Genome mining for yeast metabolic diversity

Lead Research Organisation: University of East Anglia
Department Name: Graduate Office

Abstract

Yeasts are hugely important organisms used in beer and bread making. Less well known are their key roles in a wide variety of bioindustries, such as the production of fine chemicals, nutraceuticals, pharmaceuticals and biofuels. The yeast taxonomic tree is very broad, with some species/strains particularly well adapted to certain environments and displaying numerous traits of biotechnological interest, though the genetic underpinnings of this adaptation are not yet clear. We have recently begun sequencing the genomes of strains within the National Collection of Yeast Cultures (NCYC). The resulting dataset will enable us to hunt for specific genes and gene clusters, genomically co-located groups of genes collectively involved in a single metabolic pathway, that are associated with traits of interest. Crucially, whole genome sequencing enables us to hunt for such genomic elements using computational approaches.

In this project, the student will use computational tools to search a newly developed dataset of approximately 700 diverse yeast genome sequences for metabolic genes and gene clusters. He/she will work with NCYC colleagues and Eagle Genomics Ltd. to fold the resulting software pipeline into a new yeast industrial biotechnology bioinformatics platform. Finally, he/she will work with the IFR Biorefinery Centre to associate important genes or gene clusters with key yeast trait datasets.

Publications

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Studentship Projects

Project Reference Relationship Related To Start End Student Name
BB/M011216/1 01/10/2015 30/09/2023
1653494 Studentship BB/M011216/1 01/10/2015 30/09/2019 Christopher Pyatt
 
Description New software developed to retrieve gene clusters from genome assembly data. Publicly available on GitHub.

Extent of specific gene clusters ascertained within a large group of yeasts.

Novel protein family members identified and classified (broadly) from ~1000 yeast strains.
Exploitation Route Partially constructed software module can be built upon. Completed modules can be used to mine datasets for additional gene clusters (should they become of interest). Identified CYPs can be investigated further, particularly novel ones.
Sectors Chemicals,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

 
Title FindClusters 
Description The software takes a collection of genes, and a collection of genome assemblies, and searched for those genes within all the genome assemblies. It then reports any clustered examples of the pathway. 
Type Of Technology Software 
Year Produced 2019 
Open Source License? Yes  
Impact Still new 
URL https://github.com/chrispyatt/FindClusters
 
Description Conference poster (Chicago) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation at major conference (ISMB Chicago).
Year(s) Of Engagement Activity 2018
 
Description Conference presentation (Leicester) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk about CYP aspects of project to BYG
Year(s) Of Engagement Activity 2018
 
Description Conference presentation and poster (Swansea) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk given about project to British Yeast Group Meeting
Year(s) Of Engagement Activity 2016
 
Description Conference talk (Hinxton) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk about FindCLusters software at Genome Informatics (Wellcome campus, Cambiridge)
Year(s) Of Engagement Activity 2018
 
Description Conference talk (Kent) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk about project at British Yeast Group meeting
Year(s) Of Engagement Activity 2017
 
Description Using phylogenetic to pinpoint the birth of biosynthetic gene clusters 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Research scientists and postgraduate students attended the Midsummer Phylogenetics Meeting at the University of East Anglia, 18th June 2019.
Year(s) Of Engagement Activity 2019
URL http://www.uea.ac.uk/computing/news-and-events/conferences/midsummer-phylogenetics-meeting-2019