Identification and Characterization of microRNAs in the Gonads of Litopenaeus vannamei Using High-Throughput Sequencing
Abstract
:1. Introduction
2. Materials and Methods
2.1. Experimental Shrimp and Sample Preparation
2.2. Small RNA cDNA Library Construction by High-Throughput Sequencing
2.3. Bioinformatics Analysis
2.4. Stem-Loop RT-qPCR
3. Results
3.1. Determination of L. vannamei Sex and Development Stages Based on Gonad Sections
3.2. Summary of Sequencing Data in the Gonads of L. vannamei
3.3. Identification and Prediction of miRNAs in the L. vannamei Ovaries and Testes
3.4. Screening Differentially Expressed miRNAs in the Gonads of L. vannamei
3.5. The Differentially Expressed miRNAs Targets Prediction and Functional Annotation
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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miRNA id | Expression (Testis) | Expression (Ovary) | log2FoldChange (Ovary/Testis) |
---|---|---|---|
novel_mir23 | 6437.118799 | 0.508025321 | −13.62922707 |
miR-92b-3p_3 | 22,983.4716 | 1102.313603 | −4.381990104 |
miR-12-5p_2 | 969.0430681 | 217.7167985 | −2.154108059 |
novel_mir67 | 0.172733727 | 1287.990965 | 12.86428505 |
miR-279_1 | 418.747114 | 4246.721485 | 3.342198342 |
let-7-5p_6 | 414.5091587 | 28,964.08332 | 6.126717217 |
miR-263a-5p_1 | 5.9993158 | 156.8735167 | 4.708660031 |
MiRNAs | Mature Sequence (5′-3′) | Primer Sequences (5′-3′) | |
---|---|---|---|
novel_mir23 | GAGGACGUGGUAG CCUAGUGGU | Fwd | GCGGAGGACGTGGTAGCCT |
Rev | AGTGCAGGGTCCGAGGTATT | ||
Stem | GTCGTATCCAGTGCAGGGTC | ||
CGAGGTATTCGCACTGGATACGACACCACT | |||
miR-92b-3p_3 | AATTGCACTAGTC CCGGCCTGC | Fwd | GCGCGAAGCACAGCCC |
Rev | AGTGCAGGGTCCGAGGTATT | ||
Stem | GTCGTATCCAGTGCAGG | ||
GTCCGAGGTATTCGCACTGGATACGACGCGGCC | |||
miR-12-5p_2 | TGAGTATTACATC AGGTACTGGT | Fwd | GCGCGCGGAGAACACA |
Rev | AGTGCAGGGTCCGAGGTATT | ||
Stem | GTCGTATCCAGTGCAGG | ||
GTCCGAGGTATTCGCACTGGATACGACCCGTCC | |||
novel_mir67 | UGAUGAGGUCUU GUCGUGAGGAGU | Fwd | GCGTGATGAGGTCTTGTCGTG |
Rev | AGTGCAGGGTCCGAGGTATT | ||
Stem | GTCGTATCCAGTGCAGGGTCC | ||
GAGGTATTCGCACTGGATACGACACTCCT | |||
miR-279_1 | TGACTAGATCCAC ACTCATCCA | Fwd | CGCGCGGACAGACCACA |
Rev | AGTGCAGGGTCCGAGGTATT | ||
Stem | GTCGTATCCAGTGCAGGG | ||
TCCGAGGTATTCGCACTGGATACGACTGGTGG | |||
let-7-5p_6 | TGAGGTAGTAGGT TGTATAGTT | Fwd | GCGCGCGCGGAGGAGA |
Rev | AGTGCAGGGTCCGAGGTATT | ||
Stem | GTCGTATCCAGTGCAGG | ||
GTCCGAGGTATTCGCACTGGATACGACCTTCCC | |||
miR-263a-5p_1 | AATGGCACTGGAA GAATTCACGG | Fwd | CGCGAAGGCACGGAAGA |
Rev | AGTGCAGGGTCCGAGGTATT | ||
Stem | GTCGTATCCAGTGCAGGG | ||
TCCGAGGTATTCGCACTGGATACGACCCGTGT | |||
U6 | Fwd | CTCGCTTCGGCAGCACA | |
Rev | AACGCTTCACGAATTTGCGT |
miRNA_id | Source of Variance | Sum of Squares | Degrees of Freedom | Mean Square | F Value | p-Value |
---|---|---|---|---|---|---|
let-7-5p_6 | Regression | 11.54 | 3 | 3.846 | 275.5 | 0.000 |
Residual | 0.1117 | 8 | 0.01396 | |||
Total | 11.65 | 11 | ||||
miR-263a-5p_1 | Regression | 0.3094 | 3 | 0.1031 | 36.11 | 0.000 |
Residual | 0.02285 | 8 | 0.002856 | |||
Total | 0.3322 | 11 | ||||
miR-279_1 | Regression | 0.8922 | 3 | 0.2974 | 58.52 | 0.000 |
Residual | 0.04065 | 8 | 0.005082 | |||
