Comparative Transcriptomics of Root Development in Wild and Cultivated Carrots
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. RNA Extraction and RNAseq
2.3. RNAseq Data Analysis
3. Results and Discussion
3.1. RNAseq Summary and Identification of Novel Transcripts
3.2. Differential Expression
3.2.1. cDEG.1.2: Genes Differentially Expressed in the Developing Storage Root (T2), as Compared with the Young Plant (T1)
3.2.2. cDEG.1.3—Genes Differentially Expressed in the Mature Storage Root (T3), as Compared with the Young Plant (T1)
3.2.3. cDEG.2.3—Genes Differentially Expressed in the Mature Storage Root (T3), as Compared with the Developing Storage Root (T2)
3.2.4. DEGs between Wild in Cultivated D. carota at the Three Timepoints (wcDEG.1, wcDEG.2, and wcDEG.3)
3.3. Genetic Determinants of the Carrot Storage Root Development
3.3.1. Regulation of the Carrot Storage Root Development
3.3.1.1. Transcription Factors
3.3.1.2. Post-Translational Protein Modifications
3.3.1.3. Hormonal Signaling
3.3.1.4. Redox Signaling
3.3.1.5. Regulation Complexity
3.3.2. DEGs Involved in the Carrot Storage Root Development
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Type of Comparison | Time Points | Cluster Number | Codes Used in the Text | |||
---|---|---|---|---|---|---|
Code | Description | Code | Description | Code | Description | |
cDEG. | ‘c’ refers to DEGs observed in the cultivated roots but not in the wild roots | 1.2. | Digits refer to the timepoints (T1 vs. T2, T1 vs. T3 or T2 vs. T3) used for comparison | XX | Consecutive numbering resulting from GO enrichment analysis; ‘XX’ stands for the one or two digits representing the clusters | cDEG.1.2.XX |
1.3. | cDEG.1.3.XX | |||||
2.3. | cDEG.2.3.XX | |||||
wDEG. | ‘w’ refers to DEGs observed in the wild roots but not in the cultivated roots | 1.2. | wDEG.1.2.XX | |||
1.3. | wDEG.1.3.XX | |||||
2.3. | wDEG.2.3.XX | |||||
wcDEG. | ‘wc’ refers to DEGs observed for wild vs. cultivated comparison | 1 | Digit refers to the timepoint (T1, T2, or T3) for which the wild and cultivated transcriptomes were compared | wcDEG.1.XX | ||
2 | wcDEG.2.XX | |||||
3 | wcDEG.3.XX |
Comparison | Cluster ID | Gene ID | Functional Annotation | log2FoldChange |
---|---|---|---|---|
cDEG.1.2 | 11 | LOC108218660 | transcription factor GTE4-like | 2.218323 |
cDEG.1.2 | 11 | LOC108218615 | transcription factor TCP8-like | 2.115051 |
cDEG.1.2 | 11 | LOC108227595 | transcription factor GTE8-like | 2.110012 |
cDEG.1.2 | 11 | LOC108204589 | trihelix transcription factor GT-2-like | 1.567139 |
cDEG.1.2 | 11 | LOC108208638 | trihelix transcription factor ASIL1-like | 1.502276 |
cDEG.1.2 | 11 | LOC108205163 | transcription factor EGL1-like | 1.268485 |
cDEG.1.2 | 19 | LOC108196018 | transcription factor GTE7-like | 1.534413 |
cDEG.1.2 | 19 | LOC108215981 | transcription factor IIIB 90 kDa subunit-like | 1.434734 |
cDEG.1.2 | 19 | LOC108219662 | GATA transcription factor 11-like | 1.210731 |
cDEG.1.2 | 19 | LOC108205675 | transcription factor TCP8-like | 1.074681 |
cDEG.1.2 | 20 | LOC108196925 | transcription factor MYB1R1-like | 1.705882 |
cDEG.1.2 | 27 | LOC108219074 | trihelix transcription factor PTL | 2.193835 |
cDEG.1.2 | 27 | LOC108209692 | ethylene-responsive transcription factor ERF118-like | 2.100109 |
cDEG.1.2 | 27 | LOC108209999 | transcription factor MYB1R1-like | 1.675776 |
cDEG.1.2 | 27 | LOC108200607 | GATA transcription factor 16 | 1.372083 |
cDEG.1.2 | 27 | LOC108219053 | ethylene-responsive transcription factor RAP2-13 | 1.068196 |
cDEG.1.2 | 31 | LOC108223963 | bZIP transcription factor 60-like | 1.437431 |
cDEG.1.2 | 31 | LOC108219044 | transcription factor TCP20 | 1.274651 |
cDEG.1.2 | 31 | LOC108218833 | bZIP transcription factor 17-like | 1.194341 |
cDEG.1.3 | 18 | LOC108204549 | general transcription factor 3C polypeptide 3 | 2.767626 |
