DOI: 10.5061/dryad.bh276
title: Data from: Transcriptome analysis of 20 taxonomically related benzylisoquinoline alkaloid-producing plants

description: 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.
description: Phylogenetic analysis of
 berberine bridge enzyme (BBE) gene candidates from twenty BIA-accumulating
 plant species.BBE.aln consensus
 tree.nexPhylogenetic analysis of
 aldo-keto reductase gene candidates with homology to codeinone reductase
 (COR) from twenty BIA-accumulating plant species.COR.reg.tree.nexPhylogenetic analysis of aldo-keto reductase gene candidates with homology to codeinone reductase (COR) from twenty BIA-accumulating plant species. Rooted tree.COR.rooted.tree.nexPhylogenetic analysis of carboxyl esterase (CXE) gene candidates from twenty BIA-accumulating plant species.CXE.reg.tree.nexPhylogenetic analysis of carboxyl esterase (CXE) gene candidates from twenty BIA-accumulating plant species. Rooted tree.CXE.rooted.tree.nexPhylogenetic analysis of CYP80 gene candidates from twenty BIA-accumulating plant species.CYP80.reg.tree.nexPhylogenetic analysis of CYP80 gene candidates from twenty BIA-accumulating plant species. Rooted tree.CYP80.rooted.tree.nexPhylogenetic analysis of CYP82 gene candidates from twenty BIA-accumulating plant species.CYP82.reg.tree.nexPhylogenetic analysis of CYP82 gene candidates from twenty BIA-accumulating plant species. Rooted tree,CYP82.rooted.tree.nexPhylogenetic analysis of CYP719 gene candidates from twenty BIA-accumulating plant species.CYP719.reg.tree.nexPhylogenetic analysis of CYP719 gene candidates from twenty BIA-accumulating plant species. Rooted tree.CYP719.rooted.tree.nexPhylogenetic analysis of 2-oxoglutarate / iron (II)-dependent dioxygenase (DIOX) gene candidates from twenty BIA-accumulating plant species.DIOX.reg.tree.nexPhylogenetic analysis of 2-oxoglutarate / iron (II)-dependent dioxygenase (DIOX) gene candidates from twenty BIA-accumulating plant species. Rooted tree.DIOX.rooted.tree.nexPhylogenetic analysis of FAD-dependent oxidase (FADOX) gene candidates from twenty BIA-accumulating plant species.FADOX.reg.tree.nexPhylogenetic analysis of FAD-dependent oxidase (FADOX) gene candidates from twenty BIA-accumulating plant species. Rooted tree.FADOX.rooted.tree.nexPhylogenetic analysis of norcoclaurine synthase (NCS) gene candidates from twenty BIA-accumulating plant species.NCS.reg.tree.nexPhylogenetic analysis of norcoclaurine synthase (NCS) gene candidates from twenty BIA-accumulating plant species. Rooted tree.NCS.rooted.tree.nexPhylogenetic analysis of N-methyltransferase (NMT) gene candidates from twenty BIA-accumulating plant species.NMT.reg.tree.nexPhylogenetic analysis of N-methyltransferase (NMT) gene candidates from twenty BIA-accumulating plant species. Rooted tree.NMT.rooted.tree.nexPhylogenetic analysis of short chain dehydrogenase / reductase gene candidates with homology to noscapine synthase (NOS) from 20 BIA-accumulating plant species.NOS.reg.tree.nexPhylogenetic analysis of short chain dehydrogenase / reductase gene candidates with homology to noscapine synthase (NOS) from 20 BIA-accumulating plant species. Rooted tree.NOS.rooted.tree.nexPhylogenetic analysis of BAHD-type O-acetyltransferase (OAT) gene candidates from twenty BIA-accumulating plant species.OAT.reg.tree.nexPhylogenetic analysis of BAHD-type O-acetyltransferase (OAT) gene candidates from twenty BIA-accumulating plant species. Rooted tree.OAT.rooted.tree.nexPhylogenetic analysis of O-methyltransferase (OMT) gene candidates from twenty BIA-accumulating plant species.OMT.reg.tree.nexPhylogenetic analysis of short chain dehydrogenase / reductase gene candidates with homology to salutaridine reductase (SALR) from twenty BIA-accumulating plant species.SALR.reg.tree.nexPhylogenetic analysis of short chain dehydrogenase / reductase gene candidates with homology to salutaridine reductase (SALR) from twenty BIA-accumulating plant species. Rooted tree.SALR.rooted.tree.nexPhylogenetic analysis of short chain dehydrogenase / reductase gene candidates with homology to sanguinarine reductase (SANR) from twenty BIA-accumulating plant species.SANR.reg.tree.nexPhylogenetic analysis of short chain dehydrogenase / reductase gene candidates with homology to sanguinarine reductase (SANR) from twenty BIA-accumulating plant species. Rooted tree.SANR.rooted.tree.nex