De Novo Transcriptome Analysis Reveals Flowering-Related Genes That Potentially Contribute to Flowering-Time Control in the Japanese Cultivated Gentian Gentiana triflora
Abstract
:1. Introduction
2. Results
2.1. Identification of Reference Genes Expressed in Gentian Leaves, and Gene Annotation via BLAST Analysis and Protein Motif Analysis
2.2. Expression Profiling of Flowering-Related Genes in Leaves over a Three-Month Period Prior to Flowering
2.3. Effect of Photoperiod on the Expression of BBX Genes in In Vitro–Grown Seedlings
2.4. Coexpression Cluster Analysis
3. Discussion
4. Materials and Methods
4.1. Plant Materials
4.2. RNA-Seq Analysis
4.3. Validation via qRT-PCR Analysis
4.4. Phylogenetic Analysis of the BBX and MADS-Box Family Proteins
4.5. Analysis of BBX Gene Expression in Response to Photoperiod in In-Vitro-Grown Seedlings
4.6. Gene Coexpression Analysis in Field-Grown Gentian Plants
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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Trinity Status | ||
---|---|---|
Contigs | Total number (>179 bp) | 521,292 |
Total assembled bases (bp) | 411,975,909 | |
Average of contig length (bp) | 790 | |
N50 (bp) | 1360 | |
Unigenes | Total number | 37,919 |
Total assembled bases (bp) | 39,296,556 | |
Average of contig length (bp) | 1036 | |
N50 (bp) | 1206 |
Pathway | No. of Arabidopsis FLOR-ID Genes | No. of Hit Genes |
---|---|---|
Photoperiod | 139 | 82 |
Vernalization | 90 | 63 |
Aging | 53 | 26 |
Hormones | 77 | 34 |
Ambient temperature | 38 | 20 |
Sugar | 46 | 21 |
Autonomous | 116 | 86 |
Circadian clock | 25 | 18 |
Total 1 | 325 | 212 |
Transcript ID | Gene Model | BlastP | Arabidopsis | Gentian |
---|---|---|---|---|
TRINITY_DN25746_c0_g1_i1.p1 | AT5G22290.1 | NAC domain-containing protein 89 | NAC089 | |
TRINITY_DN12869_c1_g1_i7.p1 | AT4G34530.1 | Transcription factor bHLH63 | CIB1 | |
TRINITY_DN73_c4_g1_i3.p1 | AT2G16770.1 | Basic leucine zipper 23 | bZIP23 | |
TRINITY_DN3883_c0_g3_i1.p1 | AT5G48150.3 | Scarecrow-like transcription factor PAT1 | PAT1 | |
TRINITY_DN54928_c0_g1_i3.p1 | AT1G29280.1 | Probable WRKY transcription factor 65 | WRKY65 | |
TRINITY_DN23960_c0_g1_i5.p1 | AT2G28550.3 | Ethylene-responsive transcription factor RAP2-7 | TOE1 | |
TRINITY_DN6815_c0_g2_i1.p1 | AT2G44940.1 | Ethylene-responsive transcription factor ERF034 | ||
TRINITY_DN13564_c0_g1_i1.p1 | AT2G28350.1 | Auxin response factor 10 | ARF10 | |
TRINITY_DN2158_c0_g1_i8.p1 | AT3G61150.1 | Homeobox-leucine zipper protein HDG1 | HDG1 | |
TRINITY_DN6125_c0_g1_i1.p1 | AT5G60850.1 | Dof zinc finger protein DOF5.4 | OBP4 | |
TRINITY_DN10067_c0_g2_i3.p1 | AT4G06598.1 | Uncharacterized protein At4g06598 | ||
TRINITY_DN23176_c0_g1_i1.p1 | AT2G03710.2 | Agamous-like MADS-box protein AGL3 | SEP4 | GtSEP1 |
TRINITY_DN14692_c0_g1_i4.p1 | AT1G74650.1 | MYB31 | ||
TRINITY_DN16714_c0_g1_i3.p1 | AT3G11450.1 | |||
TRINITY_DN30900_c0_g1_i2.p1 | AT3G54340.1 | Floral homeotic protein APETALA 3 | AP3 | GtAP3b |
