This week the manuscript “Development of Genomic Resources for a thraustochytrid Pathogen and Investigation of Temperature Influences on Gene Expression” was published.
Photo: Students in FHL EIMD course hard at work on bioinformatic analysis of transcriptome and genomic data from the hard clam pathogen quahog parasite unknown (QPX).
Abstract: Understanding how environmental changes influence the pathogenicity and virulence of infectious agents is critical for predicting epidemiological patterns of disease. Thraustochytrids, part of the larger taxonomic class Labyrinthulomycetes, contain several highly pathogenic species, including the hard clam pathogen quahog parasite unknown (QPX). QPX has been associated with large-scale mortality events along the northeastern coast of North America. Growth and physiology of QPX is temperature-dependent, and changes in local temperature profiles influence pathogenicity. In this study we characterize the partial genome of QPX and examine the influence of temperature on gene expression. Genes involved in several biological processes are differentially expressed upon temperature change, including those associated with altered growth and metabolism and virulence. The genomic and transcriptomic resources developed in this study provide a foundation for better understanding virulence, pathogenicity and life history of thraustochytrid pathogens.
Citation: Garcia-Vedrenne AE, Groner M, Page-Karjian A, Siegmund G-F, Singhal S, Sziklay J, Roberts SB. (2013) Development of Genomic Resources for a thraustochytrid Pathogen and Investigation of Temperature Influences on Gene Expression. PLoS ONE 8(9): e74196. doi:10.1371/journal.pone.0074196
Genome Browser Tracks also published!
Genomic feature tracks (iebed, gff) from partial genome sequencing of QPX (Quahog Parasite Unknown). Data includes putative SNPs, RNA-seq data from cultures grown at two temperatures, and putative transcript locations based on sequence similarity searches. Feature tracks (and corresponding fasta file) developed to be viewed with Integrative Genomics Viewer (http://www.broadinstitute.org/igv/). Fileset includes sesssion file (.xml) to load all features.
All data are also available at http://eagle.fish.washington.edu/QPX_genome/