Anthocyanins Profiling Analysis and RNA-Seq Revealed the Dominating Pigments and Coloring Mechanism in Cyclamen Flowers

SIMPLE SUMMARY: Flower color is a complex plant trait that is mainly controlled by the accumulation of pigments, such as anthocyanins. However, the great diversity of flower color in plants cannot be attributed to a single pigment. Therefore, a more comprehensive approach is needed to fully understand the whole pigment spectrum. In this study, we used metabolomics to profile more than 100 plant pigment in red-flowered cyclamen. By comparing the anthocyanins metabolome in white-flowered cyclamen, we were able to identify key anthocyanins that are highly abundant in red flowers, but low in white flowers. Thus, we can pinpoint the pigments underlying specific flower color phenotype. To further reveal the gene expression network that ultimately controlling the production of pigments, we also performed RNA-Seq using the same plant materials. The transcriptomics revealed a significant altered gene expression profile between red flowers compared to white flowers. More importantly, differential expression analysis allowed us to identify key genes governing the pigment metabolome and flower color. Collectively, our study significantly advanced our understanding of the molecular basis of flower color in cyclamen. ABSTRACT: Pigments in cyclamen (Cyclamen purpurascens) endows flowers with great ornamental and medicinal values. However, little is known about the biosynthetic pathways of pigments, especially anthocyanins, in cyclamen flowers. Herein, anthocyanins profiling and RNA-Seq were used to decipher the molecular events using cyclamen genotypes of red (HXK) or white (BXK) flowers. We found that red cyclamen petals are rich in cyanidin-3-O-rutinoside, cyanidin-3-O-glucoside, delphinidin-3-O-glucoside, malvidin-3-O-glucoside, peonidin-3-O-rutinoside, quercetin-3-O-glucoside, and ruti. In addition, our transcriptomics data revealed 3589 up-regulated genes and 2788 down-regulated genes comparing the BXK to HXK. Our rich dataset also identified eight putative key genes for anthocyanin synthesis, including four chalcone synthase (CHS, g13809_i0, g12097_i0, g18851_i0, g36714_i0), one chalcone isomerase (CHI, g26337_i0), two flavonoid 3-hydroxylase (F3′H, g14710_i0 and g15005_i0), and one anthocyanidin synthase (ANS, g18981_i0). Importantly, we found a 2.5 order of magnitude higher expression of anthocyanin 3-O-glucosyltransferase (g8206_i0), which encodes a key gene in glycosylation of anthocyanins, in HXK compared to BXK. Taken together, our multiomics approach demonstrated massive changes in gene regulatory networks and anthocyanin metabolism in controlling cyclamen flower color.