Transcriptome Analyses Throughout Chili Pepper Fruit Development Reveal Novel Insights into the Domestication Process

Abstract

Chili pepper (Capsicum spp.) is an important crop, as well as a model for fruit development studies and domestication. Here, we performed a time-course experiment to estimate standardized gene expression profiles with respect to fruit development for six domesticated and four wild chili pepper ancestors. We sampled the transcriptomes every 10 days from flowering to fruit maturity, and found that the mean standardized expression profiles for domesticated and wild accessions significantly differed. The mean standardized expression was higher and peaked earlier for domesticated vs. wild genotypes, particularly for genes involved in the cell cycle that ultimately control fruit size. We postulate that these gene expression changes are driven by selection pressures during domestication and show a robust network of cell cycle genes with a time shift in expression, which explains some of the differences between domesticated and wild phenotypes.

A method to analyze time expression profiles demonstrated in a database of chili pepper fruit development

“…For each combination of accession time of development, 2 RNA-Seq libraries (biological replicates) were constructed, thus a total of RNA-Seq libraries were employed to estimate time expression profiles. Additionally, some of the accessions were sampled in times larger than 60 DAA, but those data were not used for time profile estimation; please see Supplementary material in 22 . In total we obtained data from 179 RNA-Seq libraries, that comprise the 168 used for time profiles estimation plus some extra samples from times larger than 60 DAA as well as libraries from plantlet stage for one domesticated and one wild accession.…”

“…Descriptions of these 179 libraries are in data frame “library.desc”, while raw counts of map reads for all genes at each one of the libraries is in data frame “readcounts”, both within the Salsa package. Sequencing, filtering and mapping of the raw reads to the reference Capsicum genome are presented in the supplementary methods and results in 22 . In total more that 3 billions of raw reads where map to the reference genome, and these data have been deposited in NCBI’s gene expression omnibus (GEO) 25 , and are accessible through GEO Series accession number GSE165448 ( https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE165448 ).…”

“…Finally, we calculate the SEP for a gene i as a vector , where and , i.e., we use the pair to calculate an standardized version of the gene expression pattern which has mean of 0 and standard deviation, S (), equal to 1. For details of this procedure please see the “Supplementary Material” in 22 as well as Additional file 1 .…”

“…Chili pepper ( Capsicum spp.) is an important crop, as well as a model for fruit development studies and domestication 22 . We developed a methodology to examine time expression profiles by testing neighboring time intervals and then obtaining “Standardized Expression Profiles” (SEPs), which can be easily interpreted and tested.…”

“…All curated data and functions to analyze them are included in the R 23 package “Salsa” 24 . This data mining tool arouse during the course of a previous project, and has proven to be useful to reveal novel insights about the domestication of chili pepper 22 ; please see https://www.mdpi.com/2223-7747/10/3/585 . Here we explain the rationale of the methodology, present a panorama of its possibilities and exemplify the use of this tool.…”