Identification and Characterization of Salt-Responsive MicroRNAs in Vicia faba by High-Throughput Sequencing
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials, Growth Conditions, and Salt Stress Treatments
2.2. sRNA Library Construction and Sequencing
2.3. Data Filtering and Mapping Reads
2.4. Classification of sRNAs
2.5. Predictions of sRNAs
2.6. Analyzing sRNA Expression
2.7. Target Prediction
2.8. Screening the Differentially Expressed sRNAs (DESs)
2.9. GO Enrichment Analysis
2.10. Pathway Enrichment Analysis
3. Results
3.1. sRNA Sequencing
3.2. Annotation of sRNAs and miRNA Identification
3.3. Identification of Differentially Expressed miRNAs
3.4. Target Prediction and Functional Analysis of the miRNAs
4. Discussion
Salt Stress-Responsive miRNAs and Their Targets in Faba Bean
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Sample Name | Sequence Type | Raw Tag Count | Clean Tag Count | Percentage (%) | Number of Mapped Tags | Percentage (%) |
---|---|---|---|---|---|---|
HC-4 | SE50 | 51420111 | 47942551 | 93.24 | 36387118 | 75.9 |
HSA | SE50 | 43734868 | 40682196 | 93.02 | 26272525 | 64.58 |
IC-1 | SE50 | 48229628 | 43865674 | 90.95 | 21451106 | 48.9 |
IS-4 | SE50 | 53763194 | 41563472 | 77.31 | 20568122 | 49.49 |
Type | HC-4 | HSA | IC-1 | IS-1 | ||||
---|---|---|---|---|---|---|---|---|
Count | (%) | Count | (%) | Count | (%) | Count | (%) | |
Total | 47942551 | 100 | 40682196 | 100 | 43865674 | 100 | 41563472 | 100 |
Intergenic | 9985569 | 20.83 | 10292988 | 25.3 | 9475423 | 21.6 | 8197558 | 19.72 |
Mature (miRNA) | 3224519 | 6.73 | 1653404 | 4.06 | 6841472 | 15.6 | 5633410 | 13.55 |
Rfam other sncRNA | 73325 | 0.15 | 94167 | 0.23 | 24135 | 0.06 | 35172 | 0.08 |
snRNA | 1405 | 0 | 4831 | 0.01 | 2381 | 0.01 | 959 | 0 |
unmap | 11040957 | 23.03 | 13725210 | 33.74 | 21005681 | 47.89 | 20270917 | 48.77 |
rRNA | 1773606 | 3.7 | 1100198 | 2.7 | 244021 | 0.56 | 358242 | 0.86 |
Hairpin | 38 | 0 | 9 | 0 | 80 | 0 | 147 | 0 |
snoRNA | 30566 | 0.06 | 14138 | 0.03 | 9971 | 0.02 | 6058 | 0.01 |
Precursor | 27019 | 0.06 | 11116 | 0.03 | 24531 | 0.06 | 40935 | 0.1 |
Repeat | 21771765 | 45.41 | 13683732 | 33.64 | 6237390 | 14.22 | 7018371 | 16.89 |
tRNA | 13782 | 0.03 | 102403 | 0.25 | 589 | 0 | 1703 | 0 |
Sample | Known miRNA Count | Novel miRNA Count | Known piRNA Count | Novel piRNA Count | Known siRNA Count | Novel siRNA Count |
---|---|---|---|---|---|---|
IS-4 | 1301 | 51 | 0 | 0 | 0 | 2578 |
HSA | 1118 | 38 | 0 | 0 | 0 | 1879 |
HC-4 | 1018 | 44 | 0 | 0 | 0 | 1919 |
IC-1 | 1465 | 48 | 0 | 0 | 0 | 2241 |
Conserved miRNA Family | DESs in HC-4-vs.-HSA (Sensitive Genotype) | DESs in IC-1-vs.-IS-4 (Tolerant Genotype) | Target Gene Family | ||
---|---|---|---|---|---|
Number of Upregulated Members | Number of Downregulated Members | Number of Upregulated Members | Number of Downregulated Members | ||
miRNA156 | 20 | 6 | 11 | 7 | Squamosa promoter-binding proteins |
miRNA157 | 2 | 1 | 2 | 1 | Squamosa promoter-binding proteins |
