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| Status |
Public on Aug 04, 2024 |
| Title |
Transcriptomic landscape of seedstick in Arabidopsis thaliana funiculus after fertilisation |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
In Angiosperms, the continuation of plant species is intricately dependent on the funiculus multifaceted role in nutrient transport, mechanical support, and dehiscence of seeds. SEEDSTICK (STK) is a MADS-box transcription factor involved in seed size and abscission, and one of the few genes identified as affecting funiculus growth. Given the importance of the funiculus to a correct seed development, allied with previous phenotypic observations of stk mutants, we performed a transcriptomic analysis of stk funiculi from floral stage 17, using RNA-sequencing, to infer on the deregulated networks of genes. The generated dataset of differentially expressed genes was enriched with cell wall biogenesis, cell cycle, sugar metabolism and transport terms, all in accordance with stk phenotype observed in funiculi from floral stage 17. We selected eight differentially expressed genes for transcriptome validation using qPCR and/or promoter reporter lines. Those genes were involved with abscission, seed development or novel functions in stk funiculus, such as hormones/secondary metabolites transport, for transcriptome validation using qPCR and/or promoter reporter lines. Overall, the analysis performed in this study allowed delving into the STK-network established in Arabidopsis funiculus, fulfilling a literature gap. Simultaneously, our findings reinforced the reliability of the transcriptome, making it a valuable resource for candidate genes selection for functional genetic studies in the funiculus. This will enhance our understanding on the regulatory network controlled by STK, on the role of the funiculus and identified processes and new candidate genes that will enable a better understanding on the role of this sporophytic structure and how seed development may be affected by itthem.
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| Overall design |
Stage 17 funiculi (according to Smyth et al. 1990) were used for mRNA extraction in both stk and wt samples, in duplicate.
Grants:
. "National funding" (Grant ID UIDB/50006/2020, Fundacão para a Ciencia e Tecnologia and Ministerio da Ciencia, Tecnologia e Ensino Superior)
. "PhD scholarship" (Grant ID SFRH/BD/143579/2019, Fundacao para a Ciência e Tecnologia)
. "PhD scholarship" (Grant ID LCF/BQ/DR20/11790010, "la Caixa" Foundation (ID 100010434))
. "Grant-in-Aid for Early-Career Scientists" (Grant ID 18K14729, Japanese Society for the Promotion of Science)
. "Grant-in-Aid for Early-Career Scientists" (Grant ID 20K15817, Japanese Society for the Promotion of Science)
. "Grant-in-Aid for Transformative Research Areas" (Grant ID 22H05677, Japanese Society for the Promotion of Science)
. "Grant-in-Aid for Transformative Research Areas" (Grant ID 23H04740, Japanese Society for the Promotion of Science)
. "Fellowship" (Grant ID 22H04980, Japanese Society for the Promotion of Science)
. "Fellowship" (Grant ID 22K21352, Japanese Society for the Promotion of Science)
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| Contributor(s) |
Ferreira MJ, Silva J, Takeuchi H, Suzuki T, Higashiyama T, Coimbra S |
| Citation(s) |
39134964 |
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| Submission date |
Nov 08, 2023 |
| Last update date |
Sep 11, 2024 |
| Contact name |
Sílvia Coimbra |
| E-mail(s) |
scoimbra@fc.up.pt
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| Organization name |
LAQV/REQUIMTE, Faculty of Sciences, University of Porto
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| Department |
Biology
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| Lab |
Sexual plant reproduction and development Laboratory
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| Street address |
Rua do Campo Alegre s/n
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| City |
Porto |
| ZIP/Postal code |
4169-007 |
| Country |
Portugal |
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| Platforms (1) |
| GPL19580 |
Illumina NextSeq 500 (Arabidopsis thaliana) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA1037133 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE247348_Processed_datafile_Ferreira_et_al.txt.gz |
242.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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