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

In recent decades, honeybee populations have declined, dramatically owing to destructive honey harvesting practices and the loss of foraging grounds and nesting sites. Among them, Apis laboriosa Smith, 1871 (Hymenoptera, Apidae), an important pollinator species found in the Himalayan region, holds significant economic and ecological value. However, conservation efforts and intraspecific taxonomic studies regarding it have been rather limited, and thus its full geographic range remains elusive. This study is the first to research A. laboriosa in Sichuan. Through a systematic study integrating morphological feature analysis and genomic data, the following conclusions are drawn. Whole-genome resequencing data analysis reveals that the Sichuan population forms a new monophyletic group (Bootstraps = 100). In the past ten thousand years, the population sizes of A. laboriosa in four different regions of China have been decreasing rapidly. Measures should be taken to protect them across the entire distribution range, especially the populations in Tibet and Sichuan, due to their relatively large genetic differences and low intra-population genetic diversity. Based on the significant difference analysis, the following four wing vein morphological features with extremely significant differences were identified: the width of the right forewing (FB), the cubital index a/b (Ci), the forewing vein angle (E9), and the forewing vein angle (K19). These findings are expected to offer a valuable reference for future A. laboriosa conservation endeavors, particularly in protecting populations with a high level of genetic differentiation.

Apis laboriosa Smith is the largest bee in the genus Apis, and it is mainly distributed in Yunnan and Tibet regions in China. In this study, two complete m

The Asian honey bee (Apis cerana) is a key native pollinator in Asia, contributing substantially to both natural and agricultural ecosystems. However, climate change and human activities increasingly threaten its pollination services and long-term survival. Understanding patterns of genetic differentiation and local adaptation is therefore essential for protecting native populations. Sichuan Province in China, with its complex mountains, deep valleys, and pronounced climatic heterogeneity, offers an excellent natural laboratory for studying these processes in A. cerana. We collected 139 worker bees from 22 locations across Sichuan and generated whole-genome resequencing data. By integrating these data with genomes from eight well-established subspecies, we show that bees from Xinlong, Jiuzhaigou, and Kangding form three genetically differentiated populations that are distinct from all known subspecies. These populations display moderate to high genetic differentiation and unique demographic histories relative to previously described subspecies. Selective-sweep analyses further identified 200–300 candidate genes under positive selection in each population. These genes are enriched in functions related to chemical sensing, flight musculature, cell-cycle regulation, osmotic balance, and stress response, consistent with adaptation to patchy nectar resources, a short spring reproductive window, and large diurnal temperature swings. Our findings uncover three previously unrecognized genetic resources of A. cerana and provide genomic insights into their local adaptation, offering a valuable foundation for conservation and breeding programs.