The genome sequence of the garden bumblebee, Bombus hortorum (Linnaeus, 1761)

We present a genome assembly from an individual female Bombus hortorum (the garden bumblebee; Arthropoda; Insecta; Hymenoptera; Apidae). The genome sequence is 296 megabases in span. The majority of the assembly is scaffolded into 18 chromosomal pseudomolecules.


Introduction
The garden bumblebee, Bombus hortorum, is one of the seven most common species of bumblebee in the UK. It is widespread, being found in most habitats apart from upland areas. It is a large bumblebee species with a long face and a very long proboscis, meaning it favours deep flowers with a relatively long corolla such as foxglove (Digitalis purpurea) and honeysuckle (Lonicera periclymenum). It visits a wide range of flowers, particularly those with deep or complex blooms, meaning it is frequently found in gardens. This species expresses a preference for red clover (Trifolium pratense) when available (Brown et al., 1992). In common with other species in the Genus, the high degree of floral visitation undertaken by this species indicates its important role as a pollinator.
Bombus hortorum is a eusocial, annual species, with queens emerging from overwinter diapause from around March onwards. Workers can be seen from late April, with the number of workers increasing throughout the spring to reach around 100 workers in a mature nest (Edwards & Jenner, 2005). The first males can be produced from June and new queens from July. Nests are always constructed under cover, but if underground they are often only shallowly so (Kells & Goulson, 2003).

Genome sequence report
The genome was sequenced from a single female B. hortorum collected from Wytham Woods, Oxfordshire, UK (latitude 51.77, longitude -1.339). A total of 82-fold coverage in Pacific Biosciences single-molecule long reads and 113-fold coverage in 10X Genomics read clouds were generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 23 missing/ misjoins, reducing the assembly length by 0.001% and the scaffold number by 31.1%, and increasing the scaffold N50 by 38.9%. The final assembly has a total length of 296 Mb in 43 sequence scaffolds with a scaffold N50 of 17 Mb (Table 1). Of the assembly sequence, 88.9% was assigned to 18 chromosomal-level scaffolds (numbered by sequence length) ( Figure 1-Figure 4; Table 2). The assembly has a BUSCO (Simão et al., 2015) v5.1.2 completeness of 97.5% using the hymenoptera_odb10 reference set. While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited.

Methods
A single female B. hortorum was collected using a net from Wytham Woods, Oxfordshire, UK (latitude 51.77, longitude -1.339) by Liam Crowley, University of Oxford. The specimen was snap-frozen in dry ice using a CoolRack before transferring to the Wellcome Sanger Institute (WSI) for genome sequencing and assembly.
DNA was extracted at the WSI Scientific Operations core from the head and thorax using the Qiagen MagAttract HMW DNA kit, according to the manufacturer's instructions. RNA was extracted from abdomen tissue in the Tree of Life Laboratory at the WSI using TRIzol (Invitrogen), according to the manufacturer's instructions. RNA was then eluted in 50 μl        The genome sequence is released openly for reuse. The B. hortorum genome sequencing initiative is part of the Darwin Tree of Life (DToL) project. All raw sequence data and the assembly have been deposited in INSDC databases. The genome will be annotated using the RNA-Seq data and presented through the Ensembl pipeline at the European Bioinformatics Institute. Raw data and assembly accession identifiers are reported in Table 1. e1007273. https://doi.org/10.21956/wellcomeopenres.18990.r46468