miRNA159 | 27 | 8 | 8 | 28 | MYB transcription factors/TCP transcription factors |
miRNA160 | 4 | 4 | 11 | 43 | Auxin Response factors |
miRNA162 | 9 | 3 | 8 | 8 | Dicer Like protein/E3 ubiquitin-protein ligase RNF144A-like isoform X1 |
miRNA164 | 3 | 2 | 12 | 33 | NAC domain protein/NAC transcription factor-like protein |
miRNA165 | 0 | 1 | 2 | 2 | Homeo domain-Zip transcription factors/homeobox-leucine zipper protein ATHB-14-like/bZIP transcription factor |
miRNA166 | 39 | 91 | 82 | 80 | Homeobox-leucine zipper protein ATHB-15-like isoform X2/bZIP transcription factor |
miRNA167 | 38 | 26 | 27 | 31 | Transmembrane protein, putative/translation initiation factor eIF-2B delta subunit |
miRNA168 | 19 | 13 | 24 | 9 | Argonautes/protamine P1 family protein |
miRNA169 | 3 | 1 | 2 | 4 | HAP2/NFY transcription factors/CCAAT-binding transcription factor |
miRNA171 | 19 | 14 | 12 | 42 | Scarecrow-like transcription factors/GRAS family transcription regulator |
miRNA172 | 1 | 0 | 0 | 1 | AP2 domain transcription factors/AP2-like ethylene-responsive transcription factor/myb-like transcription factor family protein |
miRNA319 | 6 | 3 | 6 | 12 | MYB transcription factors/TCP transcription factors |
miRNA390 | 3 | 8 | 4 | 5 | TAS3-primary transcripts/LRR receptor-like kinase family protein |
miRNA391 | 1 | 0 | 0 | 1 | TAS3-primary transcripts/zinc finger CCCH domain protein |
miRNA393 | 8 | 1 | 2 | 2 | F-Box protein/transport inhibitor response 1 protein/Ubiquitin |
miRNA394 | 2 | 0 | 2 | 2 | F-Box protein/Zinc finger CCCH domain-containing protein ZFN-like |
miRNA396 | 36 | 16 | 31 | 26 | Growth regulating factors/F-box protein interaction domain protein /BZIP transcription factor bZIP80 |
miRNA397 | 2 | 2 | 4 | 4 | Laccases |
miRNA398 | 2 | 7 | 3 | 13 | Cu/Zn superoxide dismutases (CSD)/BAG family molecular chaperone regulator-like protein |
miRNA399 | 3 | 3 | 8 | 4 | Phosphate transporter/ubiquitin-conjugating enzyme E2/OBP3-responsive protein |
miRNA408 | 1 | 6 | 16 | 5 | Plantacyanins/uclacyanin-2-like/basic blue-like protein |
miRNA2111 | 2 | 5 | 6 | 2 | DNA replication factor CDT1-like protein/calcineurin-like phosphoesterase, family protein |
miRNA482 | 0 | 2 | 1 | 1 |
miRNA ID | Count (HC-4) | Count (HSA) | TPM (HC-4) | TPM (HSA) | log2 Ratio (HSA/HC-4) | Regulation Profile (Up/Down) (HSA/HC-4) | p-Value | FDR |
---|---|---|---|---|---|---|---|---|
novel_mir1 | 193 | 869 | 5.12 | 31.31 | 2.612408 | Up | 1.81E-153 | 2.31 × 10−152 |
novel_mir5 | 24 | 124 | 0.64 | 4.47 | 2.804131 | Up | 3.67E-25 | 2.05 × 10−24 |
novel_mir6 | 0 | 48 | 0.001 | 1.73 | 10.75656 | Up | 1.12E-18 | 5.58 × 10−18 |
novel_mir7 | 227 | 1120 | 6.02 | 40.35 | 2.744733 | Up | 1.78E-208 | 2.63 × 10−207 |
novel_mir9 | 0 | 82 | 0.001 | 2.95 | 11.5265 | Up | 2.42E-31 | 1.47 × 10−30 |
novel_mir10 | 14 | 894 | 0.37 | 32.21 | 6.44384 | Up | 8.00E-307 | 1.47 × 10−305 |
novel_mir13 | 33 | 115 | 0.88 | 4.14 | 2.234055 | Up | 2.47E-18 | 1.21 × 10−17 |
