An ecological model organism flies into the genomics era

Despite the very rapid 'genomicization' of the field of Molecular Ecology in recent years, there have been relatively few annotated whole-genome assemblies of nonmodel organisms published. Instead, molecular ecologists have more frequently utilized next-generation sequencing technologies to develop genome-wide markers or to generate transcriptome data. Whole-genome assemblies are more expensive and require considerable computational resources and bioinformatic expertise. However, the availability of an annotated genome offers exciting opportunities to address fundamental questions in ecology and evolution that are difficult to address with moderate sets of markers or by transcriptome sequencing. Such questions include elucidating the roles of natural and sexual selection in shaping diversity, determining the roles of regulatory and protein-coding change in the evolution of traits, and determining the genomic architecture of sex-specific trait variation. Arguably, these questions are most tractable--and most interesting--in well-characterized species for which there is already some knowledge of natural and sexual selection, and of the traits that are most likely to link to fitness. In this issue, Mueller et al. (2016) present the assembly and annotation of the genome of the blue tit (Cyanistes caeruleus), a model ecological species. In addition, by sequencing the transcriptome of male and female blue tits, the authors identify and annotate sex-biased gene expression and conclude that noncoding RNA genes are likely to play a significant role in sex-biased expression. By making their assembly and annotation publically available and accessible via a genome browser, Mueller et al. (2016) offer exciting possibilities for further research into the genomic basis of adaptation, and investigation of the roles of natural and sexual selection, in this well-studied ecological model species.