Scientia Agricultura Sinica ›› 2023, Vol. 56 ›› Issue (4): 711-728.doi: 10.3864/j.issn.0578-1752.2023.04.010

• HORTICULTURE • Previous Articles     Next Articles

Genome-Wide Identification and Expression Analysis of DIR Gene Family in Cucumber

ZHANG KaiJing1(), HE ShuaiShuai1, JIA Li2, HU YuChao1, YANG DeKun1, LU XiaoMin1, ZHANG QiAn2, YAN CongSheng2()   

  1. 1College of Agriculture, Anhui Science and Technology University, Fengyang 233100, Anhui
    2Institute of Horticulture, Anhui Academy of Agricultural Sciences/Key Laboratory of Horticultural Crop Germplasm Innovation and Utilization (Co-construction by Ministry and Province)/Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crop, Anhui Province, Hefei 230031
  • Received:2022-04-13 Accepted:2022-06-07 Online:2023-02-16 Published:2023-02-24

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Abstract:

【Objective】 Based on the cucumber (Cucumis sativus L.) genome information and transcriptome sequencing big-data, the DIR gene family in cucumber was identified with bioinformatics methods, and the expression pattern analysis of DIR family genes in different tissues and stresses response were analyzed. It would lay an important foundation for further study on the biological function of cucumber DIR genes. 【Method】 With the reported HMM model file of DIR gene, the probable DIR genes ID from the cucumber protein database was firstly identified using HMMSearch program in the HMMER software package. The cucumber DIR genes were ultimately verified using online tools Pfam and SMART. The tools of ExPASy, TBtools, GSDS, MEME, MEGA, MCScanX and Circos were used to analyze the physicochemical characteristics, chromosomal distributions, gene structure, phylogenetic tree and synteny of cucumber DIR genes. Based on cucumber transcriptome sequencing big-data of different tissues and under different stresses, transcriptome sequencing analysis was re-analyzed using cucumber V3 version genome information. The data of cucumber DIR genes in different transcriptome sequencing analysis were retrieved. The expression heatmaps of DIR gene family were drawn using TBtools software, and the expression patterns of cucumber DIR genes in different tissues and stresses response were analyzed. 【Result】 Total of 23 DIR genes were identified from cucumber genome, which distributed to 7 chromosomes. The number of amino acids of these DIR genes ranged from 78 to 684, and the molecular weight ranged from 8.70 to 73.82 kD. Phylogenetic analysis divided the cucumber DIR genes into 3 subgroups, the structure and motif of the genes in each subgroup were similar. Synteny analysis showed that the 12 cucumber DIR genes were collinearity with 19 Arabidopsis DIR genes and with 27 kinds of linear relationships, and 12 cucumber DIR genes were collinearity and with 11 rice DIR genes with 19 kinds of linear relationships. While only 8 cucumber DIR genes were conservative, which were not collinearity with any DIR gene in Arabidopsis and rice. Tissue-specific expression analysis revealed that some cucumber DIR genes had low or no expression levels in all tissues including root, stem, flower, fruit, leaf and so on, some cucumber DIR genes had high expression levels in all tissues, and some DIR genes had specific expression levels in some tissues, but no or low expression levels in other tissues. This suggested that different cucumber DIR genes had tissue specific expression patterns. The expression profiles analysis of cucumber DIR genes under biotic and abiotic stresses conditions revealed that cucumber DIR gene, CsaV3_4G023490, were up-regulated expression in response to all stresses, which meant this gene played an important role in the process of cucumber growth and development. 【Conclusion】 Total of 23 DIR genes were identified in cucumber, which were divided into 3 subgroups. The gene members in each subgroup were highly conserved, and the gene structure and protein conserved domain were different among 3 subgroups. The expression patterns of cucumber DIR genes in different tissues and stresses response were different, which coordinately regulated the growth and development of cucumber.

Key words: cucumber, DIR, gene family, bioinformatics, expression analysis

Table 1

The physiochemical characteristics of 23 members in the cucumber DIR gene family"

基因 ID
Gene ID		 CDS大小
CDS size (bp)		 氨基酸数目
Number of amino
acids (aa)		 分子量
Molecular weight (kD)		 等电点
pI		 不稳定性系数
Instability index		 脂肪系数
Aliphatic index		 亲水性平均值
Grand
average of hydropathicity		 亚细胞定位预测
Prediction of subcellular location
CsaV3_1G003340.1 552 183 19.94 6.06 32.24 90.00 0.255 质膜 Plasma membrane
CsaV3_1G003540.1 633 210 22.89 9.30 54.28 82.19 -0.111 线粒体 Mitochondrion
CsaV3_1G010290.1 774 257 27.81 5.69 46.08 75.53 -0.284 质膜Plasma membrane
CsaV3_2G015820.1 2055 684 73.82 9.13 33.65 92.27 -0.027 叶绿体 Chloroplast
CsaV3_2G015830.1 867 288 32.11 10.08 52.35 89.65 -0.136 质膜Plasma membrane
CsaV3_2G034820.1 639 212 22.68 9.69 21.78 78.73 -0.116 细胞外间隙 Extracellular space
CsaV3_3G011390.1 750 249 25.45 5.35 32.07 90.88 0.248 质膜Plasma membrane
CsaV3_3G015180.1 465 154 16.95 4.66 23.21 80.91 0.049 细胞外间隙 Extracellular space
CsaV3_4G006220.1 720 239 26.49 7.77 29.99 96.69 0.274 质膜Plasma membrane
CsaV3_4G006240.1 780 259 28.92 9.65 30.21 84.79 -0.055 质膜Plasma membrane
CsaV3_4G006250.1 576 191 21.26 8.63 28.03 86.81 0.163 质膜Plasma membrane
CsaV3_4G023480.1 237 78 8.70 9.85 36.49 70.00 -0.338 线粒体 Mitochondrion
CsaV3_4G023490.1 1284 427 48.16 9.48 35.62 88.85 -0.053 质膜Plasma membrane
CsaV3_4G023500.1 588 195 21.70 9.76 28.73 81.54 -0.030 质膜Plasma membrane
CsaV3_4G023510.1 528 175 19.53 9.58 23.03 95.20 -0.003 线粒体 Mitochondrion
CsaV3_5G006660.1 834 277 31.22 9.75 36.00 64.37 -0.420 线粒体 Mitochondrion
CsaV3_5G006670.1 1185 394 41.43 4.31 47.97 77.54 -0.177 细胞外间隙 Extracellular space
CsaV3_5G026130.1 990 329 34.01 5.08 33.90 79.12 -0.011 细胞外间隙 Extracellular space
CsaV3_6G006930.1 675 224 25.28 6.97 37.75 100.63 0.099 质膜Plasma membrane
CsaV3_7G003510.1 615 204 22.55 7.72 33.85 96.62 0.119 质膜Plasma membrane
CsaV3_7G005610.1 597 198 21.23 9.56 43.93 91.67 0.228 质膜Plasma membrane
CsaV3_7G005630.1 525 174 19.04 9.69 56.27 83.56 0.068 质膜Plasma membrane
CsaV3_7G022920.1 1770 589 66.23 8.49 49.45 89.63 -0.177 质膜Plasma membrane

