The genome sequences of Achlya hypogyna and Thraustotheca clavata: Insights on oomycete parasite evolution

Parasitism is the most common consumer strategy among eukaryotes and is a life history strategy that has arisen independently innumerable times across the tree of life. Nevertheless, mechanisms underlying the transition from a free-living lifestyle to a parasitic mode of existence are largely a mystery, and investigations on the genetic consequences of becoming a parasite are limited to highly specialized human pathogens. Parasitic oomycetes, especially plant pathogenic species, are widely studied and have a wealth of genomic information available, but relatively little genomic information is available for free-living or facultatively parasitic taxa. Comparisons of gene families among oomycetes, with the goal of understanding their evolution across this lifestyle spectrum, will not produce clear results without filling in these gaps in the data. With this goal in mind the focus of this research was to: 1) sequence the genome of Achlya hypogyna and Thraustotheca clavata 2) compare these proteomes to the parasitic oomycetes to identify gene families involved in parasite evolution and 3) identify and characterize the secretome A. hypogyna and T. clavata. Next-generation sequencing technologies were used to generate high quality draft genomes for A. hypogyna and T. clavata. Using a variety of bioinformatic resources and tools including evolutionary gene networks and a novel program Sequence Comparative Analysis using Networks (SCAN) we were able to generate transcriptome libraries that were used to computational predict proteomes for each species. Proteins belonging to the secretome were identified using publically available functional models and these sequences were compared with published oomycete secretomes. A custom phylogenetic pipeline was used to identify horizontal gene transfer events involving secretome proteins. This research generated a novel bioinformatic analysis tool, SCAN, which is capable of identifying quality transcriptome assembly with statistical support. With the addition of two saprolegnian oomycete genomes and the use of evolutionary gene networks we were able to identify unique gene family expansions and contractions in parasitic oomycetes. Combining our data from these two Saprolegnian oomycetes with the available secretomes from parasitic Peronosporelean taxa, we have identified and described the conserved oomycete secretome that contains effector gene families, including elicitins and protease inhibitors. Additionally, we have identified 13 horizontal gene transfer events that are key to the evolution of parasitism within this diverse group of organisms