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

Abstract

<i>Apis cerana abansis</i>, 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 <i>A. cerana abansis</i> with the help of PacBio, Illumina and Hi-C sequencing technologies in order to identify the genome differences between the <i>A. cerana abansis</i> and the published genomes of different <i>A. cerana</i> strains. The sequencing methods, assembly and annotation strategies of <i>A. cerana abansis</i> were more comprehensive than previously published <i>A. cerana</i> genomes. Then, the intraspecific genetic diversity of <i>A. cerana</i> was revealed at the genomic level. We re-identified the repeat content in the genome of <i>A. cerana abansis</i>, as well as the other three <i>A. cerana</i> strains. The chemosensory and immune-related proteins in different <i>A. cerana</i> 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 <i>A. cerana</i><i>abansis</i> lost the largest number of chemoreceptors compared to other strains, and hypothesized that gene loss/gain might help different <i>A. cerana</i> strains to adapt to their respective environments. Our work contains more complete and precise assembly and annotation results for the <i>A. cerana</i> genome, thus providing a resource for subsequent in-depth related studies.