Comparative Transcriptome Analysis Reveals Novel Candidate Resistance Genes Involved in Defence against Phytophthora cactorum in Strawberry
Abstract
:1. Introduction
2. Results
2.1. Transcriptome of Resistant and Susceptible Strawberry Genotypes Inoculated with P. cactorum
2.2. Analysis of Differentially Expressed Genes in F. vesca Genotypes
2.3. GO Term Enrichment Analysis of DEGs
2.4. Genes Involved in Defence against P. cactorum
2.5. Expression of Defence-Related Genes in the RPc-1 Locus
2.6. Differential Expression Analysis of Transcription Factor Genes
2.7. Flavonoid, Isoprenoid and Phytohormone Signalling Pathway Genes
2.8. Pathogenesis-Related Genes
2.9. Validation of Genes Expressed Only in the Resistant Genotypes
2.10. Detection of Genes Distinct for the Resistant Genotypes
3. Discussion
4. Materials and Methods
4.1. Plant Material and Pathogen Inoculation
4.2. Disease Scoring and Statistical Analysis
4.3. RNA Isolation, Library Preparation and Sequencing
4.4. De Novo Transcriptome Assembly and Data Analysis
4.5. RNA-Seq Data Validation by Semi-Quantitative Reverse Transcription-PCR (RT-PCR)
4.6. Isolation of Genomic DNA and PCR Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene ID | RNA Abundance 48 h after Inoculation (Mean Transcripts per Million ± SE) | Annotation Based on NCBI Non-Redundant Database and InterProScan Domain Analysis | Putative Role in Defence | Reference | ||
---|---|---|---|---|---|---|
NCGR1218 | NCGR1603 | Bukammen | ||||
FvH4_7g05680.1 | 0 ± 0.0 | 28 ± 1.0 | 33 ± 1.0 | Protein DJ-1 homolog D-like | Cellular defence response against oxidative stress, and chloroplast development | [49,50] |
FvH4_1g22440.1 | 0 ± 0.0 | 28 ± 1.0 | 35 ± 3 | Putative galactose oxidase with kelch/beta-propeller | Production of H2O2 from galactose and O2; interaction with ASK1/MAP3K5 | [51,52] |
FvH4_6g53350.1 | 0 ± 0.0 | 27 ± 2.0 | 32 ± 2.0 | Protease HtpX homolog, peptidase M48 | Stress-controlled protease in E. coli; proteolytic quality control of misfolded proteins | [53,54] |
FvH4_7g20440.1 | 0 ± 0.0 | 16 ± 1.0 | 19 ± 1.0 | Zinc finger BED domain-containing protein DAYSLEEPER | Influence on global gene expression in Arabidopsis thaliana; BED-NLRs act as immune receptors in wheat (Triticum aestivum) | [55,56] |
FvH4_5g03090.1 | 0 ± 0.0 | 11 ± 3.0 | 11 ± 3.0 | Putative Clostridium epsilon toxin ETX/mosquitocidal toxin MTX2; agglutinin domain | Resistance to Fusarium graminearum | [57] |
FvH4_3g14180.1 | 0 ± 0.0 | 10 ± 1.0 | 12 ± 1.0 | Kinase RLK-Pelle-LRR-XI-1 family, protein kinase domain | Immune receptor against diverse pathogens; also involved in growth and development | [58,59] |
FvH4_5g16110.1 | 0 ± 0.0 | 8 ± 0.5 | 8 ± 0.4 | Putative disease resistance RPP13-like protein 1, leucine-rich repeat | Resistance to biotrophic oomycete Peronospora parasitica | [60] |
FvH4_6g34080.1 | 0 ± 0.0 | 7 ± 0.4 | 7 ± 0.4 | Putative transcription factor C2H2 family, zinc finger, RING-type | Response to abiotic stresses in plants | [61,62] |
FvH4_5g32170.1 | 0 ± 0.0 | 6 ± 2.0 | 5 ± 1.0 | Proteinase inhibitor PSI-1.2, proteinase inhibitor I20 | Expression induced upon wounding and involved in plant defence against herbivory | [63,64] |
