RNA-seq Analysis of Salt-Stressed Versus Non Salt-Stressed Transcriptomes of Chenopodium quinoa Landrace R49
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material
2.2. RNA Extraction
2.3. Library Preparation and RNA Sequencing
2.4. RNA Sequence Analysis
2.5. Functional Annotation of Reference Transcriptome and Gene Ontology Over-Representation Analysis
2.6. Real-time Quantitative Reverse Transcription-Polymerase Chain Reaction (RT-qPCR)
2.7. Statistical Analysis
3. Results
3.1. Phenotype Response and Transcriptome Sequencing
3.2. Functional Annotation and GO
3.3. RNA-seq Validation by Real-Time RT-qPCR
3.4. Expression Levels in Roots vs. Shoots
4. Discussion
4.1. Salinity Induces Transcriptome-Wide Changes in Quinoa
4.2. Comprehensive Analysis of DEGs induced by Salt Stress and Biological Insight
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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(Treatment) Time | |||
---|---|---|---|
(0) T1 | (300) T1 | (300) T3 | |
Total Bases | 4,971,425,434 | 4,581,155,576 | 4,883,948,526 |
Read Count | 49,222,034 | 45,357,976 | 48,355,926 |
GC (%) | 43.34 | 43.31 | 43.51 |
Average Length (bp) | 101 | 101 | 101 |
Inputs Reads | 47,543,290 | 43,853,712 | 46,700,950 |
Mapped Reads | 34,220,702 | 31,442,862 | 33,862,731 |
Mapped Rate (%) | 71.98 | 71.7 | 72.51 |
Q20 (%) | 96.59 | 96.7 | 96.58 |
Q30 (%) | 91.71 | 91.96 | 91.68 |
Gene | Gene Ontology (GO) | Annotation | Kal’s Z-test | |||
---|---|---|---|---|---|---|
300) T1 > (0) T1 | (300) T3 > (0) T1 | |||||
Fold Change | FDR p-Value | Fold Change | FDR p-Value | |||
AUR62029344-RA | GO:0006355 Regulation of transcription, DNA-templated | NAC domain-containing protein 72 | 2.68 | 0.00 | 2.45 | 0.00 |
AUR62026261-RA | homeobox-leucine zipper protein HAT5 | 2.90 | 0.00 | 2.49 | 0.00 | |
AUR62021507-RA | heat stress transcription factor C-1 | 4.06 | 0.00 | 2.50 | 0.00 | |
AUR62004541-RA | homeobox-leucine zipper protein ATHB-12-like | 4.64 | 0.00 | 5.11 | 0.00 | |
AUR62023642-RA | ethylene-responsive transcription factor ERF014-like | −3.12 | 0.00 | −4.13 | 0.00 | |
AUR62004723-RA | ethylene-responsive transcription factor ERF014-like | −2.68 | 0.00 | −3.85 | 0.00 | |
AUR62025525-RA | ethylene-responsive transcription factor ERF071 | −2.27 | 0.00 | −4.07 | 0.00 | |
AUR62032882-RA | ethylene-responsive transcription factor ERF021-like | −6.55 | 0.01 | − ∞ | 0.00 | |
AUR62032288-RA | GO:0006952 Defense response | acidic chitinase | − ∞ | 0.00 | −103.63 | 0.00 |
AUR62027590-RA | LRR receptor-like serine/threonine-protein kinase FLS2 | −2.59 | 0.00 | −3.27 | 0.00 | |
AUR62033289-RA | GO:0006950 Response to stress | putative 4-hydroxy-4-methyl-2-oxoglutarate aldolase 3 | 2.79 | 0.00 | 4.93 | 0.00 |
AUR62037323-RA | universal stress protein A-like protein | 4.57 | 0.00 | 6.98 | 0.00 | |
