The western honeybee, Apis mellifera is a prominent model organism in the field of sociogenomics
and a recent upgrade substantially improved annotations of the reference genome.
Nevertheless, genome assemblies based on short-sequencing reads suffer from problems in regions
comprising e.g. multi-copy genes. We used single-molecule nanopore-based sequencing
with extensive read-lengths to reconstruct the organization of the major royal jelly protein
(mrjp) region in three species of the genus Apis. Long-amplicon sequencing provides evidence
for lineage-specific evolutionary fates of Apis mrjps. Whereas the most basal species, A. florea,
seems to encode ten mrjps, different patterns of gene loss and retention were observed for
A. mellifera and A. dorsata. Furthermore, we show that a previously reported pseudogene in
A. mellifera, mrjp2-like, is an assembly artefact arising from short read sequencing.