Exploring Environmental Adaptation In Apis Cerana Based On Pan-genomics

The Apis cerana,is an important pollinator,providing pollination services to numerous wild plants and crops.Its widespread natural distribution makes it an ideal species for studying the molecular mechanisms of insect adaptation to different environments.In recent years,the population of A.cerana has declined and is declining,so understanding how A.cerana populations adapt to their external environmental conditions and elucidating the underlying mechanisms could inform conservation efforts.Several large-scale whole-genome resequencing projects have been performed for A.cerana,which not only revealed its population genetic structure but also uncovered some genes linked to its adaptations.However,previous analyses mainly used a single reference genome and focused on small-sized genetic variations,such as single nucleotide polymorphisms(SNPs)and small insertions/deletions(Indels).Many studies across various organisms have shown that relying on a single reference genome and small-scale genetic variations may overlook crucial genetic information for a species.Therefore,this study aims to construct a pan-genome sequence for the A.cerana and utilize it for population genomics research to comprehensively reveal the molecular mechanisms of its environmental adaptation.In this study,we first constructed and characterized the pan-genome of A.cerana based on a chromosome-level reference genome for its ancestral group and 525 whole-genome resequencing data sets.Then,we investigated the presence/absence variation(PAV)patterns and genotyped structural variations(SVs)across A.cerana populations and used these mapped variants to explore the potential role of SVs in the environmental adaptation of A.cerana.The main results are as follows:1.We utilized PacBio high-fidelity(HiFi)long-read sequencing and high-throughput chromosome conformation capture(Hi-C)techniques to generate a chromosome-scale reference genome sequence for the central ancestral population group of A.cerana.2.We constructed the pan-genome for A.cerana based on the reference genome of its ancestral population group and 525 whole-genome resequencing data sets(Figure 1).Our results revealed that the pan-genome of A.cerana is～345.2 Mb in length,including 127.5 Mb of sequences that are absent from the reference genome.3.We identified 16,587 protein-coding genes in the pan-genome,and 31.32%of them were flexible,that is,variably present,across A.cerana populations;These flexible genes were enriched in biological processes such as response to external stimuli,indicating their potential roles in adaptation.4.We identified and characterized SVs across A.cerana populations.After cross-validation,a total of 19,955 population SV sets were identified.Most SVs showed low linkage disequilibrium(LD)with nearby SNPs and Indels,suggesting that SVs is an important source of genetic variation.5.After performing environmental association analysis,we identified 44 SVs that 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 provides a representative high-quality genome and 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,which can further deepen people’s understanding of this species..