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De novo transcriptomic analysis of light-induced flavonoid pathway, transcription factors in the flower buds of Lonicera japonica

  • Hailing Fang
  • Xiwu Qi
  • Yiming Li
  • Xu Yu
  • Dongbei Xu
  • Chengyuan LiangEmail author
  • Weilin Li
  • Xin Liu
Original Article
  • 23 Downloads
Part of the following topical collections:
  1. Functional Genomics

Abstract

Key message

Transcriptomic analysis of the relationship between gene expression patterns and flavonoid contents in the flower buds of Lonicera japonica under light-induced conditions, especially the flavonoid pathway genes and transcription factors.

Abstract

Flos Lonicerae Japonicae (FLJ), the flower buds of Lonicera japonica Thunb., has been used to treat some human diseases including severe respiratory syndromes and hand-foot-and-mouth diseases owing to its putative antibacterial, and antiviral effects. Luteoloside is a flavonoid that is used by the Chinese Pharmacopoeia to evaluate the quality of FLJ. Light is an important environmental factor that affects flavonoid biosynthesis in the flower buds of L. japonica. However, how light triggers increases in flavonoid production remains unclear. To enhance our understanding of the mechanism involved in light-regulated flavonoid biosynthesis, we sequenced the transcriptomes of L. japonica exposed to three different light conditions: 100% light intensity (CK), 50% light intensity (LI50), and 25% light intensity (LI25) using an Illumina HiSeq 4000 System. A total of 77,297 unigenes with an average length of 809 bp were obtained. Among them, 43,334 unigenes (56.06%) could be matched to at least one biomolecular database. Additionally, 4188, 1545 and 1023 differentially expressed genes (DEGs) were identified by comparative transcriptomics LI25-vs-CK, LI50-vs-CK, and LI25-vs-LI50, respectively. Of note, genes known to be involved in flavonoid biosynthesis, such as 4-coumarate coenzyme A ligase (4CL), and chalcone synthase (CHS) were up-regulated. In addition, a total of 1649 transcription factors (TFs) were identified and divided into 58 TF families; 98 TFs exhibited highly dynamic changes in response to light intensity. Quantitative real-time PCR (qRT-PCR) was used to test the expression profiles of the RNA sequencing (RNA-Seq) data. This study offers insight into how transcriptional expression pattern is influenced by light in the flower buds of L. japonica, and will enhance the understanding of molecular mechanisms of flavonoid biosynthesis in response to light in L. japonica.

Keywords

Lonicera japonica Thunb. Transcription Factor Light intensity Flavonoid Transcriptome sequencing 

Abbreviations

FLJ

Flos Lonicerae Japonicae

DEGs

Differentially expressed genes

4CL

4-coumarate coenzyme A ligase

CHS

Chalcone synthase

TF

Transcription factor

qRT-PCR

Quantitative real-time PCR

RNA-seq

RNA sequencing

PAL

Phenylalanine ammonia-lyase

F3H

Flavanone 3-hydroxylase

FLS

Flavonol synthase

CHI

Chalcone isomerase

F3′H

Flavonoid 3′-hydroxylase

DFR

Dihydroflavonol 4-reductase

ANS

Anthocyanidin synthase

C4H

Cinnamic acid 4-hydroxylase

NR

Non-redundant protein sequence database

KOG

Clusters of eukaryotic orthologous Group

GO

Gene ontology

KEGG

Kyoto encyclopedia of genes and genomes

FSII

Flavonol synthase

UFGT

UDP-glucose: flavone 7-O-beta-glucosyltransferase

Notes

Acknowledgements

This work was supported by the National Natural Science Foundation of China (31500249), the Natural Science Foundation of the Jiangsu Province (BK20160603, BK20161381).

Compliance with ethical standards

Conflict of interest

No potential conflict of interest was reported by the authors.

Availability of supporting data

We have deposit our data in Sequence Read Archive (SRA) database (http://www.ncbi.nlm.nih.gov/sra/), the accession for our submission is: SRP132670.

Supplementary material

468_2019_1916_MOESM1_ESM.png (19 kb)
Supplementary material 1 (PNG 19 kb). Fig S1 Length distribution of the assembled unigenes with a distribution larger than 200 bp in L. japonica
468_2019_1916_MOESM2_ESM.png (101 kb)
Supplementary material 2 (PNG 101 kb). Fig S2 Gene ontology (GO) classifications of DEGs in pairwise comparisons (LI25-vs-CK, LI50-vs-CK, and LI25-vs-LI50). The DEGs were classified into three main categories: (A) cellular component, (B) molecular function, and (C) biological process. Each bar indicates the number of unigenes classified under each specific category
468_2019_1916_MOESM3_ESM.docx (18 kb)
Supplementary material 3 (DOCX 17 kb)
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Supplementary material 4 (DOCX 16 kb)
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Supplementary material 5 (DOCX 18 kb)
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Supplementary material 6 (DOCX 32 kb)
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Supplementary material 7 (DOCX 23 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Hailing Fang
    • 1
  • Xiwu Qi
    • 1
  • Yiming Li
    • 2
  • Xu Yu
    • 1
    • 3
  • Dongbei Xu
    • 1
  • Chengyuan Liang
    • 1
    Email author
  • Weilin Li
    • 2
  • Xin Liu
    • 2
  1. 1.Institute of BotanyJiangsu Province and Chinese Academy of SciencesNanjingPeople’s Republic of China
  2. 2.Nanjing Forestry UniversityNanjingChina
  3. 3.Missouri State UniversitySpringfieldUSA

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