A chromosome-level genome assembly and resequencing data reveal low DNA methylation and reduced diversity in the solitary bee pollinator Osmia cornuta

Abstract

Bees provide essential pollination services that contribute to ecosystem stability, as well as the sustainability of economic crop yields. Due to concerns over global and local declines, improving our understanding of these ecologically and commercially important species is crucial for determining their capacity to respond and adapt to environmental challenges. The European orchard bee (Osmia cornuta) is a solitary bee of increasing agricultural importance due to its role in the pollination of fruit crops, yet lacks genomic resources. Using cost-effective Nanopore-only long-read sequencing, we report the first genome assembly for O. cornuta, spanning 647.56Mb across 727 contigs (N50=3.94Mb) at a high level of completeness (99.88% BUSCO complete). In line with the expected number of chromosomes in this species, 16 major scaffolds were assembled to chromosome-level. Also, we provisionally investigated the epigenomic architecture of O. cornuta, finding low numbers of CG dinucleotides that were either 5-methylated or 5-hydroxymethylated, providing additional evidence for the limited role methylation plays in gene regulation in Hymenopterans. To generate improved gene annotations, we combined transcriptomic- and orthology-based approaches, leading to the prediction of 12,144 genes and 25,964 proteins, showing exceptionally high BUSCO completeness (99.64%). Lastly, through whole-genome resequencing of a representative dataset, we provisionally find patterns of reduced nucleotide diversity and lower recombination rates within O. cornuta compared to other bee species. Collectively, our study provides a novel insight into the genome architecture of a key pollinator, providing an important resource to facilitate further genomic studies. Significance statementSolitary bees are crucial pollinators for crops and wild plants, but scientists have lacked the genetic blueprints needed to understand how these species might adapt to environmental threats like climate change and habitat loss. Using modern and cost-effective technologies, we generated the complete genome of the European orchard bee, an economically important fruit pollinator. This comprehensive genetic resource provides the foundation for future research on solitary bee biology and conservation, necessary to understand their adaptive potential in the face of environmental challenges. In line with this, we analysed this species genetic variation across populations in Germany using a small, representative dataset and found surprisingly low genetic diversity and limited evidence of gene recombination during reproduction, which are factors that could restrict its capacity to evolve in response to environmental challenges.