Cloning and Expression Analysis of ATG8 (Autophagy-Related 8) Gene Family in Solanaceae
Abstract
:1. Introduction
2. Results
2.1. Cloning of the ATG8 Gene Family
2.2. Bioinformatics Analysis of the ATG8 Gene Family
2.2.1. Prediction of the Physicochemical Properties and Subcellular Localisation of ATG8 Proteins
2.2.2. Secondary and Tertiary Structure Prediction of ATG8 Proteins
2.2.3. Analysis of ATG8 Protein Phosphorylation Sites, Transmembrane Structures, Signal Peptides, and Conformational Plausibility
2.2.4. Analysis of ATG8 Gene Structures and Chromosomal Localisation
2.2.5. Analysis of Conserved Motifs and Cis-Acting Elements
2.2.6. Phylogenetic Analysis of ATG8 Gene Family
2.2.7. Synteny Analysis
2.3. Analysis of ATG8 Expression in Osthole-Induced Disease Resistance in Pepper and Tomato
2.4. Effect of the Autophagy Inhibitor 3-MA on ATG8 Gene Family Expression
3. Discussion
4. Materials and Methods
4.1. Test Strains and Vectors
4.2. Test Plants
4.3. Reagents and Culture Media
4.4. Cloning of Target Genes
4.4.1. Total RNA Extraction
4.4.2. cDNA Synthesis
4.4.3. RT-PCR
4.5. Bioinformatics Analysis
4.6. ATG8 Expression During Osthole-Induced Disease Resistance in Pepper and Tomato
4.7. Effect of the Autophagy Inhibitor 3-MA on ATG8 Gene Expression
4.8. Statistical Analysis
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Gene | Protein Length (KDa) | Molecular Weight (Mr/103) | Theoretical pI | Instability Index | Aliphatic Index | Grand Average of Hydropathy | Subcellular Localisation |
---|---|---|---|---|---|---|---|
ATG8a1-Sl | 119 | 13,744.94 | 8.78 | 40.52 | 84.45 | −0.361 | Nucleus |
ATG8a2-Sl | 119 | 13,744.94 | 8.78 | 40.52 | 84.45 | −0.361 | Nucleus |
ATG8b1-Nt | 122 | 14,031.14 | 6.61 | 32.69 | 92.70 | −0.418 | Chloroplast |
ATG8c1-Sl | 99 | 11,428.18 | 7.93 | 44.53 | 93.54 | −0.415 | Nucleus |
ATG8c2-Sl | 99 | 11,428.18 | 7.93 | 44.53 | 93.54 | −0.415 | Nucleus |
ATG8c3-Sl | 99 | 11,428.18 | 7.93 | 44.53 | 93.54 | −0.415 | Nucleus |
ATG8c4-Ca | 99 | 11,428.18 | 7.93 | 44.53 | 93.54 | −0.415 | Nucleus |
ATG8d1-Nt | 123 | 14,109.19 | 6.61 | 35.45 | 86.42 | −0.385 | Cytoplasm |
ATG8d2-Nt | 123 | 14,109.19 | 6.61 | 35.45 | 86.42 | −0.385 | Plasma membrane |
ATG8e1-Nt | 123 | 14,107.26 | 6.61 | 43.04 | 90.41 | −0.335 | Chloroplast |
ATG8e2-Nt | 123 | 14,107.26 | 6.61 | 43.04 | 90.41 | −0.335 | Chloroplast |
ATG8f1-Sl | 122 | 13,930.08 | 7.85 | 35.19 | 94.34 | −0.331 | Mitochondria Peroxisome |
ATG8f2-Sl | 122 | 13,930.08 | 7.85 | 35.19 | 94.34 | −0.331 | Nucleus |
ATG8f3-Sl | 122 | 13,930.08 | 7.85 | 35.19 | 94.34 | −0.331 | Nucleus |
ATG8f4-Sl | 122 | 13,930.08 | 7.85 | 35.19 | 94.34 | −0.331 | Nucleus |
Gene | Serine | Threonine | Tyrosine |
---|---|---|---|
ATG8a1-Sl | 4 | 1 | 1 |
ATG8a2-Sl | 4 | 3 | 0 |
ATG8b1-Nt | 4 | 1 | 0 |
ATG8c1-Sl | 8 | 3 | 0 |
ATG8c2-Sl | 8 | 3 | 0 |
