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ABSTRACT MONACELL, JAMES TRENTADUE. Identification of Heterokaryon Incompatibility Genes in Aspergillus using Array Comparative Genome Hybridization and Whole Genome Sequencing. (Under the direction of Dr. Ignazio Carbone.) Aspergillus flavus is a filamentous ascomycete most noted as a pathogen of economically important crops such as corn, peanuts, and cotton. A. flavus poses a multifaceted threat causing crop loss, contaminating food with carcinogenic mycotoxins, aflatoxins (AF) and cyclopiazonic acid (CPA), as well as infecting humans and animals. A. flavus contamination has cost millions of dollars in crop loss, several outbreaks of aflatoxins laden foods and dog foods have occurred in recent years resulting in human and animal deaths, in addition to direct infection in immuno-compromised individuals. In addition to sexual reproduction, this fungus has the potential to undergo genetic exchange between compatible strains via heterokaryon formation, or parasexuality. Heterokaryon incompatibility is the inability of two strains to undergo fusion of vegetative fungal cells. This vegetative compatibility system is dictated by a series of heterokaryon incompatibility (het) loci whose alleles must all be identical for stable hyphal fusions to occur. Het loci have been identified in several filamentous fungi. This work provides the first characterization of het loci in Aspergillus flavus and A. parasiticus. Fungal individuals can be grouped into vegetative compatibility groups (VCGs) based on their ability to undergo hyphal fusions and potentially form heterokaryons. A major goal of this work is to seek a better understanding of the mechanisms controlling heterokaryon incompatibility to improve control methods of this important agricultural pathogen. We performed array-Comparative Genome Hybridization (aCGH) for eleven VCGs and a total of 51 strains in Aspergillus section Flavi, including A. flavus, A. parasiticus, A. oryzae, A. caelatus, A. tamarii and A. nomius. We conducted an initial screening of these data for signatures of balancing selection around single-feature polymorphism markers on chromosomes 2, 3, 4, and 6, which previous work showed to associate closely with VCG. Our screening for evidence of balancing selection revealed 12 putative het loci showing distinct patterns of trans-speciation. Additionally, we sequenced the genomes of fourteen Aspergillus flavus, two A. parasiticus, one A. nomius and two strains of A. tubingensis from Aspergillus section Nigri. To find homologs of het genes in our species of interest we performed blast searches using the putative het genes in Neurospora crassa, Podospora anserina, and Sordaria macrospora, also searching against the published genomes of A. flavus (NRRL 3357), A. oryzae (RIB 40), and A. nidulans (FGSC A4). We found numerous homologs of het genes from other species as well as evidence of gene duplication in our species of interest. There was no apparent correlation between fertility, measured as the percentage of ascospore-bearing ascocarps, and het gene copy number. However, the presence of alleles with matching WD repeats in parental strains seems to correlate with fertility, suggesting that the HNWD gene family may be important in sexual reproduction. A secondary objective of this work was to develop a web-based portal frontend using the Mobyle portal framework which executes a suite of over 189 programs, including population genetic, genome assembly and analysis tools, as well as metagenomic and large- scale phylogenetic analyses. The Mobyle SNAP Workbench web portal allows end users to 1) execute and manage otherwise complex command-line programs, 2) launch multiple exploratory analyses of parameter-rich and computationally intensive methods, and 3) track the sequence of steps and parameters that were used to perform a specific analysis. A public deployment of the portal is available at http://snap.hpc.ncsu.edu/. © Copyright 2014 James T Monacell All Rights Reserved Identification of Heterokaryon Incompatability Genes in Aspergillus using Array Comparative Genome Hybridization and Whole Genome Sequencing by James Trentadue Monacell A thesis submitted to the Graduate Faculty of North Carolina State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Bioinformatics Raleigh, North Carolina 2014 APPROVED BY: _______________________________ ______________________________ Ignazio Carbone Eric Stone Committee Chair ________________________________ ________________________________ Dahlia Nielsen Gary Payne BIOGRAPHY James Trentadue Monacell was born February 26, 1986 in Atlanta, Georgia. In 2008 he received his Bachelor of Science in Computer Science with a minor in Applied Biology from Rose-Hulman Institute of Technology. Later that year he began work on his PhD at North Carolina State University. He joined the Carbone lab to research fungal genetics as well as develop online Bioinformatics tools. He married Kellie Bailey in 2011, and they had their first child, James Douglas, in 2013. ii TABLE OF CONTENTS LIST OF TABLES ........................................................................................................ vii LIST OF FIGURES ...................................................................................................... ix CHAPTER 1 Introduction ............................................................................................ 1 1.1 Background ......................................................................................................... 2 1.2 Sexual reproduction in Aspergillus flavus ........................................................... 3 1.3 Heterokaryon Incompatibility .............................................................................. 8 1.4 Research Objectives ............................................................................................. 8 1.5 References ............................................................................................................ 11 CHAPTER 2 Mobyle SNAP Workbench: A web-based analysis portal for population genetics and evolutionary genomics .......................................................... 15 2.1 Introduction .......................................................................................................... 18 2.2 Systems and Methods .......................................................................................... 19 2.3 Framework ........................................................................................................... 20 2.4 Implementation .................................................................................................... 22 2.5 Acknowledgements .............................................................................................. 23 2.6 References ............................................................................................................ 24 CHAPTER 3 Identifying heterokaryon incompatibility loci in Aspergillus flavus and Aspergillus parasiticus using array Comparative Genome Hybridization ........ 26 3.1 Abstract ................................................................................................................ 27 3.2 Introduction .......................................................................................................... 28 3.3 Materials and Methods ......................................................................................... 31 3.3.1 Multilocus sequence typing (MLST ........................................................... 31 3.3.2 Array comparative genome hybridization (aCGH ...................................... 32 3.3.3 Identifying putative het loci ........................................................................ 36 3.4 Results .................................................................................................................. 36 3.4.1 MLSTs ........................................................................................................ 36 3.4.2 Signatures of Balancing Selection .............................................................. 40 3.5 Discussion ............................................................................................................ 40 3.6 References ............................................................................................................ 48 CHAPTER 4 Characterization of putative heterokaryon incompatibility loci in Aspergillus flavus and allied species ............................................................................. 53 iii 4.1 Abstract ................................................................................................................ 54 4.2 Introduction .......................................................................................................... 55 4.3 Materials and Methods ......................................................................................... 61 4.3.1 Strains, DNA isolation and genome sequencing......................................... 61 4.3.2 Preprocessing reads and genome assembly ................................................ 67 4.3.3 Search for het homologs ............................................................................. 67 4.3.4 Phylogenetic analysis .................................................................................. 68 4.4 Results .................................................................................................................. 69 4.4.1 Genome assemblies ....................................................................................
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