AUR62031231-RA | MLP-like protein 43 | 2.14 | 0.00 | 2.37 | 0.00 | |
AUR62012039-RA | 18 kDa seed maturation protein-like | 3.82 | 0.01 | 14.18 | 0.00 | |
AUR62021371-RA | putative 4-hydroxy-4-methyl-2-oxoglutarate aldolase 3 | 4.92 | 0.00 | 4.56 | 0.00 | |
AUR62032222-RA | inhibitor of trypsin and hageman factor-like | −2.81 | 0.00 | −28.13 | 0.00 | |
AUR62017675-RA | chalcone synthase | −3.16 | 0.00 | −2.70 | 0.00 | |
AUR62020156-RA | asparagine synthetase [glutamine-hydrolyzing] | −3.70 | 0.00 | −64.32 | 0.00 | |
AUR62031453-RA | S-type anion channel SLAH2 isoform X3 | −2.35 | 0.00 | −3.15 | 0.00 | |
AUR62014092-RA | peroxidase 5 | −2.09 | 0.03 | −6.63 | 0.00 | |
AUR62009744-RA | peroxidase 57 | −2.67 | 0.00 | −10.86 | 0.00 | |
AUR62030623-RA | GO:0071554 Cell wall organization or biogenesis | expansin A10 | 4.70 | 0.00 | 2.59 | 0.00 |
AUR62024921-RA | expansin A10 | 4.93 | 0.00 | 2.90 | 0.00 | |
AUR62002580-RA | polygalacturonase At1g48100 | 2.60 | 0.00 | 2.37 | 0.00 | |
AUR62018907-RA | xyloglucan endotransglycosylase/hydrolase | −2.36 | 0.00 | −9.18 | 0.00 | |
AUR62020893-RA | xyloglucan endotransglucosylase/hydrolase 2-like | −3.08 | 0.00 | −3.77 | 0.00 | |
AUR62024859-RA | xyloglucan endotransglucosylase/hydrolase protein 22-like | −2.40 | 0.00 | −3.17 | 0.00 | |
AUR62035069-RA | COBRA-like protein 7 | −2.48 | 0.00 | −2.80 | 0.00 | |
AUR62018602-RA | expansin-A7-like | −3.07 | 0.05 | −3.78 | 0.01 | |
AUR62018634-RA | Cellulose synthase-like protein D3 | −2.45 | 0.00 | −3.84 | 0.00 | |
AUR62003130-RA | GO:0009688 Abscisic acid biosynthetic process | nodulin-related protein 1-like | 2.14 | 0.00 | 2.63 | 0.00 |
AUR62012136-RA | GO:0009737 Response to abscisic acid | protein phosphatase 2C 37-like | 2.10 | 0.00 | 2.03 | 0.00 |
AUR62023479-RA | abscisic acid receptor PYL9 | 3.14 | 0.00 | 2.10 | 0.00 | |
AUR62012310-RA | abscisic acid receptor PYL4 | −4.31 | 0.00 | −10.00 | 0.00 | |
AUR62010485-RA | abscisic acid 8’-hydroxylase 1-like | −3.44 | 0.00 | −3.63 | 0.00 | |
AUR62022950-RA | abscisic acid receptor PYL4 | −2.38 | 0.00 | −11.05 | 0.00 |
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Ruiz, K.B.; Maldonado, J.; Biondi, S.; Silva, H. RNA-seq Analysis of Salt-Stressed Versus Non Salt-Stressed Transcriptomes of Chenopodium quinoa Landrace R49. Genes 2019, 10, 1042. https://doi.org/10.3390/genes10121042
Ruiz KB, Maldonado J, Biondi S, Silva H. RNA-seq Analysis of Salt-Stressed Versus Non Salt-Stressed Transcriptomes of Chenopodium quinoa Landrace R49. Genes. 2019; 10(12):1042. https://doi.org/10.3390/genes10121042
Chicago/Turabian StyleRuiz, Karina B., Jonathan Maldonado, Stefania Biondi, and Herman Silva. 2019. "RNA-seq Analysis of Salt-Stressed Versus Non Salt-Stressed Transcriptomes of Chenopodium quinoa Landrace R49" Genes 10, no. 12: 1042. https://doi.org/10.3390/genes10121042