Comparative Transcriptome Profiling of Resistant and Susceptible Sugarcane Cultivars in Response to Infection by Xanthomonas albilineans
Abstract
:1. Introduction
2. Results
2.1. Symptom Expression and Bacterial Population Size in Inoculated Sugarcane Leaves
2.2. RNA Sequencing and Assembly
2.3. Gene Annotation of Assembled Transcripts
2.4. Differential Expression Analysis of Assembled Transcripts
2.5. Gene Ontology Functional Analysis of Differentially Expressed Genes During Infection of Sugarcane by X. Albilineans
2.6. KEGG Enrichment Analysis of DEGs During Infection of Sugarcane by X. Albilineans
2.7. Transcriptional Expression of Ten Genes Involved in Different Plant Hormone Signal Transduction Pathways
3. Discussion
3.1. Global Patterns of Gene Transcription in Sugarcane in Response to Infection by X. Albilineans
3.2. Major Gene Categories Involved in Response of Sugarcane to Infection by X. Albilineans
3.3. Major Enriched KEGG Pathways Associated with the Response of Sugarcane to Infection by X. Albilineans
3.4. Plant Hormone Signal Transduction Pathways Involved in the Response of Sugarcane to Infection by X. Albilineans
4. Materials and Methods
4.1. Plant Growth and Inoculation with the Pathogen
4.2. Leaf Tissue Sampling
4.3. Quantification of Bacterial Populations in Inoculated Plants
4.4. Library Construction and Illumina RNA-Sequencing
4.5. De Novo Transcriptome Assembly
4.6. Differential Gene Expression Analysis and Function Annotation
4.7. Quantitative Real Time RT-PCR Analysis
4.8. Statistical Analyses
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Characteristics of Transcripts/Unigenes | Number of Transcripts (451,856,714 Nucleotides) | Number of Unigenes (429,371,352 Nucleotides) |
---|---|---|
200–500 bp length | 315,474 (51%) | 239,843 (45%) |
500 bp-1 kbp length | 164,820 (27%) | 162,182 (30%) |
1–2 kbp length | 100,096 (16%) | 99,766 (19%) |
˃2 kbp | 33,880 (5.5%) | 33,864 (6%) |
Total | 614,270 (100%) | 535,655 (100%) |
Minimum length (bp) | 201 | 201 |
Average length (bp) | 736 | 802 |
Median length (bp) | 487 | 555 |
Maximum length (bp) | 17,717 | 17,717 |
N50 (bp) a | 1045 | 1102 |
N90 (bp) b | 324 | 369 |
Gene ID | KEGG Orthology | Gene description | LCP 85-384 | ROC20 | |||||
---|---|---|---|---|---|---|---|---|---|
24 hpi | 48 hpi | 72 hpi | 24 hpi | 48 hpi | 72 hpi | ||||
Cluster-4871.238958 | K14484 | Auxin-responsive protein IAA (IAA) | 1.10 | 1.19 | 1.07 | 2.57 | 3.66 | 2.83 | |
Cluster-4871.233479 | K14487 | Auxin responsive GH3 gene family (GH3) | −1.26 | −0.63 | −0.61 | 0.08 | −0.04 | 0.26 | |
Cluster-4871.390584 | K14488 | SAUR family protein (SAUR) | 4.69 | 2.90 | 3.66 | −0.42 | −1.63 | 0.73 | |
Cluster-4871.255133 | K12126 | Phytochrome-interacting factor 3 (PIF3) | −0.34 | −0.45 | −1.03 | 2.27 | 2.27 | 1.65 | |
Cluster-4871.248068 | k14496 | Abscisic acid receptor PYR/PYL family (PYL) | 1.49 | 1.30 | 1.47 | 0.90 | 0.74 | 0.69 | |
Cluster-4871.245620 | K14498 | Serine/threonine-protein kinase SRK2 (SNRK2) | 1.49 | 1.30 | 1.47 | 0.90 | 0.74 | 0.69 | |
Cluster-4871.356618 | K14510 | Serine/threonine-protein kinase CTR1 (CTR1) | 2.51 | 2.05 | 1.85 | 1.39 | 0.45 | 0.31 | |
Cluster-4871.244221 | K14513 | Ethylene-insensitive protein 2 (EIN2) | −0.69 | −0.46 | −0.46 | −1.16 | −1.04 | −1.24 | |
Cluster-4871.211143 | K14506 | Jasmonic acid-amino synthetase (JAR1) | −0.27 | −0.03 | 0.38 | −1.62 | −1.73 | −1.90 | |
Cluster-4871.226184 | K14508 | Regulatory protein NPR1 (NPR1) | 2.92 | 3.69 | 4.46 | −0.91 | −0.59 | −0.55 |
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Ntambo, M.S.; Meng, J.-Y.; Rott, P.C.; Henry, R.J.; Zhang, H.-L.; Gao, S.-J. Comparative Transcriptome Profiling of Resistant and Susceptible Sugarcane Cultivars in Response to Infection by Xanthomonas albilineans. Int. J. Mol. Sci. 2019, 20, 6138. https://doi.org/10.3390/ijms20246138
Ntambo MS, Meng J-Y, Rott PC, Henry RJ, Zhang H-L, Gao S-J. Comparative Transcriptome Profiling of Resistant and Susceptible Sugarcane Cultivars in Response to Infection by Xanthomonas albilineans. International Journal of Molecular Sciences. 2019; 20(24):6138. https://doi.org/10.3390/ijms20246138
Chicago/Turabian StyleNtambo, Mbuya Sylvain, Jian-Yu Meng, Philippe C. Rott, Robert J. Henry, Hui-Li Zhang, and San-Ji Gao. 2019. "Comparative Transcriptome Profiling of Resistant and Susceptible Sugarcane Cultivars in Response to Infection by Xanthomonas albilineans" International Journal of Molecular Sciences 20, no. 24: 6138. https://doi.org/10.3390/ijms20246138