Fig 1.
A) Chiltepin and Serrano fruits at different stages of development, marked with 20 DAA and 60/68 DAA the immature and mature stages sampled for the analysis performed in this study. B) Venn diagram for the number of genes expressed at each sampled stage of development for Chiltepin and Serrano. Numbers in each intersection represent the number of genes expressed in the sets corresponding to the intersection. C) Venn diagram for the number of differentially expressed genes (DEGs) per contrast; numbers in intersections represent the number of genes differentially expressed shared in the intersection contrasts. D) Number of downregulated and upregulated genes in each of the four contrasts. E) Heatmap representation of the DEGs found in at least one contrast, clustered by expression pattern of samples (columns) and genes (rows). Colored boxes at the beginning of every row indicate the contrast in which the corresponding gene is differentially expressed (DE); a purple box (shared) means the corresponding gene is DE in two or more contrasts. E) Heatmap representation of all DEGS clustered by expression pattern of samples (columns) and genes (rows); colored boxes indicated the contrast where the corresponding gene is differentially expressed.
Fig 2.
Gene ontology enrichment analysis of differentially expressed genes (DEGs).
X-axis indicates the number of DEGs in the corresponding GO term, and the color of the bars represents the ontology of the corresponding GO term. A) Enriched GO terms in contrast Ch20-Ch68 (Chiltepin 20 vs 68 DAA), B) Enriched GO terms in contrast St20-St60 (Serrano 20 vs 60 DAA).
Fig 3.
Metabolic pathway enrichment of differentially expressed genes (DEGs).
X-axis indicates the gene ratio (the quotient of the number of DEGs and the number of genes in the background); the bubble size represents the number of DEGs in the corresponding pathway, and the color of the bubble indicates the enrichment q value of the corresponding pathway, lower q values mean more significant enrichment. A) enriched pathways of contrast St20-St60 (Serrano 20 vs 60 DAA). B) enriched pathways in contrast Ch20-Ch68 (Chiltepin 20 vs 68 DAA).
Fig 4.
MapMan summary of changes in the expression of differentially expressed genes (DEGs) in pathways regulation: Hormones, signaling, protein modification, protein degradation and transcription factors; and secondary metabolism: Terpenoids, phenylpropanoids, flavonoids, carotenoids, glucosinolates, etc.
Each square represents a separate DEG, red indicates upregulation and blue indicates downregulation of the respective gene in the corresponding contrast. A) MapMan summary of DEGs in contrast Ch20-St20 (Chiltepin vs Serrano at 20 DAA). B) MapMan summary of DEGs in contrast Ch68-St60 (Chiltepin vs Serrano at 68(60) DAA). C) Map Man summary of DEGs in contrast Ch20-Ch68 (Chiltepin 20 vs 68 DAA). D) MapMan summary of DEGs in contrast St20-St60 (Serrano 20 vs 60 DAA).
Fig 5.
Heatmap representation of the differentially expressed genes (DEGs) of pepper orthologs of tomato fruit development and ripening genes.
Expression pattern clustered by samples (columns) and genes (rows). Colored boxes at the beginning of every row indicates the contrast in which the corresponding gene is differentially expressed (DE), a purple box (shared) means the corresponding gene is DE in two or more contrasts.
Fig 6.
Biological model for the fruit maturation process of A) Serrano pepper (St20-St60), and B) Chiltepin pepper (Ch20-Ch68).
Red boxes indicate genes induced (with at least 4-fold expression at the mature stage), blue boxes indicate gene repressed (with at least 4-fold expression at the immature stage).