RNA sequencing analysis of Cymbidium goeringii identifies floral scent biosynthesis related genes

Abstract

Background Cymbidium goeringii belongs to the Orchidaceae, which is one of the most abundant angiosperm families. Cymbidium goeringii consist with high economic value and characteristics include fragrance and multiple flower colors. Floral scent is one of the important strategies for ensuring fertilization. However, limited genetic data is available in this non-model plant, and little known about the molecular mechanism responsible for floral scent in this orchid. Transcriptome and expression profiling data are needed to identify genes and better understand the biological mechanisms of floral scents in this species. Present transcriptomic data provides basic information on the genes and enzymes related to and pathways involved in flower secondary metabolism in this plant. Results In this study, RNA sequencing analyses were performed to identify changes in gene expression and biological pathways related scent metabolism. Three cDNA libraries were obtained from three developmental floral stages: closed bud, half flowering stage and full flowering stage. Using Illumina technique 159,616,374 clean reads were obtained and were assembled into 85,868 final unigenes (average length 1194 nt), 33.85% of which were annotated in the NCBI non redundant protein database. Among this unigenes 36,082 were assigned to gene ontology and 23,164 were combined with COG groups. Total 33,417 unigenes were assigned in 127 pathways according to the Kyoto Encyclopedia of Genes and Genomes pathway database. According these transcriptomic data we identified number of candidates genes which differentially expressed in different developmental stages of flower related to fragrance biosynthesis. In q-RT-PCR most of the fragrance related genes highly expressed in half flowering stage. Conclusions RNA-seq and DEG data provided comprehensive gene expression information at the transcriptional level that could be facilitate the molecular mechanisms of floral biosynthesis pathways in three developmental phase’s flowers in Cymbidium goeringii, moreover providing useful information for further analysis on C . goeringii, and other plants of genus Cymbidium. Electronic supplementary material The online version of this article (10.1186/s12870-019-1940-6) contains supplementary material, which is available to authorized users.

Volatile Organic Compounds from Orchids: From Synthesis and Function to Gene Regulation

“…We are presented major floral scent Cymbidiums (Figure 3). [28]. Furthermore, 32 and 38 unigenes known to be associated with MVA and MEP pathways, respectively, were reported in C. goeringii.…”

“…Depending on their origin and functions, floral volatile compounds are categorized into one of three groups: terpenoids, phenylpropanoids/benzenoids, and fatty acid derivatives [20] (Figure 1). [28], monoterpenes [23,24], phenylpropanoids/benzenoids [29,30] and fatty acid derivatives/methyl jasmonate [19,31]). Abbreviations: MVA: mevalonic acid; MEP: methyl erythritol phosphate; LOX: lipoxygenase; PEP: phosphoenolpyruvate; G3P: glyceraldehyde-3-phosphate; E4P: erythrose 4-phosphate; DMAPP: dimethylallyl pyrophosphate; FPPS: farnesyl pyrophosphate synthase; FPP: farnesyl pyrophosphate; GGPP, geranylgeranyl pyrophosphate; GPP, geranyl pyrophosphate; IPP: isopentenyl pyrophosphate; DAHP: 3-deoxy-D-arabinoheptulosonate-7phosphate; Phe: phenylalanine.…”

“…Monoterpenes (Table 1) play a key role in the volatile profile [23,24]; in C. goeringii, floral volatile organic compounds include farnesol, methyl epi-jasmonate, (E)-β-farnesene, and nerolidol. Sesquiterpenes play a key role in the scent profile [28]. In the Cymbidium hybrid "Sunny Bell," linalool is the major compound found in the petal [39].…”

“…In the Cymbidium hybrid "Sunny Bell," linalool is the major compound found in the petal [39]. The volatile floral scents inside species and cultivars of Cymbidium have been reported [28,39]. Among the volatiles α-pinene, eucalyptol, trans-β-ocimene, α-copaene, and β-caryophyllene terpenoid were leading components in the volatile mixture [40,41].…”

“…In plants, monoterpenes, diterpenes, carotenoids, ubiquinones, and phytols are produced in the plastid via the MEP pathway, while all other plant terpenoids (sesquiterpenes, triterpenes, and polyterpenes) are produced using the MVA pathway. Floral volatiles with TPSs have been identified in such orchids as P. bellina [24] and C. goeringii [28]. Terpenoids are dominant in floral volatiles including those emitted by orchids.…”