Transcriptome Analysis of Sweet Cherry (Prunus avium L.) Cultivar ‘Lapins’ upon Infection of Pseudomonas syringae pv. syringae
Abstract
:1. Introduction
2. Results
2.1. Disease Development
2.2. The Transcriptome Datasets of Sweet Cherry cv. ‘Lapins’
2.3. Different Pss Strains Trigger Different Local and Distal Responses
2.4. Functional Categories and GO Enrichment Analysis
2.5. Validation of Expression Changes by Quantitative RT-PCR
3. Discussion
3.1. Disease-Related Gene Candidates in Sweet Cherry Induced by Pss Inoculation
3.2. Pss Infection Triggers a Variety of Biological Processes
3.3. Detection of Pss in Uninfected Samples
4. Materials and Methods
4.1. Plant Material and Growth Conditions
4.2. Bacterial Inoculation, Plant Sampling, Bacterial Re-Isolation, and Biochemical Characterization
4.3. Nucleic Acid Sampling
4.4. Pss DNA Quantification in Sweet Cherry Samples
4.5. Library Construction and RNA Sequencing
4.6. RNA Sequence Curation and Mapping to the Reference Transcriptome
4.7. Differential Gene Expression Analysis
4.8. Gene Ontology Enrichment Analysis
4.9. Validation of DEGs
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Sampling Loci | Pss Strain | Replicates | Number of Raw Reads | Raw Read Length (nt) | GC Content (%) | Q20 (%) | Q30 (%) | Number of Reads after Trimming | Percentage of Trimmed Reads (%) | Average Read Length after Trimming (nt) | Number of Mapped Reads | Percentage of Mapped Reads (%) | Percentage of Transcripts with Mapped Reads (%) |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Local | Mock | 1 | 60,835,050 | 151 | 46.97 | 93.33 | 88.30 | 53,581,529 | 88.08 | 131.86 | 16,754,262 | 31.27 | 73.58 |
2 | 56,187,144 | 151 | 47.78 | 94.38 | 89.62 | 50,721,363 | 90.27 | 130.61 | 16,331,122 | 32.20 | 73.87 | ||
3 | 63,132,360 | 151 | 47.13 | 95.93 | 91.59 | 58,677,218 | 92.94 | 131.63 | 18,513,496 | 31.55 | 75.29 | ||
A1M3 | 1 | 63,225,668 | 151 | 51.82 | 93.10 | 87.88 | 55,555,633 | 87.87 | 126.43 | 3,691,298 | 6.64 | 59.78 | |
2 | 56,813,968 | 151 | 46.17 | 96.77 | 92.50 | 54,199,081 | 95.40 | 133.34 | 20,805,818 | 38.39 | 74.33 | ||
3 | 57,510,590 | 151 | 49.47 | 94.32 | 89.64 | 51,953,024 | 90.34 | 131.69 | 13,244,942 | 25.49 | 71.46 | ||
11116_b1 | 1 | 57,931,388 | 151 | 45.78 | 93.15 | 87.95 | 51,048,941 | 88.12 | 133.41 | 18,382,040 | 36.01 | 74.84 | |
2 | 53,399,388 | 151 | 46.72 | 95.43 | 90.92 | 49,360,607 | 92.44 | 131.64 | 17,792,020 | 36.04 | 74.85 | ||
3 | 55,546,824 | 151 | 47.12 | 95.68 | 91.31 | 51,399,548 | 92.53 | 132.19 | 18,189,231 | 35.39 | 73.67 | ||
A1M197 | 1 | 69,961,046 | 151 | 47.66 | 96.24 | 91.91 | 66,028,852 | 94.38 | 131.24 | 20,000,527 | 30.29 | 73.68 | |
2 | 58,834,920 | 151 | 46.78 | 92.03 | 86.79 | 50,531,708 | 85.89 | 132.67 | 19,298,925 | 38.19 | 73.88 | ||
