MicroRNAs in Vitis vinifera cv. Chardonnay Are Differentially Expressed in Response to Diaporthe Species
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material
2.2. Fungal Isolates
2.3. Plant Inoculation
2.4. RNA Extraction and Quality Control
2.5. Library Preparation and Sequencing
2.6. Bioinformatics and Data Evaluation
2.7. miRNA Target Prediction and Functional Annotation
2.8. Validation of miRNA Expression Profiles by Real-Time RT-qPCR
3. Results
3.1. Plant Inoculation
3.2. The Abundance of sRNAs in Grapevines in Vitro
3.3. New and Conserved miRNAs Identified in Grapevine cv. Chardonnay in Vitro
3.4. miRNA Expression Profiles by Real-Time RT-qPCR
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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19 | 20 | 21 | 22 | 23 | 24 | 25 | Total | |
---|---|---|---|---|---|---|---|---|
DE | 287,897 | 436,557 | 518,754 | 330,042 | 331,108 | 159,806 | 113,975 | 2,178,138 |
DB | 563,942 | 801,579 | 656,600 | 556,699 | 467,013 | 211,409 | 141,876 | 3,399,118 |
C | 104,300 | 362,066 | 540,728 | 320,848 | 236,014 | 202,736 | 88,881 | 1,855,572 |
miRNA Name | miRNA Sequence | Putative Target Identified Using NCBI | Target Acc. Based on the Highest Expectations (E), psRNA Target | Inhibition |
---|---|---|---|---|
2 | CCCAGUCCCGAACCCGUCGGC | similar to aspartate aminotransferase; similar to Aspartate aminotransferase 2, transcript variant X9, misc_RNA, importin α isoform 9 | chr11.gff3_MRNA_VIT_11s0149g00200.t01 | Cleavage |
3 | AGUUACUAAUUCAUGAUCUGGC | importin α isoform 9 | chr2.gff3_MRNA_VIT_02s0033g00980.t01 | Cleavage |
5 | CCAGUCCCGAACCCGUCGGC | Vitis vinifera contig VV78X128415.10, whole genome shotgun sequence | chr7_random.gff3_MRNA_VIT_07s0151g00980.t01 | Cleavage |
6 | UCUCGGACCAGGCUUCAUUCC | Vitis vinifera microRNA MIR166a (MIR166A), microRNA, http://www.mirbase.org/cgi-bin/mature.pl?mature_acc=MIMAT0020658 | chr18.gff3_MRNA_VIT_18s0075g00480.t01 | Translocation |
8 | GGUGGCUGUAGUUUAGUGGU | Vitis vinifera contig VV78X038801.3, whole genome shotgun sequence | chr18.gff3_MRNA_VIT_18s0001g12770.t01 | Cleavage |
9 | CGGUGGACUGCUCGAGCUGC | Vitis vinifera contig VV78X196950.19, whole genome shotgun sequence | chr15.gff3_MRNA_VIT_15s0048g02810.t01 | Translocation |
10 | CUAACAGACCGGUAGACUUGAAC | Vitis vinifera contig VV78X130314.7, whole genome shotgun sequence | chr15.gff3_MRNA_VIT_15s0048g02810.t01 | Translation |
12 | CCCAGUCCCGAACCCGUCGGCU | Vitis vinifera contig VV78X156561.10, whole genome shotgun sequence | chr11.gff3_MRNA_VIT_11s0149g00200.t01 | Cleavage |
13 | GCGCCUGUAGCUCAGUGGA | Vitis vinifera contig VV78X046944.3, whole genome shotgun sequence | chr8.gff3_MRNA_VIT_08s0007g07620.t01 | Cleavage |
14 | UUCAUGGACGUUGAUAAGAUCCU | Vitis vinifera subsp. sylvestris chloroplast DNA, complete genome | chr7.gff3_MRNA_VIT_07s0005g00750.t01 | Cleavage |
15 | UAACAGACCGGUAGACUUGAAC | PREDICTED: Vitis vinifera pentatricopeptide repeat-containing protein At5g50990 (LOC100247459) | chr18.gff3_MRNA_VIT_18s0001g09480.t01 | Cleavage |
