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De Novo Transcriptomics Analysis of the Floral Scent of Chinese Narcissus

  • Yansen HeEmail author
  • Min Xu
  • Xiaojing ChenEmail author
Article
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Abstract

The Chinese narcissus is a well-known monocotyledon plant with a beautiful color, and fresh with a sweet floral scent. Lack of transcriptomic and genomic information hinders understanding of the molecular mechanisms underlying the biosynthesis of narcissus floral scent volatiles. Here we predicted the functions of identified significantly differentially expressed genes (DEGs), according to public protein annotation databases. Using RNA-sequencing (RNA-Seq) on the Illumina HiSeq system and de novo transcriptome assembly, we investigated gene expression in narcissus corona and petal tissues at the early flowering (day 1) and full-bloom (day 7) stages. Significant differences in the expression profiles of 14 fragrance-related genes were further analyzed by qRT-PCR. A total of 62,826,860,514 bases were generated by RNA-seq; clean reads were 210,658,254 bp, and the guanine-cytosine content was 47.7%–48.88%. Transcripts (n = 167,374; 67.27%) and unigenes (n = 81,442; 32.73%) had mean lengths of 1069.70 bp and 813.27 bp, respectively. The total length and N50 length values of transcripts were 179,040,048 bp and 1654 bp, while those of unigenes were 66,234,291 bp and 1406 bp. Assembled genes were annotated by comparison with the non-redundant, Protein family, Clusters of Orthologous Groups of proteins, Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes, and Gene Ontology, public protein databases. Additionally, 46 and 71 significantly differentially expressed genes encoded enzymes and transcription factors, respectively, associated with floral volatiles biosynthesis pathways, were analyzed in-depth. Our findings represent a fundamental step toward better understanding of the mechanisms of narcissus floral volatile biosynthesis.

Keywords

Transcriptomics Narcissus Floral scent Biosynthesis DEGs qRT-PCR 

Abbreviations

HS-SPME

solid-phase microextraction

GC-MS

gas chromatography/mass spectrometry

NES/LINS

nerolidol/linalool synthase

TPS

terpene synthase

AADC

pyridoxal-50 -phosphate-dependent L-aromatic amino acid decarboxylase

PAR

phenylacetaldehyde reductase

DXR

1-deoxy-d-xylulose 5-phosphate reductoisomerase

PAL

phenylalanine ammonia-lyase

BEAT

benzyl alcohol acetyltransferase

BAMT

benzoic acid carboxyl methyl transferase

SAMT

salicylic acid carboxyl methyl- transferase

HPL

Hydroperoxide lyase

2AP

2-acetyl-1-pyrroline

BADH2 (AMADH2)

betaine aldehyde dehydrogenase 2

NR

non-redundant protein sequences

Pfam

Protein family

KOG/COG/eggnog

Clusters of Orthologous Groups of proteins

Swiss-Prot

a manually annotated and reviewed protein sequence database

KEGG

Kyoto Encyclopedia of Genes and Genomes

GO

Gene Ontology

DEGs

differential expressed genes

IPP

isopentenyl diphosphate

DMAPP (DMADP)

dimethylallyl diphosphate

G3P

glyceraldehyde 3-phosphate

MEP

2-C-methyl-D-erythritol 4-phosphate

DXS

1-D-desoxyxylulose 5-phosphate synthase

DXP

1-deoxy-d-xylulose 5-phosphate

TPP

thiamine pyrophosphate

CMS

2-C-methyl-D-erythritol 4- phosphate cytidylyltransferase

CTP

cytosine 5′-triphosphate

ICME

isoprenylcysteine methylesterase

GGDP

geranylgeranyl diphosphate

Dedol-PP

dehydrodolichyl diphosphate

DDS

dedol-PP synthase

ABA

abscisic acid

GA

gibberellin

CDP-ME2P

4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate

ME-CPP

2-C-methyl-D-erythritol 2,4-cyclodiphosphate

MEcDP

2- C-methyl-D-erythritol 2,4-cyclodiphosphate

HMBPP

1-hydroxy-2-methyl-butenyl 4-disphosphate

FDP

(E, E)-Famesyl-PP

GDP

Geranyl-PP

DoI-PP

Dolichol-PP

MAS

momilactone A synthase

benzoyl-CoA

O-benzoyltransferase

DBAT

10-deacetylbaccatin III 10-O-acetyltransferase

Phe

phenylalanine

Tyr

tyrosine

TAL

tyrosine ammonia lyase

4CL

4-coumarate--CoA ligase

ALDH

aldehyde dehydrogenase

CCR

cinnamoyl CoA reductase

CCoAOMT

caffeoyl-CoA-O-methyltransferase

CAD

cinnamyl alcohol dehydrogenase

ASAT

aspartate aminotransferase

HCT

shikimate O-hydroxycinnamoyl transferase;

benzoyl-CoA

benzyl alcohol O-benzoyltransferase

bZIP

basic leucine zipper

ERF

ethylene-responsive factor

bHLH

basic helix-loop-helix

SRF

serum response factor

TCP

TEOSINTE-BRANCHED1/CYCLOIDEA/PCF

EOBI

EMISSION OF BENZENOIDS I

MAPK

mitogen-activated protein kinase

JA

jasmonate acid

BIS1

bHLH iridoid synthesis 1

qRT-PCR

real-time quantitative PCR

FPKM

fragments per kilobase of transcript per million mapped reads

FDR

false discovery rate

TFs

transcription factors

Notes

Acknowledgments

We would like to thank the Charlesworth (https://www.cwauthors.com.cn) for language editing services.

Author Contributions

HYS and XM drafted the manuscript together. HYS conceived the study and participated in the design of all experiments. XM performed qRT-PCR and statistical analysis. CXJ participated in the data analysis and discussion about the experiments. All authors read and approved the final manuscript.

Funding

This work was supported by the Natural Science Foundation of China (NSFC; 30972031) and the Science and Technology Innovation Team of Fujian Academy of Agricultural Sciences (STIT2017-2-11).

Compliance with Ethics Standards

Conflict Interest

Authors declare that they have no conflict interest.

Supplementary material

12042_2020_9253_MOESM1_ESM.docx (16 kb)
Supplementary Table 3 (DOCX 16 kb)
12042_2020_9253_MOESM2_ESM.docx (21 kb)
Supplementary Table 4 (DOCX 20 kb)

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Authors and Affiliations

  1. 1.Institute of Subtropical AgricultureFujian Academy of Agricultural SciencesZhangzhouPeople’s Republic of China
  2. 2.College of Tropical CropsHainan UniversityHaikouPeople’s Republic of China
  3. 3.College of HorticultureFujian Agriculture and Forestry UniversityFuzhouPeople’s Republic of China

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