Genome-Wide Identification and Analysis of Drought-Responsive Genes and MicroRNAs in Tobacco
Abstract
:1. Introduction
2. Results
2.1. Physiological Analysis of PRO, SOD, and MDA under Drought Conditions
2.2. Generation and Quality Assessment of the DGE Dataset
2.3. Map** DGE Tags to the Tobacco Reference Genome Database
2.4. Expression of Tobacco Root Genes under Drought Stress
2.5. Resolving Transcription Factors (TFs) among Differentially Expressed Genes
2.6. Identifying Candidate Drought Responsive Genes (DRGs) in Tobacco Roots
Gene Name 1 | Function | Homolog_Niben_ID | PlantGDB_or_unigenes_ID | Tranfactor_ID | Family | TPM-NCK | TPM-N6H | TPM-N48H |
---|---|---|---|---|---|---|---|---|
GRF6 (14-3-3 protein GF14 lambda) | Drought tolerance | NbS00060175g0001.1 | - | - | - | 161.74 | 80.67 | 123.31 |
NbS00044217g0013.1 | - | - | - | 5.89 | 8.27 | 18.9 | ||
NbS00020600g0007.1 | - | - | - | 22.98 | 13 | 33.3 | ||
NbS00007737g0010.1 | - | - | - | 158.5 | 277.48 | 121.51 | ||
ABF1 | Drought tolerance | NbS00021408g0025.1 | - | - | - | 0.88 | 18.03 | 0.6 |
ANAC055 | Drought and salt tolerance | NbS00023955g0006.1 | gnl|UG|Nta#S45443622 | Nta005482 | NAC | 108.71 | 58.51 | 39 |
NbS00008328g0013.1 | gnl|UG|Nta#S45488905 | Nta010847 | NAC | 35.06 | 60.28 | 73.51 | ||
ANAC072 | Drought and salt tolerance | NbS00007567g0016.1 | gnl|UG|Nta#S33559198 | Nta013275 | NAC | 5.3 | 3.25 | 13.8 |
NbC26152828g0003.1 | gnl|UG|Nta#S45463754 | Nta012057 | NAC | 23.57 | 48.76 | 99.01 | ||
NbS00025931g0004.1 | gnl|UG|Nta#S33566495 | Nta005129 | NAC | 7.95 | 7.68 | 23.4 | ||
NbS00028594g0003.1 | gnl|UG|Nta#S45443622 | Nta005482 | NAC | 19.15 | 21.87 | 56.7 | ||
APX2 | Drought resistance | NbS00018810g0008.1 | - | - | - | 0.88 | 2.96 | 6.6 |
bZIP1 | Drought, salt and disease tolerance | NbS00007503g0111.1 | gnl|UG|Nta#S33578426 | Nta007642 | bZIP | 84.55 | 40.48 | 28.5 |
CBF4 | Drought and freezing tolerance | NbS00018604g0003.1 | gnl|UG|Nta#S45471037 | Nta012107 | ERF | 10.9 | 0.01 | 0.01 |
CpMYB10 | Desiccation and salinity tolerance | NbS00016700g0002.1 | gnl|UG|Nta#S45484072 | Nta012264 | MYB | 2.36 | 10.05 | 1.8 |
NbS00007512g0018.1 | - | - | - | 11.49 | 10.34 | 3.3 | ||
DREB1B/CBF1 | Increased tolerance to drought, cold and salinity | NbS00009125g0101.1 | gnl|UG|Nta#S33537030 | Nta005632 | ERF | 114.31 | 11.52 | 16.2 |
DREB2A | Drought resistance | NbS00032542g0006.1 | gnl|UG|Nta#S33577665 | Nta005987 | ERF | 160.56 | 14.78 | 31.5 |
NbS00025865g0001.1 | gnl|UG|Nta#S33537030 | Nta005632 | ERF | 13.26 | 0.89 | 7.5 | ||
NbS00002425g0103.1 | gnl|UG|Nta#S33577665 | Nta005987 | ERF | 5.3 | 0.01 | 0.6 | ||
DREB3 | Drought tolerance | NbS00016353g0001.1 | - | - | - | 20.03 | 3.25 | 2.7 |
FAD3 | Drought resistance | NbS00037943g0006.1 | - | - | - | 17.97 | 27.48 | 42 |
NbS00033197g0010.1 | - | - | - | 16.2 | 9.46 | 29.7 | ||
GmERF3 | Drought tolerance | NbS00020925g0011.1 | gnl|UG|Nta#S33555957 | Nta004926 | ERF | 27.1 | 27.78 | 12.6 |
HSFA2 | Resistance to environmental stresses | NbS00009669g0213.1 | - | - | - | 0.01 | 2.07 | 17.1 |
MYB60 | Drought tolerance | NbS00046172g0003.1 | gnl|UG|Nta#S40644996 | Nta005483 | MYB | 1.77 | 1.77 | 12.3 |
NbS00009475g0003.1 | - | - | - | 5.89 | 3.25 | 0.6 | ||
NbS00009284g0003.1 | gnl|UG|Nta#S33578151 | Nta004281 | MYB | 65.4 | 108.75 | 28.8 | ||
NbS00007772g0004.1 | gnl|UG|Nta#S33578094 | Nta008536 | MYB | 1.77 | 0.89 | 10.2 | ||
NCED1 | Drought and salinity resistance | NbS00014845g0012.1 | - | - | - | 51.26 | 87.17 | 32.7 |
NtERD10B | Improved drought- and low temperature stress tolerance | NbS00041294g0010.1 | - | - | - | 0.01 | 0.01 | 7.5 |
NbS00029572g0007.1 | - | - | - | 0.01 | 0.01 | 13.2 | ||
NbS00019308g0009.1 | - | - | - | 2.36 | 5.61 | 86.41 | ||
NtERD10C | Improved drought- and low-temperature stress tolerance | NbS00018964g0003.1 | - | - | - | 75.12 | 12.41 | 21.9 |
