2026-04-13T05:56:32Zhttps://recercat.cat/oai/requestoai:recercat.cat:20.500.12327/28712025-10-22T11:23:39Zcom_2072_4428com_2072_4427col_2072_487898
RECERCAT
author
Pérez de los Cobos, Felipe
author
García-Gómez, Beatriz E.
author
Orduña-Rubio, Luis
author
Batlle, Ignasi
author
Arús, Pere
author
Tomás Matus, José
author
Eduardo, Iban
other
Producció Vegetal
group
Fructicultura
group
Genòmica i Biotecnologia
2025-10-22T11:23:39Z
2025-10-22T11:23:39Z
2024-01-02
De Los Cobos, Felipe Pérez, Beatriz Ester García-Gómez, Luis Orduña-Rubio, I. Batlle, Pere Arús, José Tomás Matus, and Iban Eduardo. 2024. “Exploring Large-scale Gene Coexpression Networks in Peach (Prunus Persica L.): A New Tool for Predicting Gene Function.” Horticulture Research, 11 (2): uhad294. doi:10.1093/hr/uhad294.
2052-7276
http://hdl.handle.net/20.500.12327/2871
https://doi.org/10.1093/hr/uhad294
Peach is a model for Prunus genetics and genomics, however, identifying and validating genes associated to peach breeding traits is a
complex task. A gene coexpression network (GCN) capable of capturing stable gene–gene relationships would help researchers overcome
the intrinsic limitations of peach genetics and genomics approaches and outline future research opportunities. In this study, we created
four GCNs from 604 Illumina RNA-Seq libraries. We evaluated the performance of every GCN in predicting functional annotations
using an algorithm based on the ‘guilty-by-association’ principle. The GCN with the best performance was COO300, encompassing
21 956 genes. To validate its performance predicting gene function, we performed two case studies. In case study 1, we used two genes
involved in fruit flesh softening: the endopolygalacturonases PpPG21 and PpPG22. Genes coexpressing with both genes were extracted
and referred to as melting flesh (MF) network. Finally, we performed an enrichment analysis of MF network and compared the results
with the current knowledge regarding peach fruit softening. The MF network mostly included genes involved in cell wall expansion
and remodeling, and with expressions triggered by ripening-related phytohormones, such as ethylene, auxin, and methyl jasmonate.
In case study 2, we explored potential targets of the anthocyanin regulator PpMYB10.1 by comparing its gene-centered coexpression
network with that of its grapevine orthologues, identifying a common regulatory network. These results validated COO300 as a powerful
tool for peach and Prunus research. This network, renamed as PeachGCN v1.0, and the scripts required to perform a function prediction
analysis are available at https://github.com/felipecobos/PeachGCN.
eng
Attribution 4.0 International
Exploring large-scale gene coexpression networks in peach (Prunus persica L.): a new tool for predicting gene function
info:eu-repo/semantics/article