De Novo Sequencing and Analysis of Lemongrass Transcriptome Provide First Insights into the Essential Oil Biosynthesis of Aromatic Grasses

Abstract

Aromatic grasses of the genus Cymbopogon (Poaceae family) represent unique group of plants that produce diverse composition of monoterpene rich essential oils, which have great value in flavor, fragrance, cosmetic, and aromatherapy industries. Despite the commercial importance of these natural aromatic oils, their biosynthesis at the molecular level remains unexplored. As the first step toward understanding the essential oil biosynthesis, we performed de novo transcriptome assembly and analysis of C. flexuosus (lemongrass) by employing Illumina sequencing. Mining of transcriptome data and subsequent phylogenetic analysis led to identification of terpene synthases, pyrophosphatases, alcohol dehydrogenases, aldo-keto reductases, carotenoid cleavage dioxygenases, alcohol acetyltransferases, and aldehyde dehydrogenases, which are potentially involved in essential oil biosynthesis. Comparative essential oil profiling and mRNA expression analysis in three Cymbopogon species (C. flexuosus, aldehyde type; C. martinii, alcohol type; and C. winterianus, intermediate type) with varying essential oil composition indicated the involvement of identified candidate genes in the formation of alcohols, aldehydes, and acetates. Molecular modeling and docking further supported the role of identified protein sequences in aroma formation in Cymbopogon. Also, simple sequence repeats were found in the transcriptome with many linked to terpene pathway genes including the genes potentially involved in aroma biosynthesis. This work provides the first insights into the essential oil biosynthesis of aromatic grasses, and the identified candidate genes and markers can be a great resource for biotechnological and molecular breeding approaches to modulate the essential oil composition.

RNA-Seq Analysis Provides the First Insights into the Phylogenetic Relationship and Interspecific Variation between Agropyron cristatum and Wheat

“…SNP discovery from NGS data was also combined with bulked segregant analysis for the fine mapping of genes in polyploid wheat (Trick et al, 2012 ; Ramirez-Gonzalez et al, 2015 ; Bassi et al, 2016 ). RNA-sequencing (RNA-Seq) has also recently become a popular technique because it is cost-effective, does not rely on a reference genome and can contribute to transcriptional analysis, gene discovery, phylogenetic analysis, and molecular marker development (Meena et al, 2016 ). In a previous study, de novo transcriptome assembly and unigene functional annotation were conducted in A. cristatum , and gene resources related to stress resistance and inflorescence development and specific to A. cristatum within the tribe Triticeae were identified (Zhang et al, 2015a ).…”

Full-length transcriptome sequences of Agropyron cristatum facilitate the prediction of putative genes for thousand-grain weight in a wheat-A. cristatum translocation line

“…High-throughput transcriptome sequencing has recently become a popular technique because it is cost-effective, does not rely on a reference genome and can contribute to transcriptional analysis, molecular marker development and gene discovery [19]. In a previous study, de novo transcriptome assembly and unigene functional annotation were conducted in A. cristatum with the Illumina sequencing technique, and gene resources that were related to traits of interest and specific to A. cristatum within the tribe Triticeae, as well as the phylogenetic relationship and interspecific variation between A. cristatum and wheat, were identified [20,21].…”

“…RNA-sequencing (RNA-Seq) has recently become a popular technique because it is cost-effective, and does not rely on a reference genome [19]. RNA-Seq of A. cristatum Z559 by the Illumina platform has enabled the successful annotation of orthologous genes related to multiple agronomic traits in A.…”

Full-length transcriptome sequences of Agropyron cristatum facilitate the prediction of putative genes for thousand-grain weight in a wheat-A. cristatum translocation line

“…RNA-sequencing (RNA-Seq) has recently become a popular technique because it is cost-effective, and it does not rely on a reference genome [19]. RNA-Seq of A. cristatum Z559 by the Illumina platform has enabled the successful annotation of orthologous genes related to multiple agronomic traits in A.…”