Data from: Pan-genome analysis highlights the role of structural variation in the evolution and environmental adaptation of Asian honeybees

The Asian honeybee, Apis cerana, is an ecologically and economically
important pollinator. Mapping its genetic variation is key to
understanding population-level health, histories, and potential capacities
to respond to environmental changes. However, most efforts to date were
focused on single nucleotide polymorphisms (SNPs) based on a single
reference genome, thereby ignoring larger-scale genomic variation. We
employed long-read sequencing technologies to generate a chromosome-scale
reference genome for the ancestral group of A. cerana. Integrating this
with 525 resequencing datasets, we constructed the first pan-genome of A.
cerana, encompassing almost the entire gene content. We found that 31.32%
of genes in the pan-genome were variably present across populations,
providing a broad gene pool for environmental adaptation. We identified
and characterized structural variations (SVs) and found that they were not
closely linked with SNP distributions, however, the formation of SVs was
closely associated with transposable elements. Furthermore, phylogenetic
analysis using SVs revealed a novel A. cerana ecological group not
recoverable from the SNP data. Performing environmental association
analysis identified a total of 44 SVs likely to be associated with
environmental adaptation. Verification and analysis of one of these, a 330
bp deletion in the Atpalpha gene, indicated that this SV may promote the
cold adaptation of A. cerana by altering gene expression. Taken together,
our study demonstrates the feasibility and utility of applying pan-genome
approaches to map and explore genetic feature variations of honeybee
populations, and in particular to examine the role of SVs in the evolution
and environmental adaptation of A. cerana.