Data from: Transcriptome analysis of 20 taxonomically related benzylisoquinoline alkaloid-producing plants

Background: Benzylisoquinoline alkaloids (BIAs) represent a diverse class
of plant specialized metabolites sharing a common biosynthetic origin
beginning with tyrosine. Many BIAs have potent pharmacological activities,
and plants accumulating them boast long histories of use in traditional
medicine and cultural practices. The decades-long focus on a select number
of plant species as model systems has allowed near or full elucidation of
major BIA pathways, including those of morphine, sanguinarine and
berberine. However, this focus has created a dearth of knowledge
surrounding non-model species, which also are known to accumulate a
wide-range of BIAs but whose biosynthesis is thus far entirely unexplored.
Further, these non-model species represent a rich source of catalyst
diversity valuable to plant biochemists and emerging synthetic biology
efforts. Results: In order to access the genetic diversity of non-model
plants accumulating BIAs, we selected 20 species representing 4 families
within the Ranunculales. RNA extracted from each species was processed for
analysis by both 1) Roche GS-FLX Titanium and 2) Illumina GA/HiSeq
platforms, generating a total of 40 deep-sequencing transcriptome
libraries. De novo assembly, annotation and subsequent full-length coding
sequence (CDS) predictions indicated greater success for most species
using the Illumina-based platform. Assembled data for each transcriptome
were deposited into an established web-based BLAST portal
(www.phytometasyn.ca) to allow public access. Homology-based mining of
libraries using BIA-biosynthetic enzymes as queries yielded ~850 gene
candidates potentially involved in alkaloid biosynthesis. Expression
analysis of these candidates was performed using inter-library FPKM
normalization methods. These expression data provide a basis for the
rational selection of gene candidates, and suggest possible metabolic
bottlenecks within BIA metabolism. Phylogenetic analysis was performed for
each of 15 different enzyme/protein groupings, highlighting many novel
genes with potential involvement in the formation of one or more alkaloid
types, including morphinan, aporphine, and phthalideisoquinoline
alkaloids. Transcriptome resources were used to design and execute a case
study of candidate N-methyltransferases (NMTs) from Glaucium flavum, which
revealed predicted and novel enzyme activities. Conclusions: This study
establishes an essential resource for the isolation and discovery of 1)
functional homologues and 2) entirely novel catalysts within BIA
metabolism. Functional analysis of G. flavum NMTs demonstrated the utility
of this resource and underscored the importance of empirical determination
of proposed enzymatic function. Publically accessible, fully annotated,
BLAST-accessible transcriptomes were not previously available for most
species included in this report, despite the rich repertoire of bioactive
alkaloids found in these plants and their importance to traditional
medicine. The results presented herein provide essential sequence
information and inform experimental design for the continued elucidation
of BIA metabolism.