A transcriptomics approach to understanding polymorphic and transcript level differences linked to isoquinoline alkaloid production in triploid varieties of narcissus pseudonarcissus

Pulman, Jane A transcriptomics approach to understanding polymorphic and transcript level differences linked to isoquinoline alkaloid production in triploid varieties of narcissus pseudonarcissus. PhD thesis, University of Liverpool.

Text PulmanJan_Sept2014_2006379.pdf - Author Accepted Manuscript Available under License Creative Commons Attribution. Download (5MB)

Abstract

The Amaryllidaceae have characteristic isoquinoline alkaloids including galanthamine that is approved for treatment of Alzheimer’s disease. The daffodil (Narcissus pseudonarcissus) is an industrial source of this alkaloid. This project undertook analysis of the daffodil transcriptome as an approach to understanding this alkaloid biosynthetic pathway. Material from the basal plate of var. Carlton was analysed using the Roche 454 GS FLX Titanium and Illumina HiSeq platforms to assemble reference transcripts (45324 transcripts from 454, 165065 from Illumina). Annotation was via a bespoke BLAST pipeline utilizing UniProt, TAIR, Rfam and RefSeq. Further functional annotation and enrichment studies were carried out using the DAVID platform encompassing KEGG, GO and EC annotations. Illumina HiSeq sequencing of a second variety, Andrew’s Choice, was used alongside the reference transcripts to identify SNPs and transcript level differences. A bioinformatics method to determine ploidy indicated both varieties were triploid, in agreement with microscopy results. The level of selected transcripts was also assessed using qPCR. Several transcripts putatively involved in alkaloid biosynthesis were identified. Comp75950_c0_s1 showed homology to a C4H gene from peppers and could be involve in protocatechuic acid biosynthesis in daffodils. Two transcripts, Daff106212 and Contig1404, were predicted to catalyse the synthesis of norbelladine from protocatechuic acid and tyramine, and its subsequence conversion to 4’-O-methylnorbelladine. Finally, transcripts HDA57HA0AK3FX and Daff88927 were suggested for the final step in galanthamine biosynthesis, an intermolecular phenol coupling. This is the first transcriptomic comparison of two daffodil varieties and is an important resource for further investigation into genes involved in Amaryllidaceae alkaloid biosynthesis.

Item Type:	Thesis (PhD)
Additional Information:	THESIS PROCESSED. JULY 2015 GRADUATION. 3 YEAR EMBARGO. (cm 10.02.15) Date: 2014-09 (completed)
Subjects:	?? Q1 ??
Depositing User:	Symplectic Admin
Date Deposited:	27 Aug 2015 13:57
Last Modified:	16 Dec 2022 04:42
DOI:	10.17638/02006379
URI:	https://livrepository.liverpool.ac.uk/id/eprint/2006379