De Novo Genome Assembly of Chinese Plateau Honeybee Unravels Intraspecies Genetic Diversity in the Eastern Honeybee, .

, widely distributed in the southeastern margin of the Qinghai-Tibet Plateau, is considered an excellent model to study the phenotype and genetic variation for highland adaptation of Asian honeybee. Herein, we assembled and annotated the chromosome-scale assembly genome of with the help of PacBio, Illumina and Hi-C sequencing technologies in order to identify the genome differences between the and the published genomes of different strains. The sequencing methods, assembly and annotation strategies of were more comprehensive than previously published genomes. Then, the intraspecific genetic diversity of was revealed at the genomic level. We re-identified the repeat content in the genome of , as well as the other three strains. The chemosensory and immune-related proteins in different strains were carefully re-identified, so that 132 odorant receptor subfamilies, 12 gustatory receptor subfamilies and 22 immune-related pathways were found. We also discovered that, compared with other published genomes, the lost the largest number of chemoreceptors compared to other strains, and hypothesized that gene loss/gain might help different strains to adapt to their respective environments. Our work contains more complete and precise assembly and annotation results for the genome, thus providing a resource for subsequent in-depth related studies.