From Genotype to Phenotype: Assembly and Annotation of Two Fungal Genomes

All organisms in an environment interact with that environment, including with both other organisms as well as the abiotic surroundings. Symbiosis is defined as a close, long-term association between organisms of different species that commonly results in novel structures and/or metabolism. Ascomycetes, also known as sac fungi, are the largest phylum of Fungi with over 64,000 currently known species. Within this diverse group, beneficial and detrimental associations with specific plant hosts are observed. I selected an antagonist, Cochliobolus kusanoi, and a mutualist, Penicillium pinophilum, for our analyses. These endophytes were isolated from Panicum virgatum. I conducted paired-end sequencing with an Illumina HiSeq 4000 system to investigate the genetic underpinnings of such complex relationships. Genome assembly was completed with several programs for performance comparison, namely Velvet, MaSuRCA, and SOAPdenovo2. The de novo assemblies were assessed for completeness with BUSCO and QUAST. The final phase of the project is annotating the two genomes by following the standard DOE-JGI Fungal Genome Annotation Pipeline recommendations and incorporating our previously collected transcriptome data for these fungi to improve the annotation. Genes related to the fungal phenotypes will be predicted and functionally annotated, and comparative analysis will enable the visualization of specific gene structures and domain compositions. I successfully created a unique and accurate workflow for future fungal genomics research beginning with DNA extraction through genome annotation.