A Chromosome-Level Genome Assembly and Resequencing Data Reveal Low DNA Methylation and Reduced Diversity in the...

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 647.56 Mb across 727 contigs (N50 = 3.94 Mb) 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.