Lost and Found: Western Honey Bee ( Apis mellifera ) Matrix Metalloproteinase 1

ABSTRACT The quality of reference genomes is of utmost importance as they and the therein annotated genes and proteins serve as basis for many downstream applications. Although the current Western honey bee ( Apis mellifera ) genome assembly (Amel_HAv3.1) represents a significant improvement over previous versions (Amel_4.0, Amel_4.5), it nevertheless lacks certain protein‐coding genes present in those earlier assemblies. One of these “lost and found” genes is locus 409868 of Amel_4.0 and Amel_4.5 which is missing due to an approximately 160 kb assembly gap on chromosome 10 in Amel_HAv3.1. Here we show that the A. mellifera genome indeed harbours locus 409868 encoding matrix metalloproteinase 1 ( mmp1 ) and that it is expressed in at least four different mRNA isoforms in honey bee workers. Orthologues from other insect species have essential tissue and organ remodelling functions during development and gene knockdowns at specific developmental time points are lethal. As adult honey bee workers show in addition an elaborate age‐based division of labour with drastic major morphological and physiological changes requiring extensive tissue and organ remodelling, leaving out mmp1 because of a missing gene in the reference genome, may mean leaving out a potential key player in development.