Characterisation of Epicoccum spp. secondary metabolism genes through de novo genome and transcriptome sequencing
type: CreativeWork
description: The Epicoccum nigrum sensu lato clade of the Didymellaceae family, previously also known as E. purpurascens, consists of a group of very common saprophytic and plant associated fungal species with a worldwide distribution. Over 70 natural products have been identified from Epicoccum nigrum sensu lato. One of the most notable is the antifungal pyronepolyene C-glucoside, epipyrone, which was isolated from an Epicoccum italicum strain (ICMP 19927) from New Zealand. To identify the genes involved in the biosynthesis of epipyrone and other secondary metabolites, the whole genome of Epicoccum italicum strain ICMP 19927 was sequenced using a range of short and long insert shotgun libraries. This was assembled and thoroughly annotated by the funannotate pipeline along with additional specialised packages. Thirty four putative secondary metabolite biosynthetic gene clusters were identified in the genome, including eight clusters containing polyketide synthases (PKS), which were predicted to be required for epipyrone biosynthesis. Protocols for epipyrone production by submerged fermentation of Epicoccum were optimised to compare two conditions that strongly differ by level of epipyrone production. Genome-wide differential expression analysis by mRNA sequencing allowed the identification of the epn gene cluster for epipyrone synthesis, which was strongly upregulated in epipyrone-inducing conditions. The cluster contains six genes, including expected genes for a highly reducing PKS (epnA) and also a glycosyltransferase (epnB), the first time a gene for this class of enzyme has been identified in a fungal biosynthetic cluster with known product. Contiguous mRNA sequence supported that adjacent epnA and epnB genes are expressed as a single polycistronic mRNA, which is very rarely observed in fungi. Various genes known to be involved in nitrogen metabolite repression were found to be differentially expressed simultaneously with epipyrone production, supporting the hypothesis that …
abstract: The Epicoccum nigrum sensu lato clade of the Didymellaceae family, previously also known as E. purpurascens, consists of a group of very common saprophytic and plant associated fungal species with a worldwide distribution. Over 70 natural products have been identified from Epicoccum nigrum sensu lato. One of the most notable is the antifungal pyronepolyene C-glucoside, epipyrone, which was isolated from an Epicoccum italicum strain (ICMP 19927) from New Zealand. To identify the genes involved in the biosynthesis of epipyrone and other secondary metabolites, the whole genome of Epicoccum italicum strain ICMP 19927 was sequenced using a range of short and long insert shotgun libraries. This was assembled and thoroughly annotated by the funannotate pipeline along with additional specialised packages. Thirty four putative secondary metabolite biosynthetic gene clusters were identified in the genome, including eight clusters containing polyketide synthases (PKS), which were predicted to be required for epipyrone biosynthesis. Protocols for epipyrone production by submerged fermentation of Epicoccum were optimised to compare two conditions that strongly differ by level of epipyrone production. Genome-wide differential expression analysis by mRNA sequencing allowed the identification of the epn gene cluster for epipyrone synthesis, which was strongly upregulated in epipyrone-inducing conditions. The cluster contains six genes, including expected genes for a highly reducing PKS (epnA) and also a glycosyltransferase (epnB), the first time a gene for this class of enzyme has been identified in a fungal biosynthetic cluster with known product. Contiguous mRNA sequence supported that adjacent epnA and epnB genes are expressed as a single polycistronic mRNA, which is very rarely observed in fungi. Various genes known to be involved in nitrogen metabolite repression were found to be differentially expressed simultaneously with epipyrone production, supporting the hypothesis that …
author: Fokin, Mikhail
license: https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm
date published: 2019
date modified: 2026-07-24T01:05:30Z
provider: University of Auckland
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: ResearchSpace@Auckland

PropertyValue
property ID: Handle
value: https://hdl.handle.net/2292/48536