cDEG.1.3 | 18 | LOC108208932 | heat stress transcription factor C-1-like | 2.14659 |
cDEG.1.3 | 18 | LOC108204669 | helicase-like transcription factor CHR28 | 1.576643 |
cDEG.1.3 | 18 | LOC108219601 | WRKY transcription factor 1-like | 1.371966 |
cDEG.1.3 | 18 | LOC108205270 | GATA transcription factor 26-like | 1.267808 |
cDEG.1.3 | 18 | LOC108227355 | transcription factor bHLH130-like | 1.150305 |
cDEG.1.3 | 19 | LOC108218615 | transcription factor TCP8-like | 3.326214 |
cDEG.1.3 | 19 | LOC108218436 | nuclear transcription factor Y subunit A-10 | 2.583937 |
cDEG.1.3 | 19 | LOC108205657 | WRKY transcription factor 21 | 2.093602 |
cDEG.1.3 | 19 | LOC108213173 | ethylene-responsive transcription factor RAP2-1-like | 1.936345 |
cDEG.1.3 | 19 | LOC108210769 | WRKY transcription factor 69 | 1.581155 |
cDEG.1.3 | 19 | LOC108215331 | WRKY transcription factor 21 | 1.340796 |
cDEG.1.3 | 19 | LOC108205942 | transcription factor MYB1R1-like | 1.16443 |
cDEG.1.3 | 19 | LOC108213035 | transcription factor bHLH68 | 0.964932 |
cDEG.1.3 | 19 | LOC108203417 | transcription factor GTE2-like | 0.924269 |
cDEG.1.3 | 19 | LOC108219684 | trihelix transcription factor ASIL2 | 0.814925 |
cDEG.1.3 | 28 | LOC108200607 | GATA transcription factor 16 | 1.452332 |
cDEG.1.3 | 28 | LOC108196925 | transcription factor MYB1R1-like | 1.179838 |
cDEG.1.3 | 34 | LOC108219539 | transcription factor TGA1-like | 2.492909 |
cDEG.1.3 | 34 | LOC108200279 | WRKY transcription factor 57 | 1.972727 |
cDEG.1.3 | 34 | LOC108227595 | transcription factor GTE8-like | 1.901753 |
cDEG.1.3 | 34 | LOC108223963 | bZIP transcription factor 60-like | 1.775269 |
cDEG.1.3 | 34 | LOC108206522 | ethylene-responsive transcription factor 4-like | 1.713784 |
cDEG.1.3 | 34 | LOC108214474 | transcription factor LHW-like | 1.695994 |
cDEG.1.3 | 34 | LOC108197784 | WRKY transcription factor 28 | 1.669975 |
cDEG.1.3 | 34 | LOC108208638 | trihelix transcription factor ASIL1-like | 1.472099 |
cDEG.1.3 | 34 | LOC108218767 | WRKY transcription factor 3 | 1.434899 |
cDEG.1.3 | 34 | LOC108194726 | trihelix transcription factor ASR3 | 1.425662 |
cDEG.1.3 | 34 | LOC108227612 | transcription factor 25 | 1.400666 |
cDEG.1.3 | 34 | LOC108194205 | ethylene-responsive transcription factor ERF008-like | 1.361216 |
cDEG.1.3 | 34 | LOC108197411 | transcription factor bHLH113-like | 1.250711 |
cDEG.1.3 | 34 | LOC108205979 | trihelix transcription factor GT-1 | 1.052866 |
cDEG.2.3 | 3 | LOC108220123 | ethylene-responsive transcription factor 2-like | 1.291574 |
cDEG.2.3 | 5 | LOC108211036 | transcription factor PCL1-like | −1.98882 |
cDEG.2.3 | 5 | LOC108224748 | nuclear transcription factor Y subunit C-1-like | −1.72038 |
cDEG.2.3 | 5 | LOC108218926 | NAC transcription factor 29-like | −1.58027 |
cDEG.2.3 | 12 | LOC108220417 | transcription factor MYB48-like | −2.28333 |
cDEG.2.3 | 12 | LOC108214397 | heat stress transcription factor A-3-like | −1.49692 |
cDEG.2.3 | 14 | LOC108211325 | ethylene-responsive transcription factor ERF010-like | 2.266422 |
cDEG.2.3 | 14 | LOC108197506 | transcription factor bHLH147 | 1.218184 |
cDEG.2.3 | 14 | LOC108192438 | nuclear transcription factor Y subunit A-1-like | 1.217534 |
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Machaj, G.; Bostan, H.; Macko-Podgórni, A.; Iorizzo, M.; Grzebelus, D. Comparative Transcriptomics of Root Development in Wild and Cultivated Carrots. Genes 2018, 9, 431. https://doi.org/10.3390/genes9090431
Machaj G, Bostan H, Macko-Podgórni A, Iorizzo M, Grzebelus D. Comparative Transcriptomics of Root Development in Wild and Cultivated Carrots. Genes. 2018; 9(9):431. https://doi.org/10.3390/genes9090431
Chicago/Turabian StyleMachaj, Gabriela, Hamed Bostan, Alicja Macko-Podgórni, Massimo Iorizzo, and Dariusz Grzebelus. 2018. "Comparative Transcriptomics of Root Development in Wild and Cultivated Carrots" Genes 9, no. 9: 431. https://doi.org/10.3390/genes9090431