Transcriptome and metabolome profiling of Narcissus pseudonarcissus ‘King Alfred’ reveal components of Amaryllidaceae alkaloid metabolism

Abstract

Amaryllidaceae alkaloids (AAs) represent a diverse class of plant specialized metabolites and many display potent pharmacological activities. The AA metabolic pathway is poorly understood and resources are minimal. To enable AA pathway elucidation and novel biosynthetic enzymes discovery, we generated comprehensive metabolomic and corresponding transcriptomic datasets from different tissues of Narcissus pseudonarcissus ‘King Alfred’. In this study, we performed untargeted UPLC-QTOF-MS metabolite analysis from different tissues, which generated exhaustive list of compounds, including several AAs, most predominant and diverse in bulbs. RNA sequencing of N. pseudonarcissus ‘King Alfred’ bulbs yielded 195,347 transcripts, after assembly. Top expressed genes belong to process like metabolism, survival, and defense including alkaloid biosynthetic genes. The transcriptome contained complete sequences for all proposed genes encoding AA-biosynthetic enzymes such as tyrosine decarboxylase (TYDC1 and TYDC2), phenylalanine ammonia-lyase (PAL1 and PAL2) and phenolic acids hydroxylases (C4H and C3H) to name a few. Furthermore, transcriptome data were validated using RT-qPCR analysis and expression study in different tissues of N. pseudonarcissus ‘King Alfred’ was performed. Here, we present the first comprehensive metabolome and transcriptome study from N. pseudonarcissus ‘King Alfred’ providing invaluable resources for metabolic engineering and biotechnological applications.

Combined Analysis of the Fruit Metabolome and Transcriptome Reveals Candidate Genes Involved in Flavonoid Biosynthesis in Actinidia arguta

“…However, most genes have been obtained and identified using traditional study technology. Since transcriptome analysis has come to be regarded as a crucial way to study the expression level, structure and function of genes in order to revealing phenotypic traits, combined analysis of transcriptome and metabolome has increasingly become a popular and practical tool for the mining of new genes involved in various metabolic pathways [ 49 ]. In this study, metabolome data, coupled with transcriptome profiling, was carried out in a combined analysis for the discovery of genes involved in flavonoid biosynthesis, thus searching for useful information to illustrate phenomenon of red coloring in A. arguta fruit.…”

Combined Analysis of the Metabolome and Transcriptome Identified Candidate Genes Involved in Phenolic Acid Biosynthesis in the Leaves of Cyclocarya paliurus

“…Since transcriptome analysis is regarded as a central way to study the expression level, structure and function of genes to identify phenotypic traits, the combined analysis of both transcriptome and metabolome has increasingly become a popular and practical tool for the mining of new genes that may be involved in various metabolic pathways [48]. Thus, this method will likely become an effective tool that can be used to investigate the mechanisms involved in the regulation of the phenolic acid biosynthesis in C. paliurus.…”

Recent Progress in Amaryllidaceae Biotechnology

“…The transcript expression analyses of the genes from the two clusters suggest a different functional role for PAL1 versus PAL2. It has been demonstrated that PAL1 is expressed at similar levels in all plant parts (root, bulb, stem, leaf, flower), whereas PAL2 is expressed in the bulb [ 59 , 65 , 66 ]. Another important gene from the phenylpropanoid pathway, cinnamate-4-hydroxylase (C4H), has been recently cloned and characterized to be present as a one single transcript in Amaryllidaceae alkaloid producing plants [ 59 , 60 , 64 , 65 , 67 ].…”

“…Another important gene from the phenylpropanoid pathway, cinnamate-4-hydroxylase (C4H), has been recently cloned and characterized to be present as a one single transcript in Amaryllidaceae alkaloid producing plants [ 59 , 60 , 64 , 65 , 67 ]. The transcript expression analyses of C4H showed that the expression was highest in the bulbs of dormant and early germination stages, and it was also high in the stems, roots and bulbs in flowering plants [ 59 , 64 , 65 , 66 ].…”

“…TYDC is an important enzyme, which catalyzes the production of tyramine from L-tyrosine [ 68 ]. It has been found that two transcript variants of TYDC are present in Amaryllidaceae alkaloid producing plants [ 59 , 65 , 66 , 69 , 70 ]. The phylogenetic analysis showed that Amaryllidaceae TYDCs can be divided into two main clusters: “TYDC1” and “TYDC2” [ 59 ].…”