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A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms

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A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms

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dc.contributor.author Xanthopoulou, Aliki es_ES
dc.contributor.author Montero-Pau, Javier es_ES
dc.contributor.author Picó Sirvent, María Belén es_ES
dc.contributor.author Boumpas, Panagiotis es_ES
dc.contributor.author Tsaliki, Eleni es_ES
dc.contributor.author Paris, Harry S. es_ES
dc.contributor.author Tsaftaris, Athanasios es_ES
dc.contributor.author Kalivas, Apostolos es_ES
dc.contributor.author Mellidou, Ifigeneia es_ES
dc.contributor.author Ganopoulos, Ioannis es_ES
dc.date.accessioned 2022-06-09T18:07:05Z
dc.date.available 2022-06-09T18:07:05Z
dc.date.issued 2021-05-12 es_ES
dc.identifier.issn 1471-2164 es_ES
dc.identifier.uri http://hdl.handle.net/10251/183164
dc.description.abstract [EN] Background Summer squash (Cucurbita pepo: Cucurbitaceae) are a popular horticultural crop for which there is insufficient genomic and transcriptomic information. Gene expression atlases are crucial for the identification of genes expressed in different tissues at various plant developmental stages. Here, we present the first comprehensive gene expression atlas for a summer squash cultivar, including transcripts obtained from seeds, shoots, leaf stem, young and developed leaves, male and female flowers, fruits of seven developmental stages, as well as primary and lateral roots. Results In total, 27,868 genes and 2352 novel transcripts were annotated from these 16 tissues, with over 18,000 genes common to all tissue groups. Of these, 3812 were identified as housekeeping genes, half of which assigned to known gene ontologies. Flowers, seeds, and young fruits had the largest number of specific genes, whilst intermediate-age fruits the fewest. There also were genes that were differentially expressed in the various tissues, the male flower being the tissue with the most differentially expressed genes in pair-wise comparisons with the remaining tissues, and the leaf stem the least. The largest expression change during fruit development was early on, from female flower to fruit two days after pollination. A weighted correlation network analysis performed on the global gene expression dataset assigned 25,413 genes to 24 coexpression groups, and some of these groups exhibited strong tissue specificity. Conclusions These findings enrich our understanding about the transcriptomic events associated with summer squash development and ripening. This comprehensive gene expression atlas is expected not only to provide a global view of gene expression patterns in all major tissues in C. pepo but to also serve as a valuable resource for functional genomics and gene discovery in Cucurbitaceae. es_ES
dc.description.sponsorship BP was funded by Ministerio de Ciencia, Innovacion y Universidades, cofunded with FEDER funds (Project No. AGL2017-85563-C2-1-R) and by PROMETEO project 2017/078 (to promote excellence groups) by the Conselleria d'Educacio, Investigacio, Cultura vertical bar Esports (Generalitat Valenciana). es_ES
dc.language Inglés es_ES
dc.publisher Springer (Biomed Central Ltd.) es_ES
dc.relation.ispartof BMC Genomics es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject Gene expression atlas es_ES
dc.subject Cucurbita pepo es_ES
dc.subject RNA-seq,Differential gene expression es_ES
dc.subject Plant growth and development es_ES
dc.subject Cucurbitaceae es_ES
dc.subject Novel genes es_ES
dc.subject Fruit growth and ripening es_ES
dc.subject.classification GENETICA es_ES
dc.title A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1186/s12864-021-07683-2 es_ES
dc.relation.projectID info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/AGL2017-85563-C2-1-R/ES/CONTROL MULTIDISCIPLINAR DE ENFERMEDADES FUNGICAS Y VIROSIS EN MELON Y SANDIA: UN NUEVO RETO/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/GENERALITAT VALENCIANA//PROMETEO%2F2017%2F078//SELECCION DE VARIEDADES TRADICIONALES Y DESARROLLO DE NUEVAS VARIEDADES DE CUCURBITACEAS ADAPTADAS A LA PRODUCCION ECOLOGICA./ es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia es_ES
dc.description.bibliographicCitation Xanthopoulou, A.; Montero-Pau, J.; Picó Sirvent, MB.; Boumpas, P.; Tsaliki, E.; Paris, HS.; Tsaftaris, A.... (2021). A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms. BMC Genomics. 22(1):1-17. https://doi.org/10.1186/s12864-021-07683-2 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.1186/s12864-021-07683-2 es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 17 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 22 es_ES
dc.description.issue 1 es_ES
dc.identifier.pmid 33980145 es_ES
dc.identifier.pmcid PMC8114506 es_ES
dc.relation.pasarela S\464777 es_ES
dc.contributor.funder GENERALITAT VALENCIANA es_ES
dc.contributor.funder AGENCIA ESTATAL DE INVESTIGACION es_ES
dc.contributor.funder European Regional Development Fund es_ES
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dc.subject.ods 02.- Poner fin al hambre, conseguir la seguridad alimentaria y una mejor nutrición, y promover la agricultura sostenible es_ES
dc.subject.ods 15.- Proteger, restaurar y promover la utilización sostenible de los ecosistemas terrestres, gestionar de manera sostenible los bosques, combatir la desertificación y detener y revertir la degradación de la tierra, y frenar la pérdida de diversidad biológica es_ES


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