Next-generation sequencing for whole-genome analysis of non-model organisms

Next generation sequencing can be used to produce low-cost genomic resources for "system specific" eukaryotic models: plants and animals which are specifically suited to a particular scientific question. While complete genome sequencing using short reads alone is not yet feasible for higher eukaryotes, current technology can provide a route to gene-space or transcriptome sequencing, even for large and uncharacterized genomes. New and adapted sequence analysis methods are necessary to facilitate these genomics projects. We have developed data analysis methods and biological insights from partial genome and transcriptome sequencing using short read technology. These methods have been applied to eleven bee species in the hymenoptera for the purposes of comparative and evolutionary genomic analysis.