Standard methods and good practices in <i>Apis</i> honey bee omics research

In the past decades, COLOSS members have joined forces multiple times to develop and condense standard methods related to research on honey bees, their pests, pathogens, and colony products. This led to the publication of four open-access <i>BEEBOOK</i> volumes that have been utilized by researchers worldwide. Among the chapters, “Standard methods for molecular research in <i>Apis mellifera</i>,” written by Evans and collaborators in 2013, has been a cornerstone for the standardization of honey bee molecular studies. However, since sequencing technologies and analyzing algorithms have made tremendous progress, many described methods require updating. In parallel, other <i>Apis</i> species’ genomes have now been sequenced, thus opening new research avenues in a comparative framework. In this chapter, we add to the methods previously covered by Evans et al. in 2013 and provide updated methodology where necessary, including worked examples and bioinformatic analysis pipelines. We also cover topics which were not previously covered in depth, such as sequencing ancient samples, population genomics, proteomics, and sampling honey bee colony products for microbiome studies, among others. Our hope is for this to become a lasting resource for honey bee scientists as the field continues to advance.