Comparative Transcriptome Analysis of Pine Trees Treated with Resistance-Inducing Substances against the Nematode Bursaphelenchus xylophilus
Abstract
:1. Introduction
2. Materials and Methods
2.1. PWN Source
2.2. Preparation of Chemical Formulations
2.3. In Vivo Pine Seedling Assay
2.4. RNA Isolation
2.5. RNA Sequencing
2.6. Genome Characterization
2.7. Transcriptome Analysis
2.8. DEG Analysis
2.9. Comparative Transcriptome and Functional Enrichment
2.10. Protein–Protein Interaction Network Analysis
2.11. Quantitative Real-Time PCR (qPCR) Analysis
3. Results
3.1. Inhibitory Effects of the ASM and MeSA Treatments against PWN Infection
3.2. Overview of the In Vivo Transcriptomes in PWN-Infected Pine Trees
3.3. Genes Induced by PWN Infection under SAR Induction
3.4. Common Systems Activated by the RISs for Response to PWN Infection
3.5. Functional Systems of ASM- and MeSA-Specific Patterns
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Sample | Read Type | GC (%) | Quality 1 | Total Reads | Total Length (bp) |
---|---|---|---|---|---|
ASM_1 | Paired end | 47 | 40 | 27,814,772 | 2,805,933,290 |
ASM_2 | Paired end | 45 | 40 | 35,228,444 | 3,554,276,515 |
ASM_3 | Paired end | 46 | 40 | 33,425,670 | 3,372,510,853 |
MeSA_1 | Paired end | 45 | 40 | 31,973,654 | 3,226,375,119 |
MeSA_2 | Paired end | 45 | 40 | 33,377,584 | 3,367,938,501 |
MeSA_3 | Paired end | 46 | 40 | 33,589,898 | 3,389,002,001 |
Untreated_1 | Paired end | 45 | 40 | 31,763,374 | 3,205,080,196 |
Untreated_2 | Paired end | 46 | 40 | 33,120,212 | 3,341,300,502 |
Untreated_3 | Paired end | 45 | 40 | 34,069,162 | 3,437,840,259 |
GO ID | Terms | Count | FDR 1 |
---|---|---|---|
GO:0048585 | Negative regulation of response to stimulus | 34 | 0 |
GO:0006855 | Drug transmembrane transport | 26 | 0 |
GO:0009817 | Defence response to fungus, incompatible interaction | 26 | 0 |
GO:0042344 | Indole glucosinolate catabolic process | 26 | 0 |
GO:0052544 | Defence response by callose deposition in cell wall | 26 | 0 |
GO:0070574 | Cadmium ion transmembrane transport | 26 | 0 |
GO:0071366 | Cellular response to indolebutyric acid stimulus | 26 | 0 |
GO:1901140 | p-Coumaryl alcohol transport | 17 | 0 |
GO:1901141 | Regulation of lignin biosynthetic process | 17 | 0 |
GO:0009737 | Response to abscisic acid | 44 | 6.44 × 10−11 |
GO ID | Terms | Count | FDR 1 |
---|---|---|---|
GO:0002215 | Defence response to nematode | 9 | 1.27 × 10−7 |
GO:0009624 | Response to nematode | 14 | 1.16× 10−5 |
GO:0006833 | Water transport | 10 | 2.37 × 10−5 |
GO:0009094 | l-Phenylalanine biosynthetic process | 5 | 2.37 × 10−5 |
GO:0003333 | Amino acid transmembrane transport | 7 | 0.0056 |
GO:0009817 | Defence response to fungus, incompatible interaction | 8 | 0.0096 |
GO:0015804 | Neutral amino acid transport | 5 | 0.0096 |
GO:0051704 | Multi-organism process | 40 | 0.0407 |
GO:0097305 | Response to alcohol | 25 | 0.0443 |
GO:0009409 | Response to cold | 14 | 0.0443 |
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Park, J.; Jeon, H.W.; Jung, H.; Lee, H.-H.; Kim, J.; Park, A.R.; Kim, N.; Han, G.; Kim, J.-C.; Seo, Y.-S. Comparative Transcriptome Analysis of Pine Trees Treated with Resistance-Inducing Substances against the Nematode Bursaphelenchus xylophilus. Genes 2020, 11, 1000. https://doi.org/10.3390/genes11091000
Park J, Jeon HW, Jung H, Lee H-H, Kim J, Park AR, Kim N, Han G, Kim J-C, Seo Y-S. Comparative Transcriptome Analysis of Pine Trees Treated with Resistance-Inducing Substances against the Nematode Bursaphelenchus xylophilus. Genes. 2020; 11(9):1000. https://doi.org/10.3390/genes11091000
Chicago/Turabian StylePark, Jungwook, Hee Won Jeon, Hyejung Jung, Hyun-Hee Lee, Junheon Kim, Ae Ran Park, Namgyu Kim, Gil Han, Jin-Cheol Kim, and Young-Su Seo. 2020. "Comparative Transcriptome Analysis of Pine Trees Treated with Resistance-Inducing Substances against the Nematode Bursaphelenchus xylophilus" Genes 11, no. 9: 1000. https://doi.org/10.3390/genes11091000