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Comparative Genomics of the Mycobacterium Ulcerans And MPhil Thesis Ken Doig (197821835) MPhil Thesis – 2012 Candidate Kenneth Douglas Doig Student No. 197821835 Title Comparative genomics of the Mycobacterium ulcerans and Mycobacterium marinum complex Status Submitted in total fulfilment of the requirements of the degree of Master of Philosophy Date September 2012 Supervisors A/Prof. Tim Stinear1 Dr. Torsten Seemann2 Prof. Richard Strugnell1 Department Microbiology and Immunology Faculty Medicine, Dentistry and Health Sciences The University of Melbourne 1. Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia 2. Victorian Bioinformatics Consortium, Monash University, Clayton, Australia MPhil_Thesis-22.doc Page 1 of 1 MPhil Thesis Ken Doig (197821835) Abstract Buruli ulcer is a neglected tropical disease which is prevalent in Western Africa. Its etiological agent, Mycobacteria ulcerans occurs in a wide range of hosts and environments across the world. In contrast to its progenitor Mycobacteria marinum, the bacteria and related strains produce a toxin mycolactone, an immunosuppressive polyketide which gives rise to its pathogenicity. Bacterial pathogenesis has a number of hallmarks such as; an evolutionary bottleneck, insertion sequence (IS) expansion, pseudogene increase, genome reduction, horizontal gene transfers (HGT) and adaption to a new niche. M. ulcerans shows all of these characteristics and is a fine model for gaining a deeper understanding of the mechanics of bacterial pathogenesis in general and specifically for M. ulcerans and related strains. This research analyses the genomic makeup of 35 isolates that produce mycolactone and five M. marinum isolates. Such analysis have recently become possible through the rapid technological development of high throughput sequencing (HTS) allowing whole genome sequences of all isolates to be compared and contrasted. Nucleotide level comparisons of the isolates has enumerated a core set of SNPs and allowed a detailed phylogeny of the isolates to be revealed showing the clonal nature of the mycolactone producing isolates that have evolved from the marine dwelling M. marinum. Also highlighted were two distinct bottlenecks, both accompanied by IS expansion, genome reduction and HGT. The first bottleneck acquired the pMUM001 virulence plasmid that confers the ability to synthesis mycolactone. A second bottleneck resulted in the creation of the more pathogenic clonal groups of isolates present in Africa and Australia, which are responsible for the majority of global Buruli ulcer cases. Genome reduction has resulted in the loss of at least 185 genes with cell wall genes being overrepresented. The balance of the cell wall genes show further signs of adaptive selection suggesting remodelling of the cell wall in response to its new niche or environment. Locating the numerous ISs within the isolates indicated the virulence plasmid pMUM001 to be the likely source of the ISs, which in turn confers genome plasticity on the bacteria. A most recent common ancestor of M. marinum has given rise to M. ulcerans and all mycolactone-producing mycobacteria that are specialized variants and have evolved to live in niche environments. Analysis of the genes that have been lost, the genes retained, and the genes now under selective pressure suggest these environments might be dark, aerobic, and extracellular. The bacterial characteristics of M. ulcerans such as, slow growth, production of an immune suppressor, cell wall remodelling, loss or modification of cell wall antigens, and biofilm-forming ability all provide a survival advantage in these environments. This research provides a detailed investigation into the genetic makeup and biological impact of this group of Mycobacteria and will allow better understanding of the transmission of Buruli ulcer and their reservoirs. MPhil_Thesis-22.doc Page 2 of 2 MPhil Thesis Ken Doig (197821835) Declaration This is to certify that: (i) the thesis comprises only my original work towards the MPhil except where indicated in the Preface, (ii) due acknowledgement has been made in the text to all other material used, (iii) the thesis is less than 50,000 words in length, exclusive of tables, maps, bibliographies and appendices. Signed: _______________________________ Date: __________ Kenneth Douglas Doig Preface The following paper is a publication arising from research completed for this thesis: Doig KD, Holt KE, Fyfe JA, Lavender CJ, Eddyani M, Portaels F, Yeboah-Manu D, Pluschke G, Seemann T, Stinear TP: On the origin of Mycobacterium ulcerans, the causative agent of buruli ulcer. BMC Genomics 2012, 13(1):258. The author contributions were as follows: K.Doig co-wrote the manuscript, analysed the data and performed the bioinformatic analysis. T.Seemann wrote some of the analysis tools. K.Holt carried out the Bayesian analysis and co-wrote the manuscript. J.Fyfe and C.Lavender provided materials and assisted with study design. M.Eddyani, F.Portaels, D.Yeboah-Manu, G.Pluschke provided materials and co-wrote the manuscript. T.Stinear conceived the study, analysed the biological data and co-wrote the manuscript. All authors read and approved the final manuscript. Acknowledgements I would like to thank both my family and supervisors for their continuous support and encouragement in the completion of this research and thesis. This research was supported in part by the National Health and Medical Research Council of Australia (628930 and 65195), the Stop Buruli Initiative of the UBS-Optimus Foundation and the Victorian Government Department of Health. MPhil_Thesis-22.doc Page 3 of 3 MPhil Thesis Ken Doig (197821835) Table of Contents 1. INTRODUCTION .................................................................................................................................................6 1.1 OVERVIEW..............................................................................................................................................................................6 1.2 RESEARCH AIMS....................................................................................................................................................................6 1.3 THE BIOLOGICAL AND TECHNOLOGICAL STUDY CONTEXT...........................................................................................7 1.3.1 Insights from Comparative Genomics of Bacterial Pathogens ..................................................................7 1.3.2 The Study Bacteria: Mycobacterium ulcerans and Mycobacterium marinum................................12 1.3.3 Short Read Sequencing, Assembly and Alignment .......................................................................................14 1.4 THESIS OUTLINE................................................................................................................................................................18 2. METHODS ......................................................................................................................................................... 19 2.1 BACTERIAL ISOLATES AND SEQUENCING ......................................................................................................................19 2.2 READ MAPPING.................................................................................................................................................................. 20 2.3 DE NOVO ASSEMBLY OF SHORT READ SEQUENCES..................................................................................................... 20 2.3.1 Analysis of de novo Assembly Parameters ......................................................................................................20 2.3.2 Locating Repeat Regions Within de novo Contigs.......................................................................................21 2.3.3 De novo Assembly Limitations..............................................................................................................................22 2.4 CORE AND PAN GENOME ANALYSIS ...............................................................................................................................23 2.5 SNP ANALYSIS ................................................................................................................................................................... 24 2.6 DN/DS ANALYSIS ..............................................................................................................................................................24 2.7 PSEUDOGENE IDENTIFICATION ....................................................................................................................................... 25 3. .................................................................................................................................................................................. 26 3. RESULTS............................................................................................................................................................ 26 3.1 SHORT READ DE NOVO ASSEMBLY OPTIMISATION ..................................................................................................... 26 3.2 ISOLATE SELECTION AND SEQUENCE ANALYSIS STRATEGY ......................................................................................28 3.3 MYCOLACTONE‐PRODUCING MYCOBACTERIA FORM A MONOPHYLETIC GROUP .................................................. 32 3.4 GEOGRAPHICAL RESTRICTION OF M. ULCERANS OVER SHORT TIME SCALES .......................................................34
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