TRINITY_DN3345_c0_g3_i1.p1 | AT3G23690.1 | Transcription factor bHLH77 | CIL2 | |
TRINITY_DN3306_c0_g1_i10.p1 | AT2G30590.1 | Probable WRKY transcription factor 21 | WRKY21 | |
TRINITY_DN23930_c0_g2_i8.p1 | AT3G53310.1 | B3 domain-containing protein REM20 | ||
TRINITY_DN617_c0_g2_i3.p1 | AT3G10760.1 | |||
TRINITY_DN7529_c0_g1_i1.p1 | AT4G34590.1 | bZIP transcription factor 11 | ATB2 | |
TRINITY_DN30234_c0_g1_i2.p1 | AT5G26930.1 | GATA transcription factor 23 | GATA23 | |
TRINITY_DN22191_c0_g1_i5.p1 | AT3G54340.1 | Floral homeotic protein APETALA 3 | AP3 | GtAP3a |
TRINITY_DN2269_c0_g4_i2.p1 | AT1G65480.2 | Protein FLOWERING LOCUS T | FT | GtFT1 |
Transcript ID | Gene Model | BlastP | Arabidopsis | Gentian |
---|---|---|---|---|
TRINITY_DN522_c0_g1_i1.p1 | AT1G14920.1 | DELLA protein GAI | GAI | |
TRINITY_DN7000_c1_g1_i1.p1 | AT4G00870.1 | Transcription factor bHLH14 | ||
TRINITY_DN5423_c0_g1_i2.p1 | AT3G19860.1 | Transcription factor bHLH121 | bHLH121 | |
TRINITY_DN22844_c0_g1_i6.p1 | AT5G01310.1 | APTX | ||
TRINITY_DN1280_c1_g1_i2.p1 | AT1G58110.1 | |||
TRINITY_DN728_c3_g1_i2.p1 | AT1G78600.1 | B-box zinc finger protein 22 | BBX22 | GtBBX22 |
TRINITY_DN2269_c0_g4_i2.p1 | AT1G65480.2 | Protein FLOWERING LOCUS T | FT | GtFT1 |
TRINITY_DN23176_c0_g1_i1.p1 | AT2G03710.2 | Agamous-like MADS-box protein AGL3 | SEP4 | GtSEP1 |
TRINITY_DN35474_c0_g1_i1.p1 | AT5G51980.2 | |||
TRINITY_DN53614_c0_g1_i5.p1 | AT1G67310.1 | Calmodulin-binding transcription activator 4 |
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Takase, T.; Shimizu, M.; Takahashi, S.; Nemoto, K.; Goto, F.; Yoshida, C.; Abe, A.; Nishihara, M. De Novo Transcriptome Analysis Reveals Flowering-Related Genes That Potentially Contribute to Flowering-Time Control in the Japanese Cultivated Gentian Gentiana triflora. Int. J. Mol. Sci. 2022, 23, 11754. https://doi.org/10.3390/ijms231911754
Takase T, Shimizu M, Takahashi S, Nemoto K, Goto F, Yoshida C, Abe A, Nishihara M. De Novo Transcriptome Analysis Reveals Flowering-Related Genes That Potentially Contribute to Flowering-Time Control in the Japanese Cultivated Gentian Gentiana triflora. International Journal of Molecular Sciences. 2022; 23(19):11754. https://doi.org/10.3390/ijms231911754
Chicago/Turabian StyleTakase, Tomoyuki, Motoki Shimizu, Shigekazu Takahashi, Keiichirou Nemoto, Fumina Goto, Chiharu Yoshida, Akira Abe, and Masahiro Nishihara. 2022. "De Novo Transcriptome Analysis Reveals Flowering-Related Genes That Potentially Contribute to Flowering-Time Control in the Japanese Cultivated Gentian Gentiana triflora" International Journal of Molecular Sciences 23, no. 19: 11754. https://doi.org/10.3390/ijms231911754
APA StyleTakase, T., Shimizu, M., Takahashi, S., Nemoto, K., Goto, F., Yoshida, C., Abe, A., & Nishihara, M. (2022). De Novo Transcriptome Analysis Reveals Flowering-Related Genes That Potentially Contribute to Flowering-Time Control in the Japanese Cultivated Gentian Gentiana triflora. International Journal of Molecular Sciences, 23(19), 11754. https://doi.org/10.3390/ijms231911754