Transcriptome regulation of carotenoids in five flesh-colored watermelon (Citrullus lanatus)

Abstract

Background: Fruit flesh color in watermelon (Citrullus lanatus) is a great index for evaluation of the appearance quality and a key contributor influencing consumers' preferences, but the molecular mechanism of this intricate trait remain largely unknown. Here, the carotenoids and transcriptome dynamics during the fruit development of cultivated watermelon with five different flesh colors were analyzed.Results: A total of 13 carotenoids and 16781 differentially expressed genes (DEGs) including 1295 transcription factors (TFs) were detected in five watermelon genotypes during the fruit development. The comprehensive accumulation patterns of carotenoids were closely related to flesh color. A number of potential structural genes and transcription factors were found to be associated with the carotenoid biosynthesis pathway using comparative transcriptome analysis. The differentially expressed genes were divided into six subclusters and distributed in different GO terms and metabolic pathways. Furthermore, we performed weighted gene co-expression network analysis and predicted hub genes in six main modules determining carotenoid contents. Cla018406 (a chaperone protein dnaJ-like protein) may be a candidate gene for β-carotene accumulation and highly expressed in orange flesh-colored fruit. Cla007686 (a zinc finger CCCH domain-containing protein) was highly expressed in the red flesh-colored watermelon, maybe a key regulator of lycopene accumulation. Cla003760 (membrane protein) and Cla021635 (photosystem I reaction center subunit II) were predicted to be hub genes and may play an essential role in yellow flesh formation.Conclusions: The composition and contents of carotenoid in five watermelon genotypes vary greatly. A series of candidate genes were revealed through combined analysis of metabolites and transcriptome. These results provide an important data resource for dissecting the candidate genes and molecular basis governing flesh color formation in watermelon fruit.

Integrated analysis of carotenoid metabolites and transcriptome identifies key genes controlling carotenoid compositions and content in sweetpotato tuberous roots (Ipomoea batatas L.)

“…KEGG enrichment analysis and NR annotation showed that, there are 27 structural genes participated in carotenoid metabolic pathway among the four combinations (LY vs. W, Y vs. W, O vs. W, OR vs. W), and the sweetpotato carotenoid metabolic pathway were mapped (Figure 3). The pathway was constructed based on KEGG and references (Suematsu et al, 2020;Xu et al, 2021;Yuan et al, 2021;KEGG, 2022). Of which 10 DEGs namely Or (1), CRTISO (1), CYP97B2 (1), CHYB (1), ZEP (2), NSY (1) and DWARF27 (3) were playing major role in carotenoid biosynthesis pathway and 17 DEGs namely CCD1 (8), CCD4 (1), CCD7 (1), NCED (4) and CYP707A (3) were related to carotenoid degradation pathway.…”

“…In recent years, several transcription factors that regulate and control the carotenoid metabolic pathway have been identified in several crop species (Ampomah-Dwamena et al, 2019;Yuan et al, 2021). In present study, we performed WGCNA to identify transcription factors that coordinately regulate the biosynthesis and accumulation of carotenoids.…”