Identification of Long Non-Coding RNAs and the Regulatory Network Responsive to Arbuscular Mycorrhizal Fungi Colonization in Maize Roots
Abstract
:1. Introduction
2. Results
2.1. Phenotypic Responses of Maize Seedlings to AM Fungus
2.2. Ultra-Deep RNA Sequencing and Mapping onto Reference Genome
2.3. Gene Ontology (GO) Term and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Enrichment Analyses of Identified DEGs
2.4. Identification and Characterization of Novel LncRNAs
2.5. Putative Target Genes of Differentially Expressed lncRNAs (DELs)
2.6. Regulatory Network of DELs
2.7. Putative Vital DELs
2.8. Real-Time PCR Verification of Five DEGs and DELs
3. Discussion
4. Materials and Methods
4.1. Plant Symbiosis with AM Fungus
4.2. RNA Extraction and Total RNA-Seq Sequencing
4.3. Pipelines for Differentially Expressed Genes (DEGs) and Novel LncRNAS Identification
4.4. Prediction of Putative Cis- and Trans-targets of DELs
4.5. GO and KEGG Pathway Enrichment Analyses
4.6. Construction of the Regulatory Network
4.7. Validation of DEGs and DELs by Quantitative RT-PCR
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Sample. | Raw Reads | Number of Clean Reads | Uniquely Mapped Reads Number | Uniquely Mapped Reads (%) | Reads Mapped to Multiple Loci (%) | Reads Unmapped: Too Short (%) |
---|---|---|---|---|---|---|
40-CK-1 | 43,293,767 | 37,470,252 | 23,577,438 | 62.92 | 5.18 | 31.90 |
40-CK-2 | 53,402,529 | 46,776,062 | 32,169,682 | 68.77 | 4.52 | 26.71 |
40-CK-3 | 55,730,952 | 49,755,232 | 32,920,777 | 66.17 | 4.89 | 28.95 |
40-GI-1 | 51,811,515 | 44,618,959 | 26,549,282 | 59.50 | 4.52 | 35.98 |
40-GI-2 | 57,804,926 | 49,070,512 | 31,196,619 | 63.58 | 4.06 | 32.36 |
40-GI-3 | 53,450,977 | 46,286,135 | 30,037,248 | 64.89 | 4.10 | 31.01 |
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Han, G.; Cheng, C.; Zheng, Y.; Wang, X.; Xu, Y.; Wang, W.; Zhu, S.; Cheng, B. Identification of Long Non-Coding RNAs and the Regulatory Network Responsive to Arbuscular Mycorrhizal Fungi Colonization in Maize Roots. Int. J. Mol. Sci. 2019, 20, 4491. https://doi.org/10.3390/ijms20184491
Han G, Cheng C, Zheng Y, Wang X, Xu Y, Wang W, Zhu S, Cheng B. Identification of Long Non-Coding RNAs and the Regulatory Network Responsive to Arbuscular Mycorrhizal Fungi Colonization in Maize Roots. International Journal of Molecular Sciences. 2019; 20(18):4491. https://doi.org/10.3390/ijms20184491
Chicago/Turabian StyleHan, Guomin, Chen Cheng, Yanmei Zheng, Xuewen Wang, Yunjian Xu, Wei Wang, Suwen Zhu, and Beijiu Cheng. 2019. "Identification of Long Non-Coding RNAs and the Regulatory Network Responsive to Arbuscular Mycorrhizal Fungi Colonization in Maize Roots" International Journal of Molecular Sciences 20, no. 18: 4491. https://doi.org/10.3390/ijms20184491