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

Abstract

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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Abbreviations

3GT:

Anthocyanin 3-O-glucosyltransferase

5GT:

Anthocyanin 5-O-glucosyltransferase

a*, b*:

Chromatic components

ABP:

Anthocyanin biosynthetic pathway

ANS:

Anthocyanin synthase

AOMT:

Anthocyanin O-methyltransferase

bHLH:

Basic helix-loop-helix

C*:

Chroma (brightness)

CHI:

Chalcone isomerase

CHS:

Chalcone synthase

CIE:

Three-Dimensional International Commission on Illumination

COG:

Cluster of orthologous groups of proteins database

DEGs:

Differentially expressed genes

DFR:

Dihydroflavonol 4-reductase

F3′H:

Flavonoid 3′-hydroxylase

F3H:

Flavanone 3-hydroxylase

FDR:

False discovery rates

FLS:

Flavonol synthase

FPKM:

Fragments per kilobase per million mapped reads

GO:

Gene ontology database

KEGG:

Kyoto encyclopedia of genes and genomes database

KOG:

EuKaryotic Orthologous Groups database

L*:

Lightness

NCBI:

National Center for Biotechnology Information

NR:

Non-resundant protein database

Pfam:

Protein family

qRT-PCR:

Quantitative reverse transcription PCR

R:

Pearson’s correlation coefficient

RNA-Seq:

RNA sequencing

SEM:

Scanning electron microscopy

SDs:

Standard deviations

SwissProt:

SwissProt protein database

TFs:

Transcription factors

UHPSFC–MS:

Ultra-high performance supercritical fluid chromatography–mass spectrometry

WD40:

WD40 proteins

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Acknowledgements

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.

Funding

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).

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Contributions

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.

Corresponding author

Correspondence to Qianqian Shi.

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All the authors have declared no conflict of interest.

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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). https://doi.org/10.1007/s12298-019-00664-6

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Keywords

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