Title: Molecular Genetic and Genomic Characterization of a Mycotoxigenic Emerging Pathogen proliferatum

Name: Bandar Almiman

This is a digitised version of a dissertation submitted to the University of Bedfordshire.

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Molecular Genetic and Genomic Characterization of a Mycotoxigenic Emerging Pathogen Fusarium proliferatum

B. F. Almiman Ph.D

2017 UNIVERSITY OF BEDFORDSHIRE

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Molecular Genetic and Genomic Characterization of a Mycotoxigenic Emerging Pathogen Fusarium proliferatum

by B. F. Almiman

A thesis submitted to the University of Bedfordshire In partial fulfil of the requirements for the degree of Doctor of Philosophy

April 2017

Abstract

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This aim of this research was to elucidate the genotypic diversity of the mycotoxigenic species Fusarium proliferatum associated with diverse hosts and distributed in wide geographic locations to gain new insights into the biology of this emerging pathogen. This study developed a novel molecular genetic marker FG1056. Multilocus typing of F. proliferatum isolates (52) using F. verticillioides (2) and F. oxysporum (3) as references was carried out with FG1056 and a set of known genetic markers (ITS, TEF1, CAL and FUM1). This distinguished up to 10 genetic groups, 2 clusters and 23 haplotypes among the F. proliferatum isolates. FG1056 marker showed the highest number of SNPs (169), informative sites (89) and haplotypes (23) relative to other markers used and was comparable to the multi locus typing. Varying patterns of relationships were observed between isolates represented in the genetic groups and their host and geographic origin. Considerable biological variability was recorded among the F. proliferatum isolates in morphology, growth, sporulation and most notably fumonisin production (up to 140-fold differences) with reference to variable temperature, water activity and duration. De novo genome assemblies with the size ranging from 43.96 - 50 Mb have been developed for four diverse F. proliferatum isolates. In silico analysis led to the identification of 12,980 genes common to all isolates and up to 134 genes potentially unique to an isolate. Using these resources, FUM gene cluster (~45.3 Kb) was identified for the first time in F. proliferatum. Order and orientation of the 16 FUM genes and the complete flanking genes (MSF1 and ZCB1 at 5’; ANK1 and GAT1 at 3’) have been determined. This study has provided new insights into the genetic and biological diversity of F. proliferatum and also developed new genetic and genomic resources, which will serve as a solid platform for further research particularly to understand the regulation of fumonisins production in the laboratory and in the field.

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Acknowledgments

First and foremost, I would like to express my gratitude to my director of study, Professor S. Sreenivasaprasad who has been involved in this work from the beginning to this time of completion for the guidance, support and constructive criticisms. I would also like to appreciate the efforts of my other supervisory team Dr Shaobo and Dr N. Worsfold for their continual encouragement and academic support when required. In addition to my supervisors, Dr S. Muthumeenakshi has willingly and voluntarily given this project much time and thought that led to the expansion and successful submission of the reports. I would like to also appreciate Dr Riccardo Baroncelli and Dr Steven for their good heart and time towards the data analysis.

I also wish to acknowledge Professor Lukasz Stephen at the Polish Academy, Poland, Professor Naresh Magan at the Cranfield University, UK, as well as the Institutes of science of food production (ISPA), Italy and University of Warwick HRI for the provision of isolates used in this research.

On a personal note, I will like to appreciate my friend Taiwo Shittu for his support, time and encourage