16 | UGCACUGCCUCUUCCCUGGCU | Vitis vinifera microRNA MIR408 gene, complete sequence, http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=MI0005917 | chr18.gff3_MRNA_VIT_18s0001g15240.t01 | Cleavage |
17 | CCUAACAGACCGGUAGACUUGAAC | PREDICTED: Vitis vinifera ATP synthase subunit α, chloroplastic-like (LOC109124299), mRNA | chr18.gff3_MRNA_VIT_18s0001g11300.t01 | Cleavage |
18 | UCCUAACAGACCGGUAGACUUGAAC | Vitis vinifera subsp. sylvestris chloroplast DNA, complete genome | chr18.gff3_MRNA_VIT_18s0001g11300.t01 | Cleavage |
19 | UCCUAACAGACCGGUAGACUUGAAC | Vitis vinifera subsp. sylvestris chloroplast DNA, complete genome | chr18.gff3_MRNA_VIT_18s0001g11300.t01 | Cleavage |
20 | UUAGAUGAUCAUCAACAAACU | Vitis vinifera ankyrin repeat-containing protein NPR4-like (LOC100260982), transcript variant X10, mRNA | chr7.gff3_MRNA_VIT_07s0005g02430.t01 | Cleavage |
21 | CAGACCGGUAGACUUGAAC | PREDICTED: Vitis vinifera ATP synthase subunit α, chloroplastic-like (LOC109124299), mRNA | chr19.gff3_MRNA_VIT_19s0090g01480.t01 | Cleavage |
23 | ACAGACCGGUAGACUUGAAC | PREDICTED: Vitis vinifera ATP synthase subunit α, chloroplastic-like (LOC109124299), mRNA | chr18.gff3_MRNA_VIT_18s0001g09480.t01 | Cleavage |
24 | UUCCACAGCUUUCUUGAACUU | Vitis vinifera microRNA MIR396b (MIR396B), microRNA | chr15.gff3_MRNA_VIT_15s0021g02580.t01 | Cleavage |
25 | AACAGACCGGUAGACUUGAAC | PREDICTED: Vitis vinifera ATP synthase subunit α, chloroplastic-like (LOC109124299), mRNA | chr18.gff3_MRNA_VIT_18s0001g09480.t01 | Cleavage |
26 | CCGGCGAUGCGCUCCUGGCC | Vitis vinifera contig VV78X197078.6, whole genome shotgun sequence | chr12.gff3_MRNA_VIT_12s0034g02480.t01 | Cleavage |
27 | CAGUCCCGAACCCGUCGGC | Vitis vinifera contig VV78X156561.10, whole genome shotgun sequence | chr11.gff3_MRNA_VIT_11s0149g00200.t01 | Cleavage |
28 | UGUUGAGCUCACCUUGUACCC | PREDICTED: Vitis vinifera kinase-interacting family protein (LOC100246194), transcript variant X1, mRNA | chr9.gff3_MRNA_VIT_09s0002g03120.t01 | Translation |
30 | CGGUGGACUGCUCGAGCUGCU | Vitis vinifera contig VV78X156561.10, whole genome shotgun sequence | chr15.gff3_MRNA_VIT_15s0048g02810.t01 | Translation |
31 | GUUGAGCUCACCUUGUACCCA | PREDICTED: Vitis vinifera kinase-interacting family protein (LOC100246194), transcript variant X1, mRNA | chr9.gff3_MRNA_VIT_09s0002g03120.t01 | Translation |
32 | CCCAGUCCCGAACCCGUCGG | Vitis vinifera contig VV78X128415.10, whole genome shotgun sequence, mRNA sequence acyl CoA binding protein domain containing protein 3 which is a Golgi protein involved in several signalling events | chr6.gff3_MRNA_VIT_06s0004g04740.t01 | Cleavage |
33 | UGAAGGUCCAAGGCCGAGGCU | PREDICTED: Vitis vinifera uncharacterized LOC100855078 (LOC100855078), ncRNA | chr14.gff3_MRNA_VIT_14s0006g03100.t01 | Cleavage |
34 | GGGAUGGGUCGACCGGUCC | Vitis vinifera contig VV78X071755.8, whole genome shotgun sequence | chr12.gff3_MRNA_VIT_12s0034g01520.t01 | Cleavage |
35 | UCGGAUAAAGGGUUAUACAUC | PREDICTED: Vitis vinifera uncharacterized LOC100853315 (LOC100853315), transcript variant X1, ncRNA | chr6.gff3_MRNA_VIT_06s0009g03800.t01 | Cleavage |
