Second-generation sequencing technologies are precipitating major shifts with regards to what kinds of genomes are being sequenced and how they are annotated. While the first generation of genome projects focused on well-studied model organisms, many of todays projects involve exotic organisms whose genomes are largely terra incognita. This complicates their annotation, because unlike first-generation projects, there are no pre-existing gold-standard gene-models with which to train gene-finders. Improvements in genome assembly and the wide availability of mRNA-seq data are also creating opportunities to update and re-annotate previously published genome annotations. Todays genome projects are thus in need of new genome annotation tools that can meet the challenges and opportunities presented by second-generation sequencing technologies.