novel_mir16 | 17 | 597 | 0.45 | 21.51 | 5.578939 | Up | 1.75E-194 | 2.51 × 10−193 |
novel_mir17 | 491 | 794 | 13.03 | 28.61 | 1.134682 | Up | 2.99E-44 | 2.03 × 10−43 |
novel_mir19 | 39 | 81 | 1.03 | 2.92 | 1.503324 | Up | 3.24E-08 | 1.14 × 10−7 |
novel_mir22 | 11 | 32 | 0.29 | 1.15 | 1.987509 | Up | 2.35E-05 | 7.14 × 10−5 |
novel_mir29 | 82 | 180 | 2.18 | 6.49 | 1.57389 | Up | 9.97E-18 | 4.82 × 10−17 |
novel_mir37 | 492 | 817 | 13.06 | 29.43 | 1.172133 | Up | 6.79E-48 | 4.77 × 10−47 |
novel_mir38 | 6941 | 74963 | 184.18 | 2700.76 | 3.874177 | Up | 0 | 0 |
novel_mir39 | 164 | 1013 | 4.35 | 36.5 | 3.068809 | Up | 2.05E-212 | 3.08 × 10−211 |
novel_mir40 | 31 | 86 | 0.82 | 3.1 | 1.918572 | Up | 1.06E-11 | 4.35 × 10−11 |
novel_mir41 | 114 | 2010 | 3.02 | 72.42 | 4.583768 | Up | 0 | 0 |
novel_mir42 | 259 | 1808 | 6.87 | 65.14 | 3.245162 | Up | 0 | 0 |
novel_mir43 | 50 | 130 | 1.33 | 4.68 | 1.815082 | Up | 6.45E-16 | 3 × 10−15 |
novel_mir45 | 736 | 2609 | 19.53 | 94 | 2.266969 | Up | 0 | 0 |
novel_mir46 | 143 | 220 | 3.79 | 7.93 | 1.065123 | Up | 3.38E-12 | 1.41 × 10−11 |
novel_mir48 | 919 | 1754 | 24.39 | 63.19 | 1.373407 | Up | 9.10E-129 | 1.04 × 10−127 |
novel_mir8 | 50 | 0 | 1.33 | 0.001 | −10.3772 | Down | 1.20E-12 | 5.13 × 10−12 |
novel_mir11 | 926 | 75 | 24.57 | 2.7 | −3.18587 | Down | 4.68E-136 | 5.50 × 10−135 |
novel_mir15 | 35 | 0 | 0.93 | 0.001 | −9.86109 | Down | 4.71E-09 | 1.73 × 10−8 |
novel_mir20 | 35 | 0 | 0.93 | 0.001 | −9.86109 | Down | 4.71E-09 | 1.74 × 10−8 |
novel_mir23 | 794 | 252 | 21.07 | 9.08 | −1.21443 | Down | 3.39E-35 | 2.17 × 10−34 |
novel_mir25 | 59 | 0 | 1.57 | 0.001 | −10.6165 | Down | 8.33E-15 | 3.76 × 10−14 |
novel_mir27 | 2970 | 65 | 78.81 | 2.34 | −5.0738 | Down | 0 | 0 |
novel_mir28 | 16 | 0 | 0.42 | 0.001 | −8.71425 | Down | 0.000168 | 0.000477 |
novel_mir33 | 709 | 173 | 18.81 | 6.23 | −1.5942 | Down | 1.26E-46 | 8.65 × 10−46 |
novel_mir34 | 479 | 22 | 12.71 | 0.79 | −4.00797 | Down | 1.78E-85 | 1.64 × 10−84 |
novel_mir36 | 41 | 0 | 1.09 | 0.001 | −10.0901 | Down | 1.72E-10 | 6.84 × 10−10 |
novel_mir44 | 34 | 0 | 0.9 | 0.001 | −9.81378 | Down | 8.17E-09 | 2.97 × 10−8 |
novel_mir53 | 230 | 47 | 6.1 | 1.69 | −1.85179 | Down | 1.71E-19 | 8.64 × 10−19 |
miRNA ID | Count (IC-1) | Count (IS-4) | TPM (IC-1) | TPM (IS-4) | log2 Ratio (IS-4/IC-1) | Regulation Profile (up/down) (IC-1 vs IS-4) | p-Value | FDR |
---|---|---|---|---|---|---|---|---|
novel_mir6 | 44 | 256 | 1.87 | 11.62 | 2.6354999 | Up | 7.82× 10−41 | 4.42 × 10−40 |
novel_mir8 | 338 | 6850 | 14.38 | 310.9 | 4.434315 | Up | 0 | 0 |
novel_mir9 | 0 | 207 | 0.001 | 9.4 | 13.198445 | Up | 5.11 × 10−66 | 3.49 × 10−65 |
novel_mir18 | 0 | 188 | 0.001 | 8.53 | 13.05833 | Up | 5.02 × 10−60 | 3.27 × 10−59 |
novel_mir19 | 200 | 1538 | 8.51 | 69.81 | 3.0362027 | Up | 3.94 × 10−275 | 5.07 × 10−274 |
novel_mir22 | 0 | 587 | 0.001 | 26.64 | 14.701306 | Up | 7.53 × 10−186 | 7.83 × 10−185 |
novel_mir30 | 0 | 200 | 0.001 | 9.08 | 13.148477 | Up | 8.25 × 10−64 | 5.54 × 10−63 |
