Northern bobwhite sequencing
From raw materials to validated system: The construction of a genomic library and microarray to interpret systemic perturbations in Northern bobwhite
Manuscript accepted pending revisions in Physiological Genomics.    The limited availability of genomic tools and data for non-model species impedes computational and systems biology approaches in non-model organisms.  Here we describe the development, functional annotation, and utilization of genomic tools for the avian wildlife species Northern bobwhite (Colinus virginianus) to determine the molecular impacts of exposure to 2,6-dinitrotoluene (2,6-DNT), a field-contaminant of military concern.  Massively-parallel pyrosequencing of a normalized multi-tissue library of Northern bobwhite cDNAs yielded 71,384 unique transcripts which were annotated using gene ontology (GO), pathway information and protein domain analysis.  Comparative genome analyses with model organisms revealed functional homologies in 8,825 unique Northern bobwhite genes that are orthologous to 48% of Gallus gallus protein-coding genes. Pathway analysis and GO enrichment of genes differentially expressed in livers of birds exposed for 60d to 10 and 60 mg/kg/d 2,6-DNT revealed several impacts validated by RT-qPCR including:  prostaglandin pathway-mediated inflammation, increased expression of a heme synthesis pathway in response to anemia and a shift in energy metabolism toward protein catabolism via inhibition of control points for glucose and lipid metabolic pathways, PCK1 and PPARGC1, respectively.  This research effort provides the first comprehensive annotated gene library for Northern bobwhite. Transcriptome analysis provided insights into the metabolic perturbations underlying several observed toxicological phenotypes in a 2,6-DNT-exposure case study.  Further, the systemic impact of dinitrotoluenes on liver function appears conserved across species as PPAR signaling is similarly affected in fathead minnow liver tissue after exposure to 2,4-DNT.