Fig. 1

The distribution of DIR gene family on cucumber chromosomes The genes marked in red are tandem duplication gene pairs, and the genes marked in blue are segmental duplication gene pairs"

Fig. 2

Phylogenetic analysis of DIR genes from cucumber and Arabidopsis"

Fig. 3

Exon-intron structures of DIR genes and a schematic diagram of the amino acid motifs of DIR proteins in cucumber"

Table 2

The motifs information of cucumber DIR proteins"

基序
Motif		 序列
Sequence		 氨基酸数目
Number of amino acid		 Pfam注释
Pfam annotation
motif 1 FGTVVVIDBPLTEGPELGSKLIGRAQGFYASASQDGFGLLM 41 Dirigent
motif 2 JSFFGRNPILEKVREMPVVGGTGKFRFARG 30 Dirigent
motif 3 THLRFYFHDILSGKNPTAIAV 21 Dirigent
motif 4 AMNFAFTSGKYNGSS 15 Dirigent
motif 5 YAKAKTHYLDFTTGDAVVEYN 21 -
motif 6 EDENSFARTVNRKRLGLRKEK 21 -
motif 7 TITVLALFLFSSSSCSALPMVKKQKHKPC 29 -
motif 8 VPPVSNTSRTR 11 -
motif 9 MAGISPISPTHFLFLSFLL 19 -
motif 10 ENQHVTDGVDTJJHFSVYLSY 21 -

Fig. 4

Syntenic relationships of DIR gene family in cucumber, Arabidopsis and rice"

Fig. 5

Cis-elements analysis of the promoters of cucumber DIR family genes A: The number of various cis-elements in the promoters of each cucumber DIR gene. B: The relative proportions of different cis-elements in the promoters of cucumber DIR genes are displayed by the doughnut chart. Cis elements with the same or similar functions were represented in the same color"

Fig. 6

The expression heatmap of DIR gene family in different tissues of cucumber"

Fig. 7

The expression heatmaps of cucumber DIR gene family under abiotic stress treatments A: The expression patterns of cucumber DIR family genes under high temperature stress; HT0h_1, HT0h_2 and HT0h_3 were three replicates of the control treatment, HT3h_1 and HT3h_3 were two repetitions of high temperature treatment for 3 h, HT6h_1 and HT6h_3 were two repetitions of high temperature treatment for 6 h. B: The expression patterns of cucumber DIR family genes under low temperature stress; CT: Control, CS_2h: Low temperature treatment for 2 h, CS_6h: Low temperature treatment for 6 h; CS_12h: Low temperature treatment for 12 h. C: The expression patterns of cucumber DIR family genes under salt and silicon stresses; CT_1, CT_2 and CT_3 were three replicates of the control treatment, Na_1, Na_2 and Na_3 were three repetitions of salt stress treatment, Si_1 and Si_2 were two repetitions of silicon stress treatment. The data in the boxes indicated original FPKM values"

Fig. 8

The expression heatmaps of cucumber DIR gene family under biotic stress treatments A: The expression patterns of cucumber DIR family genes under downy mildew stress; S: Susceptible plants, R: Resistant plants, 1dpi, 2dpi, 3dpi, 4dpi and 6dpi were 1, 2, 3, 4 and 6 days post inoculation, respectively. B: The expression patterns of cucumber DIR family genes under powdery mildew stress; S: susceptible plants, R: Resistant plants, CT: Control, 48hpi: 48 hours post inoculation. C: The expression patterns of cucumber DIR family genes under root-knot nematode stress; S: Susceptible plants, R: Resistant plants, CT: Control, 1dpi, 2dpi and 3dpi were 1, 2 and 3 days post inoculation, respectively. The data in the boxes indicated original FPKM values"

Fig. 9

The expression patterns heatmap of cucumber DIR gene family under the abiotic and biotic stresses HT: High temperature stress; CS: Low temperature stress; Si: Silicon stress; DM: Downy mildew stress; PM: Powdery mildew stress; RKN: Root knot nematode stress. Gray color represents no change in expression level, red color represents up-regulated expression, green color represents down-regulated expression, and brown color represents both up-regulated and down-regulated expression"

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