Soltu.DM.10G017110.1	190	20.95	8.63	18.93	89.16	0.112	1-20	72	Cell membrane. Cell wall
StDIR31	Soltu.DM.10G017130.1	124	13.52	9.43	22.84	80.16	0.198	-	-	Cell membrane
StDIR32	Soltu.DM.10G017170.1	184	20.29	9.63	28.12	92.17	0.167	1-20	-	Cell membrane. Cell wall
StDIR33	Soltu.DM.11G026480.1	336	34.33	4.74	33.36	84.49	0.136	1-31	186	Cell membrane
StDIR34	Soltu.DM.12G003100.1	247	25.75	5.26	29.03	91.62	0.225	1-25	146 223	Cell membrane

基因名Gene name	基因ID Gene ID	蛋白长度Length of protein/aa	分子量Molecular weight/kD	等电点pI	不稳定系数Instability index	脂肪系数Aliphatic index	亲水性平均值Grand average of hydropathicity	信号肽Signal peptide/aa	N-糖基化位点N-Glyc position	亚细胞定位Subcellular location
StDIR1	Soltu.DM.01G001610.1	192	21.26	9.76	31.2	100.47	0.167	1-24	41	Chloroplast
StDIR2	Soltu.DM.01G012660.1	189	21.17	9.57	28	86.19	0.155	1-24	-	Cell membrane. Chloroplast
StDIR3	Soltu.DM.01G012790.1	191	21.29	9.37	24.95	77.12	-0.019	1-24	-	Cell wall. Chloroplast Mitochondrion
StDIR4	Soltu.DM.01G019610.1	174	19.40	6.5	10.61	99.71	0.21	-	-	Cell membrane
StDIR5	Soltu.DM.01G050810.1	127	13.56	5.6	9.14	92.13	0.231	1-20	-	Cell wall
StDIR6	Soltu.DM.01G050820.1	188	20.76	9.1	31.15	90.27	0.062	1-22	-	Cell membrane. Cell wall
StDIR7	Soltu.DM.02G003630.1	190	21.10	8.76	27.85	92.37	-0.015	1-22	-	Cell membrane
StDIR8	Soltu.DM.02G003640.1	185	20.57	9.1	25.39	91.19	0.001	1-17	-	Cell membrane
StDIR9	Soltu.DM.02G022680.1	318	34.60	9.56	27.65	91.01	0.041	-	289 315	Endoplasmic reticulum
StDIR10	Soltu.DM.04G003460.1	185	20.66	9.58	32.65	101.84	0.038	-	25	Cell membrane
StDIR11	Soltu.DM.04G007230.1	335	35.58	5.17	35.6	83.52	-0.05	1-30	-	Cell membrane
StDIR12	Soltu.DM.05G023520.1	137	14.84	9.45	29.19	95.33	0.299	1-28	-	Chloroplast. Peroxisome
StDIR13	Soltu.DM.05G025340.1	400	41.21	4.29	41.77	88.55	0.023	1-30	-	Cell membrane
StDIR14	Soltu.DM.05G025350.1	240	26.46	6.34	34.48	78.38	-0.238	1-25	-	Nucleus
StDIR15	Soltu.DM.06G015540.1	188	20.75	6.13	46.29	78.4	0.116	1-25	-	Cell membrane
StDIR16	Soltu.DM.06G031100.1	329	33.10	4.66	24.04	86.69	0.235	1-30	-	Cell membrane
StDIR17	Soltu.DM.07G013170.1	187	20.55	9.49	22.41	93.8	0.195	1-22	-	Chloroplast
StDIR18	Soltu.DM.07G017590.1	177	19.60	6.36	19.62	103.05	0.193	1-22	127	Cell membrane Mitochondrion
StDIR19	Soltu.DM.08G028530.1	189	21.53	6.35	25.21	70.69	-0.086	1-24	-	Cell membrane
StDIR20	Soltu.DM.08G028540.1	189	21.16	6.9	20.34	91.9	0.1	1-26	-	Cell membrane. Cell wall. Chloroplast
StDIR21	Soltu.DM.09G028090.1	246	25.71	5.02	31.88	87.24	0.178	1-17	145 222	Cell membrane
StDIR22	Soltu.DM.10G004800.1	190	21.33	9.73	33.17	87.74	0.017	1-22	26	Cell membrane
StDIR23	Soltu.DM.10G017030.1	184	20.24	9.21	23.79	96.9	0.188	1-20	59	Cell membrane. Cell wall. Chloroplast. Mitochondrion
StDIR24	Soltu.DM.10G017040.1	194	20.93	9.27	20.18	101.6	0.176	1-26	-	Cell membrane. Cell wall. Chloroplast
StDIR25	Soltu.DM.10G017050.1	128	14.03	9.7	14.52	75.47	0.008	1-22	128	Cell membrane
StDIR26	Soltu.DM.10G017060.1	173	19.23	5.45	22.87	77.23	-0.086	-	-	Cell wall
StDIR27	Soltu.DM.10G017070.1	194	20.90	9.3	17.68	105.62	0.213	1-26	-	Cell membrane
StDIR28	Soltu.DM.10G017090.1	193	21.18	9.52	16.09	82.28	0.069	1-23	75	Cell membrane
StDIR29	Soltu.DM.10G017100.1	174	19.35	5.81	20.61	79.02	-0.113	-	-	Cell wall
StDIR30	Soltu.DM.10G017110.1	190	20.95	8.63	18.93	89.16	0.112	1-20	72	Cell membrane. Cell wall
StDIR31	Soltu.DM.10G017130.1	124	13.52	9.43	22.84	80.16	0.198	-	-	Cell membrane
StDIR32	Soltu.DM.10G017170.1	184	20.29	9.63	28.12	92.17	0.167	1-20	-	Cell membrane. Cell wall
StDIR33	Soltu.DM.11G026480.1	336	34.33	4.74	33.36	84.49	0.136	1-31	186	Cell membrane
StDIR34	Soltu.DM.12G003100.1	247	25.75	5.26	29.03	91.62	0.225	1-25	146 223	Cell membrane

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