The genome sequence of the Tawny Mining Bee, Andrena fulva (Müller, 1766) [version 1; peer review: awaiting peer review]

We present a genome assembly from an individual female Andrena fulva (the Tawny Mining Bee; Arthropoda; Insecta; Hymenoptera; Andrenidae). The genome sequence is 461.7 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 14.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,011 protein coding genes.


Background
The Tawny Mining Bee, Andrena fulva, is a common and widespread mining bee in the UK. Females are large (10 mm wing length) and are one of the most distinctive within the Andrena genus, with long red hairs dorsally across the thorax and abdomen and black-haired head and legs. The smaller males (8 mm wing length) are less striking, with generally duller red-brown hairs on the body, although they may be recognised by the white hairs on the clypeus and long mandibles with a distinct tooth at the base (Paxton, 1991).
Andrena fulva is distributed throughout western Europe, east to the Balkans and north to southern Scandinavia. In the UK, it is locally common across England and Wales and may be found north to southern Scotland. It occurs in a range of habitats, in particular open grasslands, pastures and parks and gardens. It is broadly polylectic, visiting a range of flowers including beech (Fagus sylvatica), blackthorn (Prunus spinosa), buttercup (Ranunculus sp.), garlic mustard (Alliaria petiolata), current (Ribes sp.), hawthorn (Crataegus monogyna), maple (Acer sp.), oak (Quercus sp.), plum (Prunus domestica) and sallow (Salix sp.) (Chambers, 1968).
The species is univoltine, with a flight period from March to May. Males generally emerge first, before the females which mate then build and provision two or three nests (O'Toole & Raw, 1991). In accordance with the wider genus, nests are constructed underground. Nesting typically occurs on level, loose sandy soil with short, sparge vegetation (Maher et al., 2019). Females excavate a main central vertical tunnel 20 -40 cm deep, from which arise 4 or 5 radial cells (O'Toole & Raw, 1991). The excavated soil often forms a volcano-like tumulus which may be conspicuous in short lawns. Andrena fulva frequently forms dense nesting aggregations, that may persist in the same location for several years. Such aggregations are likely to be in response to resource distribution (e.g. near floral resources or suitable nesting substrate), although it had also been suