Genome-Wide Characterization of Salt-Responsive miRNAs, circRNAs and Associated ceRNA Networks in Tomatoes
Abstract
:1. Introduction
2. Results
2.1. Small RNA Sequencing of Tomato Roots
2.2. Identification and Characterization of Salt-Responsive miRNAs in Tomatoes
2.3. Prediction and Functional Category of the Putative Target Genes of Salt-Responsive miRNAs
2.4. Validation of Salt-Responsive miRNAs
2.5. Identification and Characterization of Salt-Responsive mRNAs and CircRNAs
2.6. GO and KEGG Analysis of Differentially Expressed mRNAs
2.7. Construction of Salt-Responsive circRNA–miRNA–mRNA Networks
3. Discussion
3.1. Analysis of Salt-Responsive mRNAs in Tomatoes
3.2. miRNAs Play Crucial Roles in Tomatoes under Salt Stress
3.3. ceRNA Networks Could Shed New Light on the Regulatory Roles of ncRNAs
4. Materials and Methods
4.1. Plant Materials and Preparation
4.2. Small RNA Sequencing and Identification of DE-miRNAs
4.3. Prediction and Annotation of Potential Target Genes of DE-miRNAs
4.4. Validation of miRNAs by qRT-PCR
4.5. Strand-Specific RNA Sequencing and Identification of Differentially Expressed mRNAs and circRNAs
4.6. Construction of the circRNA–miRNA–mRNA Networks
4.7. GO and KEGG Pathway Analyses of mRNAs in the CeRNA Networks
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Samples 1 | Raw Reads | Clean Reads | Length (18–30 nt) | Q20 (%) | Q30 (%) | GC (%) |
---|---|---|---|---|---|---|
MCK1 | 19,164,692 | 18,960,794 | 16,466,635 | 99.38 | 98.35 | 51 |
MCK2 | 18,813,751 | 18,678,235 | 13,675,379 | 99.59 | 98.72 | 52 |
PCK1 | 18,479,610 | 18,396,518 | 13,819,122 | 99.56 | 98.64 | 55 |
PCK2 | 20,555,858 | 20,428,981 | 17,783,906 | 99.59 | 98.70 | 54 |
MT1 | 21,729,061 | 21,590,130 | 15,863,323 | 99.55 | 98.62 | 50 |
MT2 | 26,172,258 | 25,926,977 | 21,979,146 | 99.50 | 98.52 | 49 |
PT1 | 19,849,787 | 19,700,143 | 15,616,279 | 99.57 | 98.65 | 52 |
PT2 | 19,518,318 | 19,345,616 | 13,681,724 | 99.58 | 98.69 | 51 |
Samples 1 | Read Number | Base Number | GC Content (%) | Q30 (%) |
---|---|---|---|---|
M82-CK1 | 136,735,222 | 10,287,608,907 | 45 | 89.42 |
M82-CK2 | 122,505,086 | 9,237,784,418 | 45 | 87.07 |
M82-CK3 | 127,746,338 | 9,622,066,421 | 45 | 88.25 |
P-CK1 | 123,116,402 | 9,272,390,810 | 44 | 89.71 |
P-CK2 | 132,255,878 | 9,958,938,470 | 43 | 88.65 |
P-CK3 | 128,380,664 | 9,668,085,519 | 43 | 89.25 |
M82-T1 | 151,887,684 | 11,430,890,506 | 45 | 89.05 |
M82-T2 | 147,518,380 | 11,100,219,513 | 47 | 88.41 |
M82-T3 | 150,787,186 | 11,347,268,749 | 46 | 88.80 |
P-T1 | 110,834,866 | 8,292,641,368 | 43 | 89.71 |
P-T2 | 160,240,518 | 11,989,101,650 | 43 | 86.94 |
P-T3 | 148,489,644 | 11,109,924,975 | 43 | 88.08 |
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Wang, Z.; Li, N.; Yu, Q.; Wang, H. Genome-Wide Characterization of Salt-Responsive miRNAs, circRNAs and Associated ceRNA Networks in Tomatoes. Int. J. Mol. Sci. 2021, 22, 12238. https://doi.org/10.3390/ijms222212238
Wang Z, Li N, Yu Q, Wang H. Genome-Wide Characterization of Salt-Responsive miRNAs, circRNAs and Associated ceRNA Networks in Tomatoes. International Journal of Molecular Sciences. 2021; 22(22):12238. https://doi.org/10.3390/ijms222212238
Chicago/Turabian StyleWang, Zhongyu, Ning Li, Qinghui Yu, and Huan Wang. 2021. "Genome-Wide Characterization of Salt-Responsive miRNAs, circRNAs and Associated ceRNA Networks in Tomatoes" International Journal of Molecular Sciences 22, no. 22: 12238. https://doi.org/10.3390/ijms222212238