miRNA–mRNA Integrated Analysis Reveals Roles for miRNAs in a Typical Halophyte, Reaumuria soongorica, during Seed Germination under Salt Stress
Abstract
:1. Introduction
2. Results
2.1. Summary of the Small-RNA Library Dataset Obtained from Deep Sequencing of R. soongorica
2.2. Identification of Conserved miRNAs from Known Families
2.3. Discovery of Novel miRNAs in R. soongorica Seeds
2.4. Differential Expression of miRNAs during Germination of R. soongorica Seeds Exposed to Various Salt Treatments
2.5. miRNA and mRNA Correlation Analysis
3. Discussion
4. Materials and Methods
4.1. Plant Material and Salt-Stress Treatment
4.2. Small-RNA Library Construction and Sequencing
4.3. Identification of Conserved and Novel miRNAs
4.4. Relative Expression between miRNA Libraries
4.5. Prediction of miRNA Target Genes
4.6. miRNA and mRNA Correlation Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Category | Raw Reads | N% > 10% | Low Quality Reads | 5′ Adapter Contamine | 3′ Adapter Null | Poly (A/T/G/C) | Unique Reads | Clean Reads |
---|---|---|---|---|---|---|---|---|
CS-1 | 13,869,156 (100.00%) | 564 (0.00%) | 19,225 (0.14%) | 33,490 (0.24%) | 224,816 (1.62%) | 12,005 (0.09%) | 1,315,057 | 13,579,056 (97.91%) |
CS-2 | 16,819,324 (100.00%) | 639 (0.00%) | 21,867 (0.13%) | 15,406 (0.09%) | 964,063 (5.73%) | 7615 (0.05%) | 1,376,042 | 15,809,734 (94.00%) |
CS-3 | 14,212,954 (100.00%) | 543 (0.00%) | 16,330 (0.11%) | 14,962 (0.11%) | 398,880 (2.81%) | 7654 (0.05%) | 1,156,054 | 13,774,585 (96.92%) |
LS-1 | 14,552,453 (100.00%) | 527 (0.00%) | 18,159 (0.12%) | 13,581 (0.09%) | 702,302 (4.83%) | 4291 (0.03%) | 993,154 | 13,813,593 (94.92%) |
LS-2 | 12,328,793 (100.00%) | 451 (0.00%) | 19,864 (0.16%) | 13,884 (0.11%) | 179,427 (1.46%) | 7466 (0.06%) | 1,442,730 | 12,107,701 (98.21%) |
LS-3 | 13,908,660 (100.00%) | 504 (0.00%) | 15,636 (0.11%) | 11,487 (0.08%) | 290,553 (2.09%) | 4276 (0.03%) | 818,193 | 13,586,204 (97.68%) |
MS-1 | 12,887,720 (100.00%) | 535 (0.00%) | 19,878 (0.15%) | 8991 (0.07%) | 270,670 (2.10%) | 3690 (0.03%) | 1,014,692 | 12,583,956 (97.64%) |
MS-2 | 17,338,149 (100.00%) | 680 (0.00%) | 23,377 (0.13%) | 17,416 (0.10%) | 490,306 (2.83%) | 12,336 (0.07%) | 2,026,130 | 16,794,034 (96.86%) |
MS-3 | 14,594,879 (100.00%) | 532 (0.00%) | 15,790 (0.11%) | 13,876 (0.10%) | 743,198 (5.09%) | 5511 (0.04%) | 1,145,458 | 13,815,972 (94.66%) |
Read Types | Total | Sequences Mapped to Genome | Known miRNA | Novel miRNA | Ribosomal RNA | Transfer RNA | Small Nuclear RNA | Small Nucleolar RNA | Trans-Acting Small Interfering RNAs | Unannotated |
---|---|---|---|---|---|---|---|---|---|---|
CS-1 | 9,127,130 | 8,474,172 (92.85%) | 12,039 (0.14%) | 1244 (0.01%) | 1,245,902 (14.70%) | 10 (0.00%) | 2883 (0.03%) | 6680 (0.08%) | 641 (0.01%) | 7,204,773 (85.02%) |
CS-2 | 8,007,781 | 7,381,145 (92.17%) | 61,754 (0.84%) | 4490 (0.06%) | 1,644,956 (22.29%) | 15 (0.00%) | 3419 (0.05%) | 5609 (0.08%) | 3583 (0.05%) | 5,657,319 (76.65%) |
CS-3 | 9,375,007 | 8,975,019 (95.73%) | 20,397 (0.23%) | 1423 (0.02%) | 1,497,323 (16.68%) | 5 (0.00%) | 2433 (0.03%) | 3034 (0.03%) | 1038 (0.01%) | 7,449,366 (83.00%) |
LS-1 | 7,270,911 | 6,886,984 (94.72%) | 16,112 (0.23%) | 1515 (0.02%) | 1,366,452 (19.84%) | 9 (0.00%) | 3193 (0.05%) | 5135 (0.07%) | 1646 (0.02%) | 5,492,922 (79.76%) |
LS-2 | 8,520,845 | 7,737,807 (90.81%) | 32,024 (0.41%) | 3086 (0.04%) | 1,356,215 (17.53%) | 9 (0.00%) | 2832 (0.04%) | 7026 (0.09%) | 2159 (0.03%) | 6,334,456 (81.86%) |
LS-3 | 9,018,168 | 8,779,523 (97.35%) | 7119 (0.08%) | 604 (0.01%) | 1,482,050 (16.88%) | 6 (0.00%) | 2286 (0.03%) | 3677 (0.04%) | 419 (0.00%) | 7,283,362 (82.96%) |
MS-1 | 8,981,640 | 8,581,120 (95.54%) | 5456 (0.06%) | 138 (0.00%) | 1,452,970 (16.93%) | 7 (0.00%) | 2749 (0.03%) | 1702 (0.02%) | 121 (0.00%) | 7,117,977 (82.95%) |
MS-2 | 10,925,787 | 9,849,558 (90.15%) | 112,529 (1.14%) | 4902 (0.05%) | 1,888,880 (19.18%) | 10 (0.00%) | 4224 (0.04%) | 5038 (0.05%) | 6472 (0.07%) | 7,827,503 (79.47%) |
MS-3 | 6,096,367 | 5,522,031 (90.58%) | 51,689 (0.94%) | 2498 (0.05%) | 927,311 (16.79%) | 9 (0.00%) | 1767 (0.03%) | 4458 (0.08%) | 3196 (0.06%) | 4,531,103 (82.06%) |
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Zhang, H.; Liu, X.; Yang, X.; Wu, H.; Zhu, J.; Zhang, H. miRNA–mRNA Integrated Analysis Reveals Roles for miRNAs in a Typical Halophyte, Reaumuria soongorica, during Seed Germination under Salt Stress. Plants 2020, 9, 351. https://doi.org/10.3390/plants9030351
Zhang H, Liu X, Yang X, Wu H, Zhu J, Zhang H. miRNA–mRNA Integrated Analysis Reveals Roles for miRNAs in a Typical Halophyte, Reaumuria soongorica, during Seed Germination under Salt Stress. Plants. 2020; 9(3):351. https://doi.org/10.3390/plants9030351
Chicago/Turabian StyleZhang, Huilong, Xiaowei Liu, Xiuyan Yang, Haiwen Wu, Jianfeng Zhu, and Huaxin Zhang. 2020. "miRNA–mRNA Integrated Analysis Reveals Roles for miRNAs in a Typical Halophyte, Reaumuria soongorica, during Seed Germination under Salt Stress" Plants 9, no. 3: 351. https://doi.org/10.3390/plants9030351