Genome-Wide Identification and Expression Analysis of Eggplant DIR Gene Family in Response to Biotic and Abiotic Stresses
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identification and Chromosomal Mapping of DIR Family Genes in Eggplant
2.2. Gene Structure Analysis and Phylogenetic Tree Construction of DIR Family Genes in Eggplant
2.3. Gene Duplication and Synteny Analysis of DIR Family Genes
2.4. RNA-Seq Reanalysis of Eggplant Transcriptome Sequencing Data
2.5. Organ-Specific Expression Analysis of DIR Family Genes in Eggplant
2.6. The Expression Profiles Analysis of Eggplant DIR Family Genes under Stresses
3. Results
3.1. Genome-Wide Identification of DIR Family Genes in Eggplant
3.2. Phylogenetic Analysis of DIR Family Genes in Eggplant, Pepper and Arabidopsis
3.3. Gene Structure and Conserved Motifs Analyses of Eggplant DIR Genes
3.4. The Synteny Analysis of DIR Genes among Eggplant, Arabidopsis and Rice
3.5. The Cis-Acting Elements Analysis of Eggplant DIR Genes
3.6. Organ-Specific Expression Analysis of Eggplant DIR Genes
3.7. The Expression Profiles of Eggplant DIR Genes under Abiotic Stresses
3.8. The Expression Profiles of Eggplant DIR Genes under Biotic Stresses
3.9. The Regulation Patterns Analysis of Eggplant DIR Family Genes under Stresses
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene Name | Gene ID | Number of Amino Acid (aa) | Molecular Weight (kDa) | Theoretical pI | Instability Index | Aliphatic Index | Grand Average of Hydropathicity | Subcellular Location |
---|---|---|---|---|---|---|---|---|
SmDIR1 | SMEL4.1_01g003540.1 | 156 | 16.97 | 9.36 | 45.55 | 76.92 | −0.108 | Mitochondrion |
SmDIR2 | SMEL4.1_01g003550.1 | 343 | 36.23 | 6.13 | 11.54 | 95.54 | 0.171 | Plasma Membrane |
SmDIR3 | SMEL4.1_01g031140.1 | 191 | 21.33 | 9.57 | 28.14 | 79.69 | −0.017 | Plasma Membrane |
SmDIR4 | SMEL4.1_02g003080.1 | 190 | 21.06 | 9.67 | 24.42 | 94.95 | 0.065 | Mitochondrion |
SmDIR5 | SMEL4.1_02g009260.1 | 186 | 20.69 | 7.06 | 36.88 | 91.24 | 0.196 | Plasma Membrane |
SmDIR6 | SMEL4.1_02g018810.1 | 194 | 21.19 | 9.08 | 28.43 | 93.87 | 0.111 | Extracellular Space |
SmDIR7 | SMEL4.1_04g004510.1 | 190 | 21.37 | 9.42 | 29.75 | 91.79 | 0.022 | Plasma Membrane |
SmDIR8 | SMEL4.1_05g003580.1 | 244 | 27.03 | 5.90 | 43.08 | 79.88 | −0.167 | Plasma Membrane |
SmDIR9 | SMEL4.1_05g003590.1 | 438 | 44.86 | 4.34 | 40.80 | 87.99 | 0.075 | Extracellular Space |
SmDIR10 | SMEL4.1_05g019870.1 | 249 | 26.06 | 5.46 | 36.58 | 85.42 | 0.115 | Plasma Membrane |
SmDIR11 | SMEL4.1_06g013950.1 | 146 | 16.14 | 8.82 | 27.09 | 91.51 | 0.135 | Plasma Membrane |
SmDIR12 | SMEL4.1_06g020190.1 | 212 | 23.63 | 9.73 | 29.47 | 89.62 | 0.094 | Plasma Membrane |
