DNA Methylation Analysis of Dormancy Release in Almond (Prunus dulcis) Flower Buds Using Epi-Genotyping by Sequencing
Abstract
:1. Introduction
2. Results
2.1. Evaluation of the Quality of the Epi-GBS Analysis
2.2. Differentyally Methylated Genes Detected
2.3. Differentyally Methylated Genes Related to Bud Dormancy
3. Discussion
4. Materials and Methods
4.1. Plant Material and Experimental Design
4.2. Epi-GBS Protocol
4.3. Bioinformatic Analysis of DNA Methylation
4.4. Gene Finding and Annotation
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Abbreviations
5mC | 5′ Methylated Cytosine |
AP180 | ASSEMBLY PROTEIN 180 |
ARF | AUXIN RESPONSE FACTOR |
CytP450 | Cytochrome P-450 |
DMF | Differentially Methylated Fragment |
DMG | Differentially Methylated Gene |
epiGBS | Epi-Genotyping By Sequencing |
FAR1 | FAR-RED IMPAIRED RESPONSE 1 |
GDSL | Gly, Asp, Ser, and Leu motif |
GO | Gene Ontology |
GPI | Glycerophosphatidylinositol |
H3K27me3 | Trymethylation of Histone 3 on Lis (K) residue 27 |
HSP | HYDROPHOBIC SEED PROTEIN |
LEA | LATE EMBRYOGENESIS ABUNDANT |
LHY | LATE ELONGATED HYPOCOTYL |
LRR-TIR | LEUCINE RICH REPEAT-TOLL INTERLEUKIN 1 RECEPTOR |
MADS | MCM1-AGAMOUS-DEFICIENS-SRF |
MAPK | MITOGEN-ACTIVATED PROTEIN KINASE |
NGS | Next Generation Sequencing |
NF-Y | NUCLEAR FACTOR-Y |
PTMs | Post-Translational Modifications |
SAM | S-ADENOSYL METHIONINE |
VPS1 | VACUOLAR PROTEIN SORTING 1 |
WDSAM1 | Tryptophan-Aspartic acid-Sterile Alpha Motif 1 |
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Differentially Methylated Fragments | ||
---|---|---|
D–P genotype comparison | ||
Hypo (<) | Hyper (>) | Stages |
307 | 370 | A and B |
677 DMFs | ||
A–B stage comparison | ||
Hypo (<) | Hyper (>) | Genotype |
3 | 20 | D |
21 | 27 | P |
3 | 7 | D and P |
10 DMFs |
Differentially Methylated Genes | |||
---|---|---|---|
Methylation State | Gene Position | Gene Hits | Genes Identified |
Hypermethylated | Upstream | 36 | |
Inside | 291 | ||
Downstream | 134 | ||
Total | 461 | 423 | |
Hypomethylated | Upstream | 19 | |
Inside | 201 | ||
Downstream | 80 | ||
Total | 300 | 281 | |
Equally-methylated | Upstream | 6 | |
Inside | 41 | ||
Downstream | 8 | ||
Total | 55 | 27 | |
Total DMGs | 816 | 731 |
Methylation State | Gene Position | Differentially Methylated Genes | ||
---|---|---|---|---|
‘Desmayo Largueta’ | ‘Penta‘ | Common | ||
Hyper-methylated | Upstream | 7 | 3 | 1 |
Inside | 5 | 2 | 2 | |
Downstream | 5 | 9 | 4 | |
Total | 17 | 14 | 7 | |
Hypo-methylated | Upstream | 1 | - | - |
Total | 18 | 14 | 7 |
FragmentID | Comparison | Chromosome | Gene Position | Prupe.Gene Code |
---|---|---|---|---|
fragment1289 | AB | Pp01 | Downstream | Prupe.1G287200 |
fragment1294 | AB | Pp01 | Upstream | Prupe.1G125600 |
fragment3735 | PAPB | Pp01 | Downstream | Prupe.1G099900 |
fragment32 | AB | Pp03 | Downstream | Prupe.3G130700 |
fragment341 | AB | Pp06 | Downstream | Prupe.6G307900 |
fragment797 | AB | Pp02 | Inside | Prupe.2G074400 |
fragment1708 | DADB | Pp02 | Inside | Prupe.2G019300 |
fragment4206 | PAPB | Pp02 | Inside | Prupe.2G019300 |
fragment341 | DADB | Pp02 | Downstream | Prupe.2G031100 |
fragment255 | DADB | Pp02 | Upstream | Prupe.2G053300 |
fragment92 | DADB | Pp02 | Inside | Prupe.2G057100 |
fragment92 | DADB | Pp02 | Inside | Prupe.2G057800 |
fragment797 | DADB | Pp02 | Upstream | Prupe.2G074300 |
fragment3707 | PAPB | Pp04 | Downstream | Prupe.4G186400 |
fragment4154 | PAPB | Pp04 | Downstream | Prupe.4G253800 |
fragment238 | AB | Pp04 | Downstream | Prupe.4G270800 |
fragment3299 | PAPB | Pp06 | Downstream | Prupe.6G307900 |
fragment1289 | DADB | Pp02 | Inside | Prupe.2G146000 |
fragment341 | DADB | Pp03 | Upstream | Prupe.3G026400 |
fragment797 | DADB | Pp03 | Downstream | Prupe.3G130700 |
fragment2263 | DADB | Pp05 | Inside | Prupe.5G036900 |
fragment157 | PAPB | Pp06 | Upstream | Prupe.6G014500 |
fragment1289 | DADB | Pp05 | Downstream | Prupe.5G038500 |
fragment483 | PAPB | Pp02 | Upstream | Prupe.2G039500 |
fragment507 | DADB | Pp06 | Inside | Prupe.6G097800 |
fragment1708 | DADB | Pp06 | Upstream | Prupe.6G331300 |
fragment2727 | DADB | Pp06 | Upstream | Prupe.6G331300 |
fragment849 | PAPB | Pp01 | Downstream | Prupe.1G105700 |
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Prudencio, Á.S.; Werner, O.; Martínez-García, P.J.; Dicenta, F.; Ros, R.M.; Martínez-Gómez, P. DNA Methylation Analysis of Dormancy Release in Almond (Prunus dulcis) Flower Buds Using Epi-Genotyping by Sequencing. Int. J. Mol. Sci. 2018, 19, 3542. https://doi.org/10.3390/ijms19113542
Prudencio ÁS, Werner O, Martínez-García PJ, Dicenta F, Ros RM, Martínez-Gómez P. DNA Methylation Analysis of Dormancy Release in Almond (Prunus dulcis) Flower Buds Using Epi-Genotyping by Sequencing. International Journal of Molecular Sciences. 2018; 19(11):3542. https://doi.org/10.3390/ijms19113542
Chicago/Turabian StylePrudencio, Ángela S., Olaf Werner, Pedro J. Martínez-García, Federico Dicenta, Rosa M. Ros, and Pedro Martínez-Gómez. 2018. "DNA Methylation Analysis of Dormancy Release in Almond (Prunus dulcis) Flower Buds Using Epi-Genotyping by Sequencing" International Journal of Molecular Sciences 19, no. 11: 3542. https://doi.org/10.3390/ijms19113542