Transcriptome Sequencing and Expression Analysis of Terpenoid Biosynthesis Genes in Litsea cubeba

Abstract

BackgroundAromatic essential oils extracted from fresh fruits of Litsea cubeba (Lour.) Pers., have diverse medical and economic values. The dominant components in these essential oils are monoterpenes and sesquiterpenes. Understanding the molecular mechanisms of terpenoid biosynthesis is essential for improving the yield and quality of terpenes. However, the 40 available L. cubeba nucleotide sequences in the public databases are insufficient for studying the molecular mechanisms. Thus, high-throughput transcriptome sequencing of L. cubeba is necessary to generate large quantities of transcript sequences for the purpose of gene discovery, especially terpenoid biosynthesis related genes.ResultsUsing Illumina paired-end sequencing, approximately 23.5 million high-quality reads were generated. De novo assembly yielded 68,648 unigenes with an average length of 834 bp. A total of 38,439 (56%) unigenes were annotated for their functions, and 35,732 and 25,806 unigenes could be aligned to the GO and COG database, respectively. By searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG), 16,130 unigenes were assigned to 297 KEGG pathways, and 61 unigenes, which contained the mevalonate and 2-C-methyl-D-erythritol 4-phosphate pathways, could be related to terpenoid backbone biosynthesis. Of the 12,963 unigenes, 285 were annotated to the terpenoid pathways using the PlantCyc database. Additionally, 14 terpene synthase genes were identified from the transcriptome. The expression patterns of the 16 genes related to terpenoid biosynthesis were analyzed by RT-qPCR to explore their putative functions.ConclusionRNA sequencing was effective in identifying a large quantity of sequence information. To our knowledge, this study is the first exploration of the L. cubeba transcriptome, and the substantial amount of transcripts obtained will accelerate the understanding of the molecular mechanisms of essential oils biosynthesis. The results may help improve future genetic and genomics studies on the molecular mechanisms behind the chemical composition of essential oils in L. cubeba fruits.

Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis

“…This finding opens the possibility of identifying uncataloged new transcripts and rare or specific genes in the coffee transcriptome. Three possible explanations may account for this high number of no hits : i) Illumina technology improves the chance to identify rare transcripts and new gene isoforms [51]; ii) we used, for the first time, Arabica flowers and fruits during their initial development, which are not well represented in CafEST assembly; and iii) de novo transcriptome assembly using RNA-seq single-end technique typically generates a high number of unigenes [52]. …”

Deyeuxia angustifolia's trancriptional response to elevated CO2 concentration in Sanjiang plain, Northeast China

“…7 Species distributions of the top seven BLASTX matches to the nr protein database We, furthermore, estimated the genes or proteins names, or ORFs of the assembled unigenes, and predicted the conserved domains, gene ontology terms and potential metabolic pathways. The average length of D. angustifolia unigenes was shorter compared with previous transcriptomic studies using the same platform in other plants, such as Litsea cubeba [17], Dendrocalamus latiflorus [18], Chorispora bungeana [19], and Ipomoea batatas [15].A large numbers of unigenes were allocated to many different GO categories and COG classifications. Using the KEGG database, most representative transcripts were distributed to specific pathways, such as cellular processes, metabolism, environmental information processing and genetic information processing.…”

A New Diterpene from Litsea cubeba Fruits: Structure Elucidation and Capability to Induce Apoptosis in HeLa Cells

“…May Chang oil has been widely studied for its chemical components, which are mainly monoterpenes and sesquiterpenes. The major chemical constituent of this oil is citral, which comprises geranial (E-citral) and neral (Z-citral) [3][4][5][6]. The oil has been found to have bio-activities such as anti-inflammatory, antioxidant, pesticidal, antimicrobial, anticancer and neuropharmacological properties [7][8][9][10][11][12].…”