FvH4_3g28530.1 | 0 ± 0.0 | 4 ± 0.5 | 3 ± 0.3 | Glucan endo-1,3-beta-glucosidase 11-like | Response to pathogen infection in plants | [65,66] |
FvH4_6g00620.1 | 0 ± 0.0 | 4 ± 0.2 | 5 ± 0.5 | Putative transcription factor C2H2 family | Response to abiotic stresses in plants | [61,62] |
FvH4_5g16070.1 | 0 ± 0.0 | 4 ± 0.2 | 3 ± 0.2 | Putative disease resistance RPP13-like protein 1 | Resistance to biotrophic oomycete Peronospora parasitica | [60] |
FvH4_6g40960.1 | 0 ± 0.0 | 4 ± 0.2 | 3 ± 0.3 | Cyclic nucleotide-gated ion channel 1-like | Active role in plant immunity in several pathosystems | [67,68] |
FvH4_6g49500.1 | 0 ± 0.0 | 3 ± 0.8 | 3 ± 0.1 | TMV resistance protein N-like, Toll/interleukin-1 receptor homology (TIR) domain | Resistance to Tobacco mosaic virus in Nicotiana benthamiana | [69] |
FvH4_6g51870.1 | 0 ± 0.0 | 3 ± 0.4 | 2 ± 0.3 | Putative transcription factor C2H2 family, zinc finger, RING-type | Response to abiotic stresses in plants | [61,62] |
FvH4_3g45070.1 | 0 ± 0.0 | 3 ± 0.1 | 7 ± 1.0 | Putative transcription factor C2H2 family, zinc finger, RING-type | Response to abiotic stresses in plants | [61,62] |
FvH4_3g11010.1 | 0 ± 0.0 | 2 ± 0.2 | 4 ± 1.0 | Berberine bridge enzyme-like 8, FAD linked oxidase, N-terminal | Enhanced resistance to Botrytis cinerea | [70] |
FvH4_5g35070.1 | 0 ± 0.0 | 2 ± 0.4 | 4 ± 0.3 | Putative pentatricopeptide repeat protein | Defence against biotic stress (Pseudomonas syringae pv. tomato and Botrytis cinerea) and abiotic stress | [71,72] |
FvH4_5g11120.1 | 0 ± 0.0 | 2 ± 0.2 | 3 ± 0.1 | Putative powdery mildew resistance protein, RPW8 | Broad spectrum mildew resistance in Arabidopsis thaliana | [73] |
FvH4_5g35080.1 | 0 ± 0.0 | 2 ± 0.5 | 4 ± 0.4 | Putative pentatricopeptide repeat protein | Defence against biotic stress (Pseudomonas syringae pv. tomato and Botrytis cinerea) | [71,72] |
FvH4_6g18970.1 | 0 ± 0.0 | 2 ± 0.3 | 2 ± 0.1 | Probable disease resistance protein At5g66900 | Unknown | _ |
FvH4_1g15330.1 | 0 ± 0.0 | 1 ± 0.2 | 1 ± 0.2 | Probable disease resistance protein At5g66910 | Unknown | _ |
FvH4_5g31070.1 | 0 ± 0.0 | 1 ± 0.3 | 2 ± 0.1 | Putative pentatricopeptide repeat protein | Defence against biotic stress (Pseudomonas syringae pv. tomato and Botrytis cinerea) and abiotic stress | [71,72] |
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Gogoi, A.; Lysøe, E.; Eikemo, H.; Stensvand, A.; Davik, J.; Brurberg, M.B. Comparative Transcriptome Analysis Reveals Novel Candidate Resistance Genes Involved in Defence against Phytophthora cactorum in Strawberry. Int. J. Mol. Sci. 2023, 24, 10851. https://doi.org/10.3390/ijms241310851
Gogoi A, Lysøe E, Eikemo H, Stensvand A, Davik J, Brurberg MB. Comparative Transcriptome Analysis Reveals Novel Candidate Resistance Genes Involved in Defence against Phytophthora cactorum in Strawberry. International Journal of Molecular Sciences. 2023; 24(13):10851. https://doi.org/10.3390/ijms241310851
Chicago/Turabian StyleGogoi, Anupam, Erik Lysøe, Håvard Eikemo, Arne Stensvand, Jahn Davik, and May Bente Brurberg. 2023. "Comparative Transcriptome Analysis Reveals Novel Candidate Resistance Genes Involved in Defence against Phytophthora cactorum in Strawberry" International Journal of Molecular Sciences 24, no. 13: 10851. https://doi.org/10.3390/ijms241310851