Combinations of Small RNA, RNA, and Degradome Sequencing Uncovers the Expression Pattern of microRNA–mRNA Pairs Adapting to Drought Stress in Leaf and Root of Dactylis glomerata L.
Abstract
:1. Introduction
2. Results
2.1. Transcriptome Sequencing of Orchardgrass under Drought Treatment
2.2. Construction of Global Small RNAs Library
2.3. Degradome Sequencing Analysis
2.4. Correlation Analysis of miRNA–Target Pairs
3. Discussion
3.1. Small RNAs and Their Expression Pattern in Plants under Drought Stress
3.2. Target Parsing of Small RNAs in Orchardgrass
3.3. Insights to the Correlation of miRNAs and their Targets
4. Materials and Methods
4.1. Plant Material and Water Deficit Treatment
4.2. Transcriptome Sequencing and De Novo Assembly Analysis
4.3. Small RNA Sequencing and miRNAs Identification
4.4. Degradome Sequencing and Target Identification
4.5. Verification by qRT-PCR
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
GO | Gene ontology |
KEGG | Kyoto encyclopedia of genes and genomes |
MAPK | Mitogen-activated protein kinase |
CDPK | Calcium-dependent protein kinase |
miRNA | microRNA |
SPL | Squamosa promoter binding protein-like |
PARE | Parallel analysis of RNA ends |
RACE | 5′-rapid amplification of cDNA ends |
DEG | Differently expressed gene |
AGO | Protein argonaute 2 |
MYBAS2 | MYB-related protein |
NAC74 | NAC domain-containing protein 74 |
PERK2 | Protein kinase R (PKR)-like endoplasmic reticulum kinase 2 |
STP13 | Sugar transport protein 13 |
BIPE3 | Luminal-binding protein 3 |
DEmiR | DIFFERENTLY expressed miRNA |
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Comparison | miR_Name | Regulation | Gene_ID | Gene Annotation | Regulation |
---|---|---|---|---|---|
CKL vs. CKR | ata-miR164c-3p | down | comp50213_c0 | - | down |
ata-miR164c-3p | down | comp59407_c0 | Heat shock 70kda protein 5 | down | |
PC-3p-68901_67 | down | comp50628_c0 | 11beta-hydroxysteroid dehydrogenase | down | |
sbi-MIR396d-p3_2ss2CA18TC | down | comp57297_c0 | Proton-dependent oligopeptide transporter | down | |
tae-miR319_L-1R+1 | down | comp59014_c0 | - | down | |
ata-miR164c-3p | down | comp59034_c0 | - | down | |
bdi-miR160e-5p_L+1R-1 | up | comp42625_c0 | Peroxidase | down | |
far-MIR1122-p5_1ss9AG | down | comp58564_c0 | ATP-dependent Clp protease ATP-binding subunit clpc | Up | |
tae-miR1130b-3p_L+4R-6_1ss6CT | up | comp59143_c0 | - | down | |
D18dR vs. CKR | ata-miR164c-3p | down | comp59407_c0 | Heat shock 70kda protein 5 | up |
bdi-miR5049-5p_R-2_2ss4TC20TC | down | comp44426_c0 | Naringenin 3-dioxygenase | up | |
bdi-miR5049-5p_R-2_2ss4TC20TC | down | comp55619_c0 | Naringenin 3-dioxygenase | up | |
far-MIR1122-p5_1ss9AG | down | comp55619_c0 | Proton-dependent oligopeptide transporter | up | |
far-MIR1122-p5_1ss9AG | down | comp58684_c0 | - | up | |
bdi-MIR1135-p3_2ss17CT20GT | up | comp58684_c0 | - | up | |
sbi-MIR396d-p3_2ss2CA18TC | down | comp57297_c0 | - | up |
Comparison | KEGG ID | Gene_ID | Regulation | KEGG_Name |
---|---|---|---|---|
CK_L vs. CK_R | ko00360 | comp42625_c0 | down | Phenylalanine metabolism |
ko00680 | comp42625_c0 | down | Methane metabolism | |
ko00940 | comp42625_c0 | down | Phenylpropanoid biosynthesis | |
D18d_R vs. CK_R | ko03060 | comp59407_c0 | up | Protein export |
ko00941 | comp55619_c0 | up | Flavonoid biosynthesis |
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Ji, Y.; Chen, P.; Chen, J.; Pennerman, K.K.; Liang, X.; Yan, H.; Zhou, S.; Feng, G.; Wang, C.; Yin, G.; et al. Combinations of Small RNA, RNA, and Degradome Sequencing Uncovers the Expression Pattern of microRNA–mRNA Pairs Adapting to Drought Stress in Leaf and Root of Dactylis glomerata L. Int. J. Mol. Sci. 2018, 19, 3114. https://doi.org/10.3390/ijms19103114
Ji Y, Chen P, Chen J, Pennerman KK, Liang X, Yan H, Zhou S, Feng G, Wang C, Yin G, et al. Combinations of Small RNA, RNA, and Degradome Sequencing Uncovers the Expression Pattern of microRNA–mRNA Pairs Adapting to Drought Stress in Leaf and Root of Dactylis glomerata L. International Journal of Molecular Sciences. 2018; 19(10):3114. https://doi.org/10.3390/ijms19103114
Chicago/Turabian StyleJi, Yang, Peilin Chen, Jing Chen, Kayla K. Pennerman, Xiaoyu Liang, Haidong Yan, Sifan Zhou, Guangyan Feng, Chengran Wang, Guohua Yin, and et al. 2018. "Combinations of Small RNA, RNA, and Degradome Sequencing Uncovers the Expression Pattern of microRNA–mRNA Pairs Adapting to Drought Stress in Leaf and Root of Dactylis glomerata L." International Journal of Molecular Sciences 19, no. 10: 3114. https://doi.org/10.3390/ijms19103114