SRK2E/OST1/SnRK2.6 | Response to dehydration stress | NbS00019609g0014.1 | - | - | - | 3.83 | 7.98 | 18 |
NbS00018358g0015.1 | - | - | - | 2.36 | 2.96 | 9.9 | ||
PP2Ac-1 | Drought resistance; maintain RWC and membrane stability | NbS00043074g0007.1 | - | - | - | 12.67 | 8.57 | 21.9 |
NbS00020903g0004.1 | - | - | - | 81.02 | 52.01 | 110.41 | ||
RD22 | Response to drought stress | NbS00017616g0005.1 | - | - | - | 3.54 | 9.16 | 22.8 |
RD29A and RD29B | low-temperature-responsive and desiccation-responsive | NbS00001669g0005.1 | - | - | - | 9.43 | 3.84 | 1.8 |
SIPK | osmotic stress/pathogen resistance | NbS00060107g0004.1 | - | - | - | 36.53 | 42.85 | 78.91 |
WIPK | osmotic stress/pathogen resistance | NbS00041241g0001.1 | gnl|UG|Nta#S37452582 | Nta004233 | ERF | 7.66 | 0.59 | 1.5 |
NbS00028162g0009.1 | gnl|UG|Nta#S37452581 | Nta012156 | ERF | 40.07 | 6.8 | 9.9 | ||
NbS00017618g0003.1 | gnl|UG|Nta#S37452582 | Nta004233 | ERF | 58.33 | 5.91 | 2.1 | ||
ZPT2-1 (renamed from EPF1) | Drought tolerance | NbS00017486g0002.1 | - | - | - | 15.32 | 4.43 | 4.5 |
NbS00002494g0018.1 | - | - | - | 44.78 | 33.1 | 19.8 |
2.7. Small RNA Sequencing
2.8. Known Tobacco miRNAs Expressed in Different Tissues and Drought Responsive miRNAs in Tobacco Roots
2.9. Potential Targets of Drought Responsive miRNAs
miRNA_family | Regulated | Target_GSS_ID | Mapped_Niben_ID | NCK_TPM | N6H_TPM | N48H_TPM | Description |
---|---|---|---|---|---|---|---|
miR160 | down | ET792241 | NbS00018737g0003.1 | 0.59 | 1.18 | 1.20 | ARF Transcription factor |
miR160 | down | ET792303 | NbS00005871g0012.1 | 0.01 | 0.01 | 0.60 | ARF Transcription factor |
miR160 | down | FH226342 | NbS00059497g0003.1 | 4.71 | 3.84 | 4.20 | ARF Transcription factor |
miR160 | down | FH226342 | NbS00026905g0003.1 | 6.78 | 3.84 | 4.50 | ARF Transcription factor |
miR160 | down | FH226421 | NbS00028965g0003.1 | 3.54 | 2.66 | 1.20 | ARF Transcription factor |
miR160 | down | FH226421 | NbS00036438g0004.1 | 0.01 | 0.59 | 0.01 | ARF Transcription factor |
miR395 | up | ET937275 | NbS00014405g0001.1 | 2.36 | 1.48 | 0.90 | unknown protein |
miR395 | up | ET937275 | NbS00009197g0109.1 | 12.37 | 3.25 | 2.40 | unknown |
miR395 | up | ET937275 | NbS00006001g0005.1 | 11.78 | 17.43 | 2.10 | unknown protein |
3. Discussion
4. Experimental Section
4.1. Plant Materials, Growth Conditions and Stress Treatments
4.2. Physiological Analyses
4.3. DGE, Small RNA Library Construction, and Solexa Sequencing
4.4. Analysis and Map** of Digital Gene Expression Tags
4.5. Identification of Differentially Expressed Genes and Cluster Analysis
4.6. Analysis of Small RNA Sequencing Data and Identification of Drought Responsive miRNAs
4.7. Quantitative Real-Time PCR (qRT-PCR) Analysis
5. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
© 2015 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/).
Share and Cite
Yin, F.; Qin, C.; Gao, J.; Liu, M.; Luo, X.; Zhang, W.; Liu, H.; Liao, X.; Shen, Y.; Mao, L.; et al. Genome-Wide Identification and Analysis of Drought-Responsive Genes and MicroRNAs in Tobacco. Int. J. Mol. Sci. 2015, 16, 5714-5740. https://doi.org/10.3390/ijms16035714
Yin F, Qin C, Gao J, Liu M, Luo X, Zhang W, Liu H, Liao X, Shen Y, Mao L, et al. Genome-Wide Identification and Analysis of Drought-Responsive Genes and MicroRNAs in Tobacco. International Journal of Molecular Sciences. 2015; 16(3):5714-5740. https://doi.org/10.3390/ijms16035714
Chicago/Turabian StyleYin, Fuqiang, Cheng Qin, Jian Gao, Ming Liu, **rong Luo, Wenyou Zhang, Hongjun Liu, **nhui Liao, Yaou Shen, Likai Mao, and et al. 2015. "Genome-Wide Identification and Analysis of Drought-Responsive Genes and MicroRNAs in Tobacco" International Journal of Molecular Sciences 16, no. 3: 5714-5740. https://doi.org/10.3390/ijms16035714