Functional Analysis of Long Non-Coding RNAs Reveal Their Novel Roles in Biocontrol of Bacteria-Induced Tomato Resistance to Meloidogyne incognita
Abstract
:1. Introduction
2. Results
2.1. Inducement Mechanisms of Sneb821
2.2. Sequencing and Characteristics of Transcripts
2.3. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) Analysis
2.4. Construction of the CeRNA Network and Predicted Interaction between lncRNAs, miRNAs, and mRNAs
2.5. Verification of Differentially Expressed lncRNAs
2.6. Function Verification of lncRNAs
3. Discussion
3.1. ROS Participate in Sneb821-induced Tomato Resistance to M. incognita
3.2. Certain lncRNAs Participate in Sneb821-induced Tomato Resistance to M. incognita
3.3. Inducement Resistance Function in lncRNAs through the ceRNA Network
3.4. lncRNA48734 and lncRNA44664 in Sneb821-induced Tomato Resistance to M. incognita
4. Materials and Methods
4.1. Plant Materials, Biocontrol Bacteria and Nematode Inoculum
4.2. RNA Extraction and Library Construction
4.3. lncRNA Analysis
4.4. RT-PCR Validation
4.5. Quantitative Real-Time PCR Validation
4.6. Prediction of lncRNA Targets and miRNA eTMs from mRNA
4.7. ceRNA Network Analysis
4.8. GO and KEGG Pathway Analysis
4.9. Transient Overexpression and Agrobacteria Infiltration
4.10. ROS Level Determination and DAB Staining
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
lncRNA | Long non-coding RNA |
siRNA | Small interfering RNA |
miRNA | MicroRNA |
tasiRNA | Trans-acting siRNA |
RKN | Root-knot nematode |
GRF | Growth-regulating factors |
SPL | Squamosal promoter-binding protein-like |
ORF | Open reading frame |
JA | Jasmonate acid |
TOE1 | Target of early activation tagged 1 |
FT | Flowering locus T |
PGPR | Plant growth-promoting rhizobacteria |
ROS | Reactive oxygen species |
ceRNA | Competing endogenous RNA |
TCS | Two-component system |
J2 | Second-stage juvenile |
J3 | Third-stage juvenile |
dpi | Days post-inoculation |
GUS | β-Glucuronidase |
NB | Nutrient broth |
qRT-PCR | Quantitative real-time PCR |
GO | Gene ontology |
KEGG | Kyoto encyclopedia of genes and genomes |
CaMV | Cauliflower mosaic virus |
SOD | Superoxide |
POD | Peroxidase |
DAB | Diaminobenzidine |
eTMs | Endogenous target mimics |
CSD | Cu/Zn-superoxide dismutase |
HR | Hypersensitive response |
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Sample | Clean Reads | Mapped Reads | Mapped Ratio |
---|---|---|---|
RKNT 1 | 123068008 | 108742693 | 88.36% |
RKNT 2 | 118020220 | 105048103 | 89.01% |
RKNT 3 | 129145372 | 114727340 | 88.84% |
Sneb821T1 | 115966444 | 104203875 | 89.86% |
Sneb821T 2 | 126689802 | 114918861 | 90.71% |
Sneb821T 3 | 109378368 | 99030869 | 90.54% |
lncRNA | mRNA | GO Terms | KEGG Pathway |
---|---|---|---|
lncRNA18894 | Solyc04g073990.2.1 | transferase activity | - |
lncRNA21563 | Solyc08g079800.2.1 | - | plant hormone signal transduction |
lncRNA24059 | Solyc12g043100.1.1 | - | endocytosis |
lncRNA25797 | Solyc10g005130.2.1 | DNA binding | - |
lncRNA35115 | Solyc04g049800.2.1 | transcription cofactor activity | - |
lncRNA39939 | Solyc02g069710.2.1 | - | ribosome |
Solyc02g032200.2.1 | - | plant-pathogen interaction | |
lncRNA8668 | Solyc10g005240.2.1 | - | biosynthesis of amino acids |
lncRNA44664 | Solyc10g083510.1.1 | cell proliferation | - |
lncRNA45969 | Solyc06g065850.2.1 | - | biosynthesis of amino acids |
lncRNA48734 | Solyc05g012040.2.1 | - | oxidative phosphorylation |
Solyc09g098130.1.1 | - | plant-pathogen interaction | |
lncRNA51612 | Solyc06g071180.2.1 | - | spliceosome |
lncRNA7183 | Solyc02g063170.2.1 | cell death | - |
lncRNA | miRNA | mRNA | Annotation |
---|---|---|---|
lncRNA18894 | miR167b-5p | Solyc04g073990.2.1 | Annexin |
lncRNA21563 | miR5303 | Solyc08g079800.2.1 | Growth-regulating factor 12 |
lncRNA24059 | miR162 | Solyc12g043100.1.1 | Pentatricopeptide repeat-containing protein |
lncRNA25797 | miR162 | Solyc10g005130.2.1 | Dicer double-stranded RNA-binding fold |
lncRNA35115 | miR172a | Solyc04g049800.2.1 | AP2-like ethylene-responsive transcription factor |
lncRNA39939 | miR396a-3p | Solyc02g069710.2.1 | Sodium/calcium exchanger protein |
Solyc02g032200.2.1 | Tir-lrr, resistance protein fragment | ||
lncRNA8668 | unconservative_6_25673 | Solyc10g005240.2.1 | Transcription factor Myb |
lncRNA44664 | miR396a-5p | Solyc10g083510.1.1 | Growth-regulating factor 2 |
lncRNA45969 | miR1919a | Solyc06g065850.2.1 | Flotillin domain protein |
lncRNA48734 | miR156d-5p | Solyc05g012040.2.1 | Squamosa promoter binding protein 3 |
Solyc09g098130.1.1 | Cc-nbs-lrr, resistance protein | ||
lncRNA51612 lncRNA7183 | miR396a-3p unconservative_11_40977 | Solyc06g071180.2.1 Solyc02g063170.2.1 | Dynein light chain 1 cytoplasmic Homology |
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Yang, F.; Zhao, D.; Fan, H.; Zhu, X.; Wang, Y.; Liu, X.; Duan, Y.; Xuan, Y.; Chen, L. Functional Analysis of Long Non-Coding RNAs Reveal Their Novel Roles in Biocontrol of Bacteria-Induced Tomato Resistance to Meloidogyne incognita. Int. J. Mol. Sci. 2020, 21, 911. https://doi.org/10.3390/ijms21030911
Yang F, Zhao D, Fan H, Zhu X, Wang Y, Liu X, Duan Y, Xuan Y, Chen L. Functional Analysis of Long Non-Coding RNAs Reveal Their Novel Roles in Biocontrol of Bacteria-Induced Tomato Resistance to Meloidogyne incognita. International Journal of Molecular Sciences. 2020; 21(3):911. https://doi.org/10.3390/ijms21030911
Chicago/Turabian StyleYang, Fan, Dan Zhao, Haiyan Fan, Xiaofeng Zhu, Yuanyuan Wang, Xiaoyu Liu, Yuxi Duan, Yuanhu Xuan, and Lijie Chen. 2020. "Functional Analysis of Long Non-Coding RNAs Reveal Their Novel Roles in Biocontrol of Bacteria-Induced Tomato Resistance to Meloidogyne incognita" International Journal of Molecular Sciences 21, no. 3: 911. https://doi.org/10.3390/ijms21030911