Total | 0.9328 | 11 | ||||
novel_mir67 | Regression | 4.534 | 3 | 1.511 | 197.1 | 0.000 |
Residual | 0.06134 | 8 | 0.007667 | |||
Total | 4.596 | 11 | ||||
miR-12-5p_2 | Regression | 6.314 | 3 | 2.105 | 282.7 | 0.000 |
Residual | 0.05956 | 8 | 0.007445 | |||
Total | 6.374 | 11 | ||||
miR-92b-3p_3 | Regression | 63.06 | 3 | 21.02 | 3057 | 0.000 |
Residual | 0.05501 | 8 | 0.006877 | |||
Total | 63.11 | 11 | ||||
novel_mir23 | Regression | 26.51 | 3 | 8.837 | 280.5 | 0.000 |
Residual | 0.2521 | 8 | 0.03151 | |||
Total | 26.76 | 11 |
Pathway-Term | p-Value | q-Value | Pathway ID |
---|---|---|---|
IL-17 signaling pathway | 8.68 × 10−16 | 2.98 × 10−13 | ko04657 |
Hepatitis B | 3.42 × 10−7 | 5.87 × 10−5 | ko05161 |
Endocrine resistance | 8.08 × 10−7 | 9.24 × 10−5 | ko01522 |
Relaxin signaling pathway | 3.666 × 10−6 | 0.0003144 | ko04926 |
AGE-RAGE signaling pathway in diabetic complications | 4.594 × 10−6 | 0.0003152 | ko04933 |
Parathyroid hormone synthesis, secretion and action | 6.455 × 10−6 | 0.000369 | ko04928 |
Other glycan degradation | 1.177 × 10−5 | 0.0005062 | ko00511 |
Phospholipase D signaling pathway | 1.181 × 10−5 | 0.0005062 | ko04072 |
MicroRNAs in cancer | 1.905 × 10−5 | 0.0007261 | ko05206 |
Insulin resistance | 2.48 × 10−5 | 0.0008508 | ko04931 |
ECM-receptor interaction | 3.992 × 10−5 | 0.0012447 | ko04512 |
Human papillomavirus infection | 0.0001299 | 0.0034973 | ko05165 |
Amoebiasis | 0.0001325 | 0.0034973 | ko05146 |
Hedgehog signaling pathway | 0.0003282 | 0.0080415 | ko04340 |
Glycosaminoglycan biosynthesis—keratan sulfate | 0.0006459 | 0.0147702 | ko00533 |
Prostate cancer | 0.0011405 | 0.0241681 | ko05215 |
Protein digestion and absorption | 0.0012572 | 0.0241681 | ko04974 |
Cell adhesion molecules (CAMs) | 0.0012683 | 0.0241681 | ko04514 |
Insect hormone biosynthesis | 0.001342 | 0.0242271 | ko00981 |
Hepatitis C | 0.0014316 | 0.0245517 | ko05160 |
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Li, W.; He, P.; Zhang, X.; Guan, J.; Chen, Y.; Zhang, L.; Zhang, B.; Zheng, Y.; Li, X.; He, Q.; et al. Identification and Characterization of microRNAs in the Gonads of Litopenaeus vannamei Using High-Throughput Sequencing. Fishes 2022, 7, 308. https://doi.org/10.3390/fishes7060308
Li W, He P, Zhang X, Guan J, Chen Y, Zhang L, Zhang B, Zheng Y, Li X, He Q, et al. Identification and Characterization of microRNAs in the Gonads of Litopenaeus vannamei Using High-Throughput Sequencing. Fishes. 2022; 7(6):308. https://doi.org/10.3390/fishes7060308
Chicago/Turabian StyleLi, Wei, Pingping He, Xingzhi Zhang, Junliang Guan, Yongxian Chen, Li Zhang, Bin Zhang, Yusi Zheng, Xin Li, Qingsong He, and et al. 2022. "Identification and Characterization of microRNAs in the Gonads of Litopenaeus vannamei Using High-Throughput Sequencing" Fishes 7, no. 6: 308. https://doi.org/10.3390/fishes7060308
APA StyleLi, W., He, P., Zhang, X., Guan, J., Chen, Y., Zhang, L., Zhang, B., Zheng, Y., Li, X., He, Q., Liu, L., Yuan, C., Wei, P., & Peng, J. (2022). Identification and Characterization of microRNAs in the Gonads of Litopenaeus vannamei Using High-Throughput Sequencing. Fishes, 7(6), 308. https://doi.org/10.3390/fishes7060308