novel_mir36 | 163 | 496 | 6.93 | 22.51 | 1.6996388 | Up | 5.04 × 10−45 | 2.99 × 10−44 |
novel_mir39 | 134 | 453 | 5.7 | 20.56 | 1.8508064 | Up | 2.78 × 10−46 | 1.67 × 10−45 |
novel_mir42 | 192 | 1707 | 8.17 | 77.48 | 3.245416 | Up | 0 | 0 |
novel_mir5 | 347 | 663 | 14.76 | 30.09 | 1.0275914 | Up | 2.31 × 10−28 | 1.10 × 10−27 |
novel_mir13 | 1404 | 298 | 59.72 | 13.53 | −2.1420523 | Down | 2.13 × 10−156 | 1.98 × 10−155 |
novel_mir14 | 62 | 10 | 2.64 | 0.45 | −2.552541 | Down | 8.44 × 10−10 | 2.72 × 10−9 |
novel_mir16 | 116 | 42 | 4.93 | 1.91 | −1.368015 | Down | 2.42 × 10−8 | 7.48 × 10−8 |
novel_mir20 | 254 | 60 | 10.8 | 2.72 | −1.9893528 | Down | 4.41 × 10−27 | 2.07 × 10−26 |
novel_mir27 | 10812 | 1387 | 459.9 | 62.95 | −2.8690419 | Down | 0 | 0 |
novel_mir29 | 1387 | 564 | 59 | 25.6 | −1.2045711 | Down | 1.14 × 10−68 | 7.94 × 10−68 |
novel_mir31 | 245 | 75 | 10.42 | 3.4 | −1.6157486 | Down | 4.83 × 10−20 | 1.98 × 10−19 |
novel_mir32 | 4098 | 1680 | 174.31 | 76.25 | −1.1928461 | Down | 3.81 × 10−196 | 4.01 × 10−195 |
novel_mir33 | 1370 | 157 | 58.27 | 7.13 | −3.0307793 | Down | 2.35 × 10−225 | 2.65 × 10−224 |
novel_mir4 | 165 | 11 | 7.02 | 0.5 | −3.811471 | Down | 1.52 × 10−34 | 7.93 × 10−34 |
novel_mir40 | 451 | 39 | 19.18 | 1.77 | −3.4377815 | Down | 1.63 × 10−84 | 1.22 × 10−83 |
novel_mir44 | 240 | 0 | 10.21 | 0.001 | −13.317695 | Down | 1.24 × 10−69 | 8.68 × 10−69 |
novel_mir46 | 759 | 263 | 32.28 | 11.94 | −1.4348377 | Down | 1.01 × 10−49 | 6.25 × 10−49 |
novel_mir48 | 6461 | 707 | 274.83 | 32.09 | −3.0983438 | Down | 0 | 0 |
novel_mir50 | 5351 | 1112 | 227.61 | 50.47 | −2.173066 | Down | 0 | 0 |
novel_mir52 | 450 | 116 | 19.14 | 5.26 | −1.8634561 | Down | 5.42 × 10−43 | 3.15 × 10−42 |
novel_mir53 | 871 | 180 | 37.05 | 8.17 | −2.1810656 | Down | 6.75 × 10−100 | 5.38 × 10−99 |
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Alzahrani, S.M.; Alaraidh, I.A.; Khan, M.A.; Migdadi, H.M.; Alghamdi, S.S.; Alsahli, A.A. Identification and Characterization of Salt-Responsive MicroRNAs in Vicia faba by High-Throughput Sequencing. Genes 2019, 10, 303. https://doi.org/10.3390/genes10040303
Alzahrani SM, Alaraidh IA, Khan MA, Migdadi HM, Alghamdi SS, Alsahli AA. Identification and Characterization of Salt-Responsive MicroRNAs in Vicia faba by High-Throughput Sequencing. Genes. 2019; 10(4):303. https://doi.org/10.3390/genes10040303
Chicago/Turabian StyleAlzahrani, Saud M., Ibrahim A. Alaraidh, Muhammad A. Khan, Hussein M. Migdadi, Salem S. Alghamdi, and Abdluaziz A. Alsahli. 2019. "Identification and Characterization of Salt-Responsive MicroRNAs in Vicia faba by High-Throughput Sequencing" Genes 10, no. 4: 303. https://doi.org/10.3390/genes10040303
APA StyleAlzahrani, S. M., Alaraidh, I. A., Khan, M. A., Migdadi, H. M., Alghamdi, S. S., & Alsahli, A. A. (2019). Identification and Characterization of Salt-Responsive MicroRNAs in Vicia faba by High-Throughput Sequencing. Genes, 10(4), 303. https://doi.org/10.3390/genes10040303