SmDIR13 | SMEL4.1_06g027190.1 | 372 | 38.41 | 4.75 | 26.34 | 96.02 | 0.230 | Plasma Membrane |
SmDIR14 | SMEL4.1_07g016780.1 | 177 | 19.52 | 5.22 | 27.96 | 95.31 | 0.124 | Plasma Membrane |
SmDIR15 | SMEL4.1_08g026590.1 | 190 | 21.28 | 7.79 | 13.38 | 88.84 | 0.088 | Plasma Membrane |
SmDIR16 | SMEL4.1_08g026600.1 | 167 | 19.13 | 6.02 | 26.49 | 66.53 | −0.298 | Plasma Membrane |
SmDIR17 | SMEL4.1_09g022870.1 | 546 | 59.69 | 8.52 | 38.73 | 97.33 | 0.354 | Plasma Membrane |
SmDIR18 | SMEL4.1_11g000960.1 | 168 | 18.76 | 6.90 | 15.68 | 99.76 | 0.123 | Plasma Membrane |
SmDIR19 | SMEL4.1_11g019830.1 | 178 | 19.93 | 9.85 | 35.35 | 100.34 | 0.069 | Plasma Membrane |
SmDIR20 | SMEL4.1_11g026460.1 | 369 | 38.79 | 4.63 | 42.99 | 84.80 | −0.063 | Extracellular Space |
SmDIR21 | SMEL4.1_12g003420.1 | 184 | 20.19 | 9.52 | 26.98 | 90.11 | 0.123 | Mitochondrion |
SmDIR22 | SMEL4.1_12g003430.1 | 194 | 20.87 | 9.24 | 22.53 | 101.55 | 0.198 | Extracellular Space |
SmDIR23 | SMEL4.1_12g003440.1 | 193 | 21.21 | 6.96 | 23.74 | 93.37 | 0.130 | Extracellular Space |
SmDIR24 | SMEL4.1_12g003620.1 | 194 | 21.36 | 7.87 | 19.27 | 79.85 | 0.055 | Extracellular Space |
Motif | Sequence | Number of Amino Acid | Pfam Annotation |
---|---|---|---|
motif 1 | FGTLTVIDDPLTIGPEPNSKJIGRAQGIYGSASQNGVSLLMALNFVFTGGKY | 52 | Dirigent |
motif 2 | YREMAIVGGTGKFRLARGYATAKTYWFB | 28 | Dirigent |
motif 3 | HAKEKVTKLHFYFHDILSGKNPTAIQIAQ | 29 | - |
motif 4 | TGDAIVEYNVVVLHY | 15 | - |
motif 5 | GSTLSILGRNPVFHE | 15 | - |
motif 6 | MPTAQGIDLGPKAVEKWFKKL | 21 | - |
motif 7 | MAIIQNSNSFQLKVIISYLLILALTITFATAGRILDEEVATPTVPPNNPDPTDQPPVSGATAAGAAAGAT | 70 | - |
motif 8 | GQHTTDGVETILHITVYJTY | 20 | - |
motif 9 | DSLSFFGVHR | 10 | - |
motif 10 | IYSGQIPFATPLGFQPPEDGVAIPNANGAMPTFNINGVPLGTGLAGTIFAGGNN | 54 | - |
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Zhang, K.; Xing, W.; Sheng, S.; Yang, D.; Zhen, F.; Jiang, H.; Yan, C.; Jia, L. Genome-Wide Identification and Expression Analysis of Eggplant DIR Gene Family in Response to Biotic and Abiotic Stresses. Horticulturae 2022, 8, 732. https://doi.org/10.3390/horticulturae8080732
Zhang K, Xing W, Sheng S, Yang D, Zhen F, Jiang H, Yan C, Jia L. Genome-Wide Identification and Expression Analysis of Eggplant DIR Gene Family in Response to Biotic and Abiotic Stresses. Horticulturae. 2022; 8(8):732. https://doi.org/10.3390/horticulturae8080732
Chicago/Turabian StyleZhang, Kaijing, Wujun Xing, Suao Sheng, Dekun Yang, Fengxian Zhen, Haikun Jiang, Congsheng Yan, and Li Jia. 2022. "Genome-Wide Identification and Expression Analysis of Eggplant DIR Gene Family in Response to Biotic and Abiotic Stresses" Horticulturae 8, no. 8: 732. https://doi.org/10.3390/horticulturae8080732