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Comparative transcriptome analyses reveal genes related to pigmentation in the petals of red and white Primula vulgaris cultivars


Primula vulgaris is an important ornamental plant species with various flower color. To explore the molecular mechanism of its color formation, comparative transcriptome analyses of the petals in red and white cultivars was performed. A total of 4451 differentially expressed genes were identified and annotated into 128 metabolic pathways. Candidate genes FLS, F3′H, DFR, ANS and AOMT in the anthocyanin pathway were expressed significantly higher in the red cultivar than the white and may be responsible for the red coloration. In the red petals, a putative transcription factors bHLH (c52273.graph_c0) was up-regulated about 14-fold, while a R2R3-MYB unigene (c36140.graph_c0) was identified as a repressor involved in anthocyanin regulation and was significantly down-regulated. In addition, the anatomy analyses and pigments composition in the red and white petals were also analyzed. The papillae on the adaxial epidermis of the red petals of P. vulgaris display a triangle-shapes, in contrast with a spherical shape for the white petals. Although flavonoids were detected in both cultivars, anthocyanins could only be identified in the red cultivar. Gossypetin and peonidin/rosinin were the most abundant pigments in red petals. This study shed light on the genetic and biochemistry mechanisms underlying the flower coloration in Primula.

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Anthocyanin 3-O-glucosyltransferase


Anthocyanin 5-O-glucosyltransferase

a*, b*:

Chromatic components


Anthocyanin biosynthetic pathway


Anthocyanin synthase


Anthocyanin O-methyltransferase


Basic helix-loop-helix


Chroma (brightness)


Chalcone isomerase


Chalcone synthase


Three-Dimensional International Commission on Illumination


Cluster of orthologous groups of proteins database


Differentially expressed genes


Dihydroflavonol 4-reductase


Flavonoid 3′-hydroxylase


Flavanone 3-hydroxylase


False discovery rates


Flavonol synthase


Fragments per kilobase per million mapped reads


Gene ontology database


Kyoto encyclopedia of genes and genomes database


EuKaryotic Orthologous Groups database




National Center for Biotechnology Information


Non-resundant protein database


Protein family


Quantitative reverse transcription PCR


Pearson’s correlation coefficient


RNA sequencing


Scanning electron microscopy


Standard deviations


SwissProt protein database


Transcription factors


Ultra-high performance supercritical fluid chromatography–mass spectrometry


WD40 proteins


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The authors thank Prof. Hui Zhang and Dr. Zhen Xue from Key Laboratory of Plant Molecular Physiology and Dr. Yan Zhu from core facility at key laboratory of plant resource, Institute of Botany, Chinese Academy of Sciences for technical assistances.


This study was funded by the National Science Foundation of China (31800599), Scientific Startup foundation for Doctor of Northwest A&F University (Z109021715), Student’s Platform for Innovation and Entrepreneurship Training Program (201710712029), Fundamental Research Funds for the Central Universities (Z109021606), General Financial Grant from the China Postdoctoral Science Foundation (2017M623267).

Author information




LL performed the experiments, analyzed the data and wrote the manuscript. YZ, XL, YZ helped prepare the plant materials and performed some experiments. QS designed the study. All authors read and approved the final manuscript.

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Correspondence to Qianqian Shi.

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Figure S1

Statistics for the annotation results. Figure S2 Statistical graph of differentially expressed unigenes between the red and white Primula vulgaris cultivars. Figure S3 Correlation of gene expression results obtained from qRT-PCR and RNA-seq analyses of color-related genes in red and white Primula vulgaris cultivars. Figure S4 Phylogenetic analysis of R2R3-MYB in Primula vulgaris and other plant species. Full-length protein sequences were aligned using Clustal W, and phylogenetic analysis was conducted with MEGA 5.0 software using the neighbor-joining method and 1000 bootstrap replicates. Figure S5 Phylogenetic analysis of bHLH in Primula vulgaris and other plant species. Full-length protein sequences were aligned using Clustal W, and phylogenetic analysis was conducted with MEGA 5.0 software using the neighbor-joining method and 1000 bootstrap replicates. Table S1 Selected genes and primers used in qRT-PCR analysis. Table S2 Overall assembly statistics for the transcriptome of red and white flowers of Primula vulgaris (DOC 2076 kb)

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Li, L., Zhai, Y., Luo, X. et al. Comparative transcriptome analyses reveal genes related to pigmentation in the petals of red and white Primula vulgaris cultivars. Physiol Mol Biol Plants 25, 1029–1041 (2019).

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  • Primula vulgaris
  • Red petal
  • Anthocyanin biosynthesis
  • Flower coloration
  • R2R3-MYB
  • Epigenetic analysis