36 | UGCACUGCCUCUUCCCUGGC | Vitis vinifera microRNA MIR408 (MIR408), microRNA | chr18.gff3_MRNA_VIT_18s0001g15240.t01 | Cleavage |
37 | CUGGAUUAUGACUGAACGCCU | PREDICTED: Vitis vinifera lysosomal Pro-X carboxypeptidase (LOC100244772), transcript variant X2, mRNA | chr4.gff3_MRNA_VIT_04s0210g00160.t01 | Cleavage |
38 | UUCCACAGCUUUCUUGAACU | Vitis vinifera microRNA MIR396c (MIR396C), microRNA | chr15.gff3_MRNA_VIT_15s0021g02580.t01 | Cleavage |
40 | AGUUACUAAUUCAUGAUCUGGCC | PREDICTED: Vitis vinifera scopoletin glucosyltransferase (LOC100260498), mRNA | chr2.gff3_MRNA_VIT_02s0033g00980.t01 | Cleavage |
41 | CCGGCGAUGCGCUCCUGGCC | mRNA sequence with expression of RPP13-like protein 1, potential disease resistance protein | chr12.gff3_MRNA_VIT_12s0034g02480.t01 | Cleavage |
42 | CCGGCGAUGCGCUCCUGGCCU | PREDICTED: Vitis vinifera putative disease resistance RPP13-like protein 1 (LOC100258269), transcript variant X4, mRNA | chr12.gff3_MRNA_VIT_12s0034g02480.t01 | Cleavage |
43 | ACCGGCGAUGCGCUCCUGGCCU | PREDICTED: Vitis vinifera auxin efflux carrier component 3 (LOC100268124), mRNA | chr1.gff3_MRNA_VIT_01s0011g01820.t01 | Cleavage |
44 | GCCCGUGGAGACGUCGUCGCCUCG | PREDICTED: Vitis vinifera oxalate--CoA ligase (LOC100256632), mRNA | chr1.gff3_MRNA_VIT_01s0011g00770.t01 | Cleavage |
45 | CGCCGUCCGAAUUGUAGUCUGGA | PREDICTED: Vitis vinifera uncharacterized LOC109123385 (LOC109123385), mRNA | chr12.gff3_MRNA_VIT_12s0134g00450.t01 | Cleavage |
46 | UCGGGUUAACAUUCCUGAACCGGGA | PREDICTED: Vitis vinifera AUGMIN subunit 7 (LOC100243653), transcript variant X1, mRNA | chr1.gff3_MRNA_VIT_01s0011g01130.t01 | Cleavage |
47 | CGGUGGACUGCUCGAGCUGCU | PREDICTED: Vitis vinifera non-specific lipid-transfer protein-like protein At5g64080 (LOC100247017), mRNA | chr15.gff3_MRNA_VIT_15s0048g02810.t01 | Translation |
48 | CCAGUCCCGAACCCGUCGGC | PREDICTED: Vitis vinifera acyl-CoA-binding domain-containing protein 3 (LOC100268114), transcript variant X6, mRNA | chr7_random.gff3_MRNA_VIT_07s0151g00980.t01 | Cleavage |
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Share and Cite
Eichmeier, A.; Kiss, T.; Penazova, E.; Pecenka, J.; Berraf-Tebbal, A.; Baranek, M.; Pokluda, R.; Cechova, J.; Gramaje, D.; Grzebelus, D. MicroRNAs in Vitis vinifera cv. Chardonnay Are Differentially Expressed in Response to Diaporthe Species. Genes 2019, 10, 905. https://doi.org/10.3390/genes10110905
Eichmeier A, Kiss T, Penazova E, Pecenka J, Berraf-Tebbal A, Baranek M, Pokluda R, Cechova J, Gramaje D, Grzebelus D. MicroRNAs in Vitis vinifera cv. Chardonnay Are Differentially Expressed in Response to Diaporthe Species. Genes. 2019; 10(11):905. https://doi.org/10.3390/genes10110905
Chicago/Turabian StyleEichmeier, Ales, Tomas Kiss, Eliska Penazova, Jakub Pecenka, Akila Berraf-Tebbal, Miroslav Baranek, Robert Pokluda, Jana Cechova, David Gramaje, and Dariusz Grzebelus. 2019. "MicroRNAs in Vitis vinifera cv. Chardonnay Are Differentially Expressed in Response to Diaporthe Species" Genes 10, no. 11: 905. https://doi.org/10.3390/genes10110905