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De novo Assembly and Comparative Analysis of Ten Petal Transcriptome (Brassicaceae) Revealed Phylogenetic Relationships and Genetic control of Flower Color Variation

ABSTRACT: Petal is not only the target of selection by horticulturalists to enhance the ornamental value of plants but also emerged as a unique model system for plant organogenesis studies. It is known that three major groups of pigments, betalains, carotenoids and anthocyanins, are responsible for the attractive natural display of flower colors. While carotenoids and betalains generally yield yellow or red colors, anthocyanins confer a diverse range of color from orange to red to violet and blue. In this study, we collected 11 species (Erysimum cheiri, Malcolmia maritime, Brassica oleracea, Raphanus sativus, Orychophragmus violaceus, Eruca sativa, Orychophragmus violaceus, Iberis amara, Aubrieta x cultorum, Lobularia maritime, Matthiola incana) belong to different tribe in Brassicaceae family with varied flower color and performed petal transcriptome analysis. de novo transcriptome assembly showed that average length of the contigs varied from 631bp in O. violaceus to 1212bp in Matthiola incana which indicated that the complexity of the genomes are different much. Protein homology between these species and those sequenced species in Brassicaceae family are consistent with the known phylogenetic relationships. However, O. violaceus has closer relationships with Sisymbrium irio than expected Brassica species. Clustering analysis of genes in anthocyanin and carotenoids synthesis pathway indicated that while silence or low expression of CCD4 (Carotenoid Cleavage Dioxygenase 4) leading to the yellow color formation in different species, purple or red color variation might result from different genes expression variation. These results not only provide transcriptome data for petal development study but also provide useful information for Brassica flower improvement for ornamental purpose.

ORGANISM(S): Lobularia maritima Iberis amara Malcolmia maritima Aubrieta x cultorum Eruca vesicaria subsp. sativa Erysimum cheiri Orychophragmus violaceus Matthiola incana Raphanus sativus Brassica oleracea

PROVIDER: GSE93879 | GEO | 2017/01/24

SECONDARY ACCESSION(S): PRJNA362874

REPOSITORIES: GEO

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Project description:Pink-flowered strawberry is a new promising ornamental flower derived from intergeneric hybridization (Fragaria × Potentilla) with bright color, prolonged flowering period and edible fruits. However, the transcriptional events underlying anthocyanins biosynthesis pathway have not been fully characterized in its petal coloration. The pigment compounds accumulated in its fruits were the same as cultivated strawberry, but different from in its flowers. To gain insights into the regulatory networks related to anthocyanin biosynthesis and identify key genes, we performed an integrated analyses of the transcriptome and metabolomes involved in red petals at three development stages (Bud stage (L), Coloration beginning stage (Z) and Big bud stage (D)) of pink-flowered strawberry. Transcript and metabolite profiles were generated through high-throughput RNA-sequencing and high-performance liquid chromatography coupled with mass spectrometry, respectively. The results showed that the main pigments of red and dark pink petals were anthocyanins, among which cyanidins were the main compounds. There were no anthocyanins detected in white-flowered hybrids. A total of 50 285 non-redundant unigenes were obtained from the transcriptome databases, among which 59 differentially expressed genes could be identified as putative homologues of flower coloration related genes. Based on a comprehensive analysis relating pigmentation compounds to gene expression profiles, the mechanism of flower color formation was examined in pink-flowered strawberry. Furthermore, a new hypothesis explaining the lack of color phenotype of the white-flowered strawberry hybrids from the level of the transcriptome. The expression patterns of FpDFR gene and FpANS gene corresponded to the accumulation patterns of cyanidin contents in pink-flowered strawberry hybrids with different shades of pink; Whereas other anthocyanin biosynthesis genes were weakly related flower color deepened. Moreover, FpANS, FpBZ1 and FpUGT75C1 genes were the key factors that lead to the inability to accumulate anthocyanins in the white petals of PFS hybrids. Meanwhile, the competitive effect of FpFLS gene and FpDFR gene may further inhibit anthocyanin synthesis. The data presented herein are important for understanding of the molecular mechanisms underlying the petal pigmentation and will be powerful for integrating into novel genes that are potential targets for breeding new valuable pink-flowered strawberry cultivars.

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De novo Assembly and Comparative Analysis of Ten Petal Transcriptome (Brassicaceae) Revealed Phylogenetic Relationships and Genetic control of Flower Color Variation

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