Comparative transcriptomic profiling of field-grown cassava genotypes across season transitions
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| Natura: | Recurso digital |
| Lingua: | inglese |
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2025
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| _version_ | 1866901852894789632 |
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| author | GISEL, ANDREAS T Webber-Birungi, Mariam STAVOLONE, LIVIA |
| author_facet | GISEL, ANDREAS T Webber-Birungi, Mariam STAVOLONE, LIVIA |
| contents | <div> <p><span lang="EN-US">Cassava is a perennial crop cultivated in tropical and subtropical areas. In its cultivation cycle, it encounters environmental stresses related to changes in temperature and water fluctuations during seasonal transitions.</span> </p> </div> <div> <p><span lang="EN-US">We profiled the transcriptomes of four field-grown genotypes to investigate the molecular basis of adaptation to season transitions. 3’mRNA-seq libraries were prepared from samples collected from storage roots to capture gene expression changes associated with shifts from rainy to dry and dry to rainy seasons. </span> </p> </div> <div> <p><span lang="EN-GB">Reproducibility and variability within the dataset were evaluated using correlation analysis and principal component analysis, providing confidence in data quality and consistency across samples.</span> </p> </div> <div> <p><span lang="EN-US">The usability of these data was proved by differential expression analysis during the rainy-to-dry and dry-to-rainy transitions, and by functional enrichment analysis. The detailed information of the experimental environmental conditions and of the workflow from planting to final DEGs analysis provided, make this dataset a useful resource for future research on plant responses to environmental fluctuations and to identify candidate genes for crop improvement strategies for climate-resilient varieties.</span> </p> <p>The following results of the data analysis of the data set published as <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB79515">PRJEB79515</a> on ENA are available:</p> <p><strong>Actionable targets:</strong> Key differentially expressed genes (sigDEGs) identified during cassava's R1-D1 and D1-R2 transitions, categorized by regulation status and associated pathways. They represent actionable targets for improving drought resilience, recovery mechanisms, and stress tolerance through pathways such as stress perception, osmotic adjustment, oxidative stress response, and protein stabilization.</p> <p><strong>Gene Annotation: </strong>Ensemble gene IDs of the significantly differentially expressed genes (sigDEGs) were used to perfom functional annotation in the Database of Annotation, Visualization, and Integrated Discovery (DAVID) platform.</p> <p><strong>GO Terms: </strong>GO enrichment in shared R1-D1 & D1-R2 genes. PlantRegMap enrichment tool was used, integrating annotations from TAIR10, UniProt-GOA, InterProScan, and RBH experimental data. topGO and Fisher’s exact tests identified significantly over-represented (p = 0.05) GO terms in the input gene set. Manihot esculenta genes were used as the background.</p> <p><strong>Growth parameters:</strong> Agronomical traits data: WAP= Weeks after planting; rep= replicates; FSRM= Fresh storage root mass (kg); Shoot=. Shoot mass (kg); PH= Plant height (cm); LA= Leaf Area (cm2); DMS= Dry matter (%)</p> <p><strong>KEGG Pathways:</strong> KEGG pathway enrichment in shared R1-D1 & D1-R2 genes. Enrichment was determined using ShinyGO V0.77 (Ge et al., 2020) intergrated with the PlantGSAD pathway database (Kanehisa et al., 2021), at FDR of 5%, using and pathway sizes of 2-2000 genes (Data S3). Manihot esculenta genes were used as the background.</p> <p>T<strong>F-Targets:</strong> All predicted Transcription Factors clustered in families of all DEGs.</p> <p><strong>Weather Data:</strong> Statistics of the weather data collected dring the experiments</p> <p> </p> </div> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_15545011 |
| institution | Zenodo |
| language | eng |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Comparative transcriptomic profiling of field-grown cassava genotypes across season transitions GISEL, ANDREAS T Webber-Birungi, Mariam STAVOLONE, LIVIA Cassava Transcriptomics Drought Resistance <div> <p><span lang="EN-US">Cassava is a perennial crop cultivated in tropical and subtropical areas. In its cultivation cycle, it encounters environmental stresses related to changes in temperature and water fluctuations during seasonal transitions.</span> </p> </div> <div> <p><span lang="EN-US">We profiled the transcriptomes of four field-grown genotypes to investigate the molecular basis of adaptation to season transitions. 3’mRNA-seq libraries were prepared from samples collected from storage roots to capture gene expression changes associated with shifts from rainy to dry and dry to rainy seasons. </span> </p> </div> <div> <p><span lang="EN-GB">Reproducibility and variability within the dataset were evaluated using correlation analysis and principal component analysis, providing confidence in data quality and consistency across samples.</span> </p> </div> <div> <p><span lang="EN-US">The usability of these data was proved by differential expression analysis during the rainy-to-dry and dry-to-rainy transitions, and by functional enrichment analysis. The detailed information of the experimental environmental conditions and of the workflow from planting to final DEGs analysis provided, make this dataset a useful resource for future research on plant responses to environmental fluctuations and to identify candidate genes for crop improvement strategies for climate-resilient varieties.</span> </p> <p>The following results of the data analysis of the data set published as <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB79515">PRJEB79515</a> on ENA are available:</p> <p><strong>Actionable targets:</strong> Key differentially expressed genes (sigDEGs) identified during cassava's R1-D1 and D1-R2 transitions, categorized by regulation status and associated pathways. They represent actionable targets for improving drought resilience, recovery mechanisms, and stress tolerance through pathways such as stress perception, osmotic adjustment, oxidative stress response, and protein stabilization.</p> <p><strong>Gene Annotation: </strong>Ensemble gene IDs of the significantly differentially expressed genes (sigDEGs) were used to perfom functional annotation in the Database of Annotation, Visualization, and Integrated Discovery (DAVID) platform.</p> <p><strong>GO Terms: </strong>GO enrichment in shared R1-D1 & D1-R2 genes. PlantRegMap enrichment tool was used, integrating annotations from TAIR10, UniProt-GOA, InterProScan, and RBH experimental data. topGO and Fisher’s exact tests identified significantly over-represented (p = 0.05) GO terms in the input gene set. Manihot esculenta genes were used as the background.</p> <p><strong>Growth parameters:</strong> Agronomical traits data: WAP= Weeks after planting; rep= replicates; FSRM= Fresh storage root mass (kg); Shoot=. Shoot mass (kg); PH= Plant height (cm); LA= Leaf Area (cm2); DMS= Dry matter (%)</p> <p><strong>KEGG Pathways:</strong> KEGG pathway enrichment in shared R1-D1 & D1-R2 genes. Enrichment was determined using ShinyGO V0.77 (Ge et al., 2020) intergrated with the PlantGSAD pathway database (Kanehisa et al., 2021), at FDR of 5%, using and pathway sizes of 2-2000 genes (Data S3). Manihot esculenta genes were used as the background.</p> <p>T<strong>F-Targets:</strong> All predicted Transcription Factors clustered in families of all DEGs.</p> <p><strong>Weather Data:</strong> Statistics of the weather data collected dring the experiments</p> <p> </p> </div> |
| title | Comparative transcriptomic profiling of field-grown cassava genotypes across season transitions |
| topic | Cassava Transcriptomics Drought Resistance |
| url | https://doi.org/10.5281/zenodo.15545011 |