ChiliCross: an R package with data of two crosses of chili pepper (Capsicum annuum L.) during fruit development

The R package "ChiliCross" contains standardized gene expression for two crosses of chili pepper (Capsicum annuum L.) during fruit development and also results of Gene Ontology (GO) enrichment analyses for sets of genes. There is also a function to plot cross results.

Gene expression data were obtained from RNA-Seq libraries constructed from accessions CM (criollo de Morelos 334, domesticated), QU (piquín Querétaro, wild) and the two F₁s: CQ resulting from CM female x QU male, and QC resulting from QU female x CM male (GEO Series accession number GSE165448). Estimation of gene expression was performed for each one of the participants in the crosses at 0, 10, 20, 30, 40, 50 and 60 Days After Anthesis (DAA). You can explore the way in which gene expression of 22,374 genes behaved in those two crosses during fruit development. Gene expression was standardized, thus the vector of gene expression of the three participants in a cross has a mean of 0 and standard deviation of 1. Gene expression was classified into 4 classes and 19 exhaustive sub-models. You can also install our R package Salsa to complement the study of gene expression for a larger set of accessions.

Acknowledgements
We thank Neftalí Ochoa-Alejo, M. Humberto Reyes-Valdés, Magda L. Arce-Rodríguez, Fernando Hernández-Godínez, Felipe Cervantes-Hernández, Corina Hayano-Kanashiro, José J. Ordaz-Ortiz and Ana Garcés-Claver for help in the obtention and processing of the data and  Alan Flores-Díaz for review of the R package. C.E-S acknowledge Conacyt scholarship for PhD studies (Grant No. 630487). This research was funded by the Consejo Nacional de Ciencia y Tecnología, México (Conacyt Project 1570).