Comparative RNA-Seq Analysis between Monoecious and Androecious Plants Reveals Regulatory Mechanisms Controlling Female Flowering in Cucurbita pepo
Abstract
:1. Introduction
2. Results
2.1. Transcriptome Sequencing of WT and Etr1b Apical Shoots at M0 and M1 Stages of Development
2.2. Differential Expressed Genes between Genotypes and Developmental Stages
2.3. Ethylene and Other Known Sex-Determining Genes in Cucurbit Species
2.4. Hormonal Pathways Regulating Female Flowering
2.5. Transcription Factors Regulating Female Flowering
2.6. Other Transcriptomic Changes Controlling Female Flowering
3. Discussion
3.1. Ethylene Genes Regulating Female Flowering in C. pepo
3.2. Other Hormone-Related Genes Regulating Female Flowering in C. pepo
3.3. Transcription Factors Associated with Female Flowers Production
3.4. Other Actors Regulating Female Flowering Transition Process
4. Materials and Methods
4.1. Plant Material
4.2. RNA Isolation and Sequencing
4.3. Bioinformatic Analysis and Graphic Representations
4.4. RNA-Seq Validation by Quantitative RT-PCR
4.5. Functional Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Genotype | Develop. Stage | No Sample | Clean Reads | Q20 (%) | Q30 (%) | GC (%) | Mapping (%) | Mapped Reads |
---|---|---|---|---|---|---|---|---|
WT | M0 | 1 | 12,863,488 | 97.81 | 93.73 | 44.92 | 98.13 | 12,622,941 |
2 | 13,356,496 | 97.87 | 93.88 | 45.02 | 97.90 | 13,076,010 | ||
3 | 12,735,924 | 97.98 | 94.36 | 45 | 97.41 | 12,406,064 | ||
M1 | 1 | 11,555,691 | 97.9 | 94.08 | 44.91 | 97.54 | 11,271,421 | |
2 | 16,244,907 | 97.91 | 93.91 | 45.23 | 97.68 | 15,868,025 | ||
3 | 11,244,769 | 98 | 94.29 | 45.16 | 98.31 | 11,054,732 | ||
etr1b | M0 | 1 | 12,843,946 | 97.66 | 93.43 | 44.91 | 97.42 | 12,512,572 |
2 | 12,246,854 | 97.95 | 94.2 | 44.85 | 98.34 | 12,043,556 | ||
3 | 14,258,714 | 98 | 94.22 | 45.16 | 98.14 | 13,993,502 | ||
M1 | 1 | 11,358,393 | 97.97 | 94.21 | 45.01 | 97.96 | 11,126,682 | |
2 | 12,456,499 | 97.89 | 94.03 | 44.73 | 97.57 | 12,153,806 | ||
3 | 11,225,221 | 97.92 | 94.1 | 44.85 | 97.77 | 10,974,899 |
TF Family | Gene ID | Annotation | M1-WT vs. M0-WT | M1-WT vs. M1-etr1b | Putative Function | Organism | Name |
---|---|---|---|---|---|---|---|
ARR-B | 111779181 | two-component response regulator ORR21-like | −4.36 | 0.00 | Cytokinin signaling [30] | A. thaliana | CpORR21 |
bHLH | 111796240 | transcription factor HEC1-like | 8.27 | 7.08 | Control of gynoecium development via auxin and cytokinin response [31] | A. thaliana | CpHEC1 |
bHLH | 111800158 | transcription factor MYC2-like | 1.73 | 4.32 | Jasmonate signaling [32] | A. thaliana | CpMYC2 |
bHLH | 111780930 | transcription factor HEC3-like isoform X3 | 5.46 | 0.00 | Control of gynoecium development via auxin and cytokinin response [31] | CpHEC3 | |
C2H2 | 111789990 | zinc finger protein 10-like | 7.39 | 5.44 | Plant growth and development [33], ABA signaling [34] | A. thaliana | CpFLZ10 |
C2H2 | 111790146 | zinc finger protein 11-like | 4.34 | 0.00 | CpFLZ11 | ||
ERF | 111791372 | ethylene-responsive transcription factor 1B | 4.45 | 2.64 | CpERF1B-1 | ||
ERF | 111800217 | ethylene-responsive transcription factor 1B-like | 4.36 | 2.15 | CpERF1B-2 | ||
ERF | 111806370 | ethylene-responsive transcription factor ERF062-like | 4.34 | 0.00 | CpERF62 | ||
G2-like | 111802196 | transcription factor HHO2-like | 5.08 | 0.00 | CpHHO2 | ||
HD-ZIP | 111781935 | homeobox-leucine zipper protein ATHB-40-like | 4.82 | 3.76 | Stamen abortion in bisexual flowers [19] | C. melo | CpHB40A |
HD-ZIP | 111801688 | homeobox-leucine zipper protein ATHB-12-like | 6.72 | 2.98 | CpHB40B | ||