3 | 57,500,624 | 151 | 45.74 | 96.28 | 91.95 | 54,062,414 | 94.02 | 134.25 | 21,404,629 | 39.59 | 74.23 | ||
Distal | Mock | 1 | 61,368,428 | 151 | 45.17 | 94.02 | 88.89 | 54,821,582 | 89.33 | 132.26 | 16,397,417 | 29.91 | 69.54 |
2 | 60,884,042 | 151 | 45.26 | 93.50 | 88.49 | 53,950,576 | 88.61 | 132.14 | 18,244,099 | 33.82 | 72.18 | ||
3 | 60,044,718 | 151 | 47.31 | 94.40 | 89.65 | 54,180,939 | 90.23 | 131.93 | 14,021,993 | 25.88 | 71.25 | ||
A1M3 | 1 | 60,741,374 | 151 | 46.02 | 93.30 | 88.19 | 53,603,105 | 88.25 | 132.87 | 16,711,876 | 31.18 | 71.91 | |
2 | 53,215,158 | 151 | 45.80 | 93.35 | 88.33 | 46,916,794 | 88.16 | 133.11 | 17,700,614 | 37.73 | 75.20 | ||
3 | 55,417,944 | 151 | 53.13 | 93.98 | 89.09 | 49,778,523 | 89.82 | 126.38 | 4,567,419 | 9.18 | 59.66 | ||
11116_b1 | 1 | 62,375,428 | 151 | 46.85 | 94.28 | 89.55 | 56,243,457 | 90.17 | 130.01 | 17,689,918 | 31.45 | 71.68 | |
2 | 56,401,534 | 151 | 51.33 | 93.98 | 89.12 | 50,643,914 | 89.79 | 126.47 | 10,970,689 | 21.66 | 67.01 | ||
3 | 56,548,966 | 151 | 46.17 | 95.62 | 91.40 | 52,320,030 | 92.52 | 132.07 | 17,770,745 | 33.97 | 72.08 | ||
A1M197 | 1 | 53,984,686 | 151 | 46.55 | 94.71 | 90.03 | 49,040,902 | 90.84 | 131.09 | 14,992,085 | 30.57 | 71.26 | |
2 | 54,615,978 | 151 | 45.94 | 93.61 | 88.62 | 48,392,367 | 88.60 | 133.17 | 14,639,217 | 30.25 | 70.58 | ||
3 | 60,384,644 | 151 | 45.74 | 94.44 | 89.64 | 54,514,976 | 90.28 | 133.59 | 17,940,683 | 32.91 | 73.16 |
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Cui, W.; Fiore, N.; Figueroa, F.; Rubilar, C.; Pizarro, L.; Pinto, M.; Pérez, S.; Beltrán, M.F.; Carreras, C.; Pimentel, P.; et al. Transcriptome Analysis of Sweet Cherry (Prunus avium L.) Cultivar ‘Lapins’ upon Infection of Pseudomonas syringae pv. syringae. Plants 2023, 12, 3718. https://doi.org/10.3390/plants12213718
Cui W, Fiore N, Figueroa F, Rubilar C, Pizarro L, Pinto M, Pérez S, Beltrán MF, Carreras C, Pimentel P, et al. Transcriptome Analysis of Sweet Cherry (Prunus avium L.) Cultivar ‘Lapins’ upon Infection of Pseudomonas syringae pv. syringae. Plants. 2023; 12(21):3718. https://doi.org/10.3390/plants12213718
Chicago/Turabian StyleCui, Weier, Nicola Fiore, Franco Figueroa, Carlos Rubilar, Lorena Pizarro, Manuel Pinto, Set Pérez, María Francisca Beltrán, Claudia Carreras, Paula Pimentel, and et al. 2023. "Transcriptome Analysis of Sweet Cherry (Prunus avium L.) Cultivar ‘Lapins’ upon Infection of Pseudomonas syringae pv. syringae" Plants 12, no. 21: 3718. https://doi.org/10.3390/plants12213718
APA StyleCui, W., Fiore, N., Figueroa, F., Rubilar, C., Pizarro, L., Pinto, M., Pérez, S., Beltrán, M. F., Carreras, C., Pimentel, P., & Zamorano, A. (2023). Transcriptome Analysis of Sweet Cherry (Prunus avium L.) Cultivar ‘Lapins’ upon Infection of Pseudomonas syringae pv. syringae. Plants, 12(21), 3718. https://doi.org/10.3390/plants12213718