Organ-level gene-regulatory networks inferred from transcriptomic data reveal context-specific regulation and highlight novel regulators of ripening and ABA-mediated responses in tomato

The organ-level GRNs can be extracted and visualized through the rGRN app in the TomViz module of the PlantaeViz platform (Santiago et al., 2024), available at https://plantaeviz.tomsbiolab.com/tomviz. Supplemental Tables 5, 8, and 11 provide metadata for the public RNA-seq, ATAC-seq, and DNase-seq...

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Detalles Bibliográficos
Autores: Fernández, José D., Navarro-Payá, David, Santiago, Antonio, Cerda, Ariel, Canan, Jonathan, Contreras-Riquelme, Sebastián, Moyano, Tomás C., Landaeta-Sepúlveda, Diego, Melet, Lorena, Canales, Javier, Johnson, Nathan R., Álvarez, José M., Matus, José Tomás, Vidal, Elena A.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2025
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/410014
Acceso en línea:http://hdl.handle.net/10261/410014
Access Level:acceso abierto
Palabra clave:Solanum lycopersicum
Gene-regulatory network
Transcriptional regulation
Tripening
Drought
Descripción
Sumario:The organ-level GRNs can be extracted and visualized through the rGRN app in the TomViz module of the PlantaeViz platform (Santiago et al., 2024), available at https://plantaeviz.tomsbiolab.com/tomviz. Supplemental Tables 5, 8, and 11 provide metadata for the public RNA-seq, ATAC-seq, and DNase-seq experiments, as well as the ChIP-seq libraries analyzed in this study. The DAP-seq data generated for this article are available in the NCBI SRA database under accession number SRA: PRJNA1236412. The scripts used to analyze RNA-seq, ATAC-seq, DNase-seq, ChIP-seq, and DAP-seq data, as well as the GENIE3 network generation pipeline and all GRNs, are available at https://github.com/ibioChile/VidalLab/tree/master/Pipelines/Tomato_GRNs_repository. In addition, the repository includes the ITAG4.2-merged GFF annotation, protein FASTA, and transcript FASTA files, which are also provided as Data S2. Genome annotation (ITAG4.2-merged, GFF3 format), Data S3. Protein sequences (ITAG4.2-merged, FASTA), Data S4. Transcript sequences (ITAG4.2-merged, cDNA FASTA).

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