MIKC_MADS | 111789058 | agamous-like MADS-box protein AGL11 isoform X2 | 5.94 | 4.04 | Seed development [35,36,37] | A. thaliana, S. lycopersicum, V. vinifera | CpAGL11 |
MIKC_MADS | 111782688 | floral homeotic protein AGAMOUS-like | 5.57 | 3.66 | Cytokinin regulation [38] | A. thaliana | CpSHP2 |
MYB | 111788261 | transcription factor MYB36-like | 5.98 | 3.25 | CpMYB36 | ||
MYB | 111809067 | transcription factor MYB62-like | 6.62 | 2.99 | Flower development via gibberellin biosynthesis and activation under phosphate starvation conditions [39] and gibberellin signaling [40] | A. thaliana | CpMYB62 |
MYB | 111797571 | transcription factor MYB73-like | −4.22 | 0.00 | Auxin response [41,42] | CpMYB73 | |
NAC | 111800590 | NAC domain-containing protein 72-like | 5.56 | 4.55 | Transcription factor RD26. Abiotic stress via ABA response [43] | A. thaliana | CpNAC72-1 |
NAC | 111808051 | NAC domain-containing protein 2-like | 4.02 | 3.81 | Transcription factor ATAF1. ABA homeostasis [44,45] | A. thaliana | CpNAC2 |
NAC | 111787610 | NAC domain-containing protein 72-like | 4.28 | 3.58 | Transcription factor RD26. Abiotic stress via ABA response [43] | A. thaliana | CpNAC72-2 |
NAC | 111791093 | NAC domain-containing protein 100-like | 5.23 | 3.05 | Leaf senescence via module EIN2-EIN3-miR164-NAC2 [46] | A. thaliana | CpNAC100 |
NAC | 111786437 | NAC domain-containing protein 55-like | 4.47 | 0.00 | Stress response mediated by ABA [47] | A. thaliana | CpNAC55 |
WRKY | 111791491 | probable WRKY transcription factor 48 | −4.67 | 0.00 | CpWRKY48 | ||
YABBY | 111802629 | protein CRABS CLAW | 4.91 | 4.19 | Carpel development [14] | C. melo | CpCRCA |
Log_2_FC | 1st Hit in A. thaliana | ||||||
---|---|---|---|---|---|---|---|
Gene ID | Annotation | T1-WT vs. T0-WT | T1_WT vs. T1_etr1b | Coverage (%) | Homology (%) | TAIR Gene ID | Name |
111796025 | bidirectional sugar transporter SWEET4-like | 3.63 | 4.12 | 88 | 55.13 | AT3G28007 | CpSWEET4 |
111811228 | protein FANTASTIC FOUR 2-like | 4.23 | 1.94 | 69 | 40.35 | AT4G02810 | CpFAF2 |
111790342 | receptor-like protein kinase FERONIA | 4.80 | 1.72 | 96 | 48.20 | AT3G51550 | CpFER-1 |
111790341 | receptor-like protein kinase FERONIA | 4.27 | 0.00 | 96 | 48.20 | AT3G51550 | CpFER-2 |
111806461 | glu S.griseus protease inhibitor-like isoform X1 | 4.00 | 0.00 | 100 | 50.00 | AT5G43580 | CpUPI |
111779138 | AT-hook motif nuclear-localized protein 22-like | −4.97 | 0.00 | 100 | 52.38 | AT3G60870 | CpAHL22 |
111809214 | protein RSI-1-like | −6.24 | 0.00 | 72 | 63.89 | AT3G09950 | CpRSI1 |
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Segura, M.; García, A.; Benítez, Á.; Martínez, C.; Jamilena, M. Comparative RNA-Seq Analysis between Monoecious and Androecious Plants Reveals Regulatory Mechanisms Controlling Female Flowering in Cucurbita pepo. Int. J. Mol. Sci. 2023, 24, 17195. https://doi.org/10.3390/ijms242417195
Segura M, García A, Benítez Á, Martínez C, Jamilena M. Comparative RNA-Seq Analysis between Monoecious and Androecious Plants Reveals Regulatory Mechanisms Controlling Female Flowering in Cucurbita pepo. International Journal of Molecular Sciences. 2023; 24(24):17195. https://doi.org/10.3390/ijms242417195
Chicago/Turabian StyleSegura, María, Alicia García, Álvaro Benítez, Cecilia Martínez, and Manuel Jamilena. 2023. "Comparative RNA-Seq Analysis between Monoecious and Androecious Plants Reveals Regulatory Mechanisms Controlling Female Flowering in Cucurbita pepo" International Journal of Molecular Sciences 24, no. 24: 17195. https://doi.org/10.3390/ijms242417195