ATG8c3-Sl | 8 | 3 | 0 |
ATG8c4-Ca | 15 | 3 | 0 |
ATG8d1-Nt | 8 | 2 | 0 |
ATG8d2-Nt | 7 | 3 | 0 |
ATG8e1-Nt | 6 | 1 | 1 |
ATG8e2-Nt | 5 | 2 | 1 |
ATG8f1-Sl | 10 | 9 | 0 |
ATG8f2-Sl | 11 | 0 | 0 |
ATG8f3-Sl | 9 | 0 | 0 |
ATG8f4-Sl | 9 | 0 | 0 |
Gene | Most Favoured Regions (%) | Additional Allowed Regions (%) | Generously Allowed Regions (%) | Disallowed Regions (%) |
---|---|---|---|---|
ATG8a1-Sl | 88.0 | 12.0 | - | - |
ATG8a2-Sl | 88.0 | 12.0 | - | - |
ATG8b1-Nt | 95.5 | 4.5 | - | - |
ATG8c1-Sl | 55.0 | 40.0 | 5.0 | - |
ATG8c2-Sl | 55.0 | 40.0 | 5.0 | - |
ATG8c3-Sl | 55.0 | 40.0 | 5.0 | - |
ATG8c4-Ca | 92.7 | 2.8 | - | - |
ATG8d1-Nt | 95.7 | 4.3 | - | - |
ATG8d2-Nt | 94.6 | 5.4 | - | - |
ATG8e1-Nt | 95.8 | 4.2 | - | - |
ATG8e2-Nt | 96.9 | 3.1 | - | - |
ATG8f1-Sl | 100.0 | - | - | - |
ATG8f2-Sl | 88.6 | 8.6 | - | 2.9 |
ATG8f3-Sl | 86.1 | 11.1 | 2.8 | - |
ATG8f4-Sl | 86.1 | 11.1 | 2.8 | - |
Name of Primer | Sequence | Gene ID |
---|---|---|
ATG8a-F | GGATGCTTTTCCACTC | JF304784 |
ATG8a-R | GTGAAGAAACAGGATACCATC | |
ATG8b-F | GTTAAGAGCTCATTCAAGCAGGA | KR336565 |
ATG8b-R | TCCCCGAATGTGTTTTCTCCA | |
ATG8c-F | GAGGAGGCAGGCAGAATCTT | MK189279 |
ATG8c-R | ACCCAAATGTATTTTCGCCGC | |
ATG8d-F | TGGCCAAGAGTTCTTTCAAGC | KR336567 |
ATG8d-R | CCAAGCTCAAGGAACCCAAAAG | |
ATG8e-F | TGAACACCCCATGGAGAGGA | KR336568 |
ATG8e-R | GGAACCCAAATGTATTTTCT | |
ATG8f-F | GGCTAAGAGCTCATTCAAGCA | NM_001247705 |
ATG8f-R | CTACAGTTCGCTCAGGACCCCGAA |
Name of Primer | Sequence | Reference |
---|---|---|
ATG8a-F | CCTGCTGATCTGACTGTGGG | [37] |
ATG8a-R | CTGTCGGAGGAAGGATATTTTTC | |
ATG8b-F | CAGTTGGGCAATTTGTCTATGTC | |
ATG8b-R | TTCAGGTCCCCGAATGTGTT | |
ATG8c-F | TATTCCCAACATTGACAAGAAAAAG | |
ATG8c-R | TGACGTAGACAAACTGCCCCA | |
ATG8d-F | CATCCGAGAGAAGTATCCCGA | |
ATG8d-R | CAGACAACAGAGCAGCCGTG | |
ATG8e-F | TTTGGAGAGGAGGCAGGCA | |
ATG8e-R | CAGACATCAGAGCAGCAGTTGG | |
ATG8a-F | CCTGCTGATCTGACTGTGGG | |
ATG8a-R | CTGTCGGAGGAAGGATATTTTTC |
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Chen, Y.; Lu, Y.; Dong, S.; Yang, C.; Yang, S. Cloning and Expression Analysis of ATG8 (Autophagy-Related 8) Gene Family in Solanaceae. Plants 2024, 13, 2924. https://doi.org/10.3390/plants13202924
Chen Y, Lu Y, Dong S, Yang C, Yang S. Cloning and Expression Analysis of ATG8 (Autophagy-Related 8) Gene Family in Solanaceae. Plants. 2024; 13(20):2924. https://doi.org/10.3390/plants13202924
Chicago/Turabian StyleChen, Yahan, Yunshuang Lu, Shibo Dong, Chengde Yang, and Shunyi Yang. 2024. "Cloning and Expression Analysis of ATG8 (Autophagy-Related 8) Gene Family in Solanaceae" Plants 13, no. 20: 2924. https://doi.org/10.3390/plants13202924
APA StyleChen, Y., Lu, Y., Dong, S., Yang, C., & Yang, S. (2024). Cloning and Expression Analysis of ATG8 (Autophagy-Related 8) Gene Family in Solanaceae. Plants, 13(20), 2924. https://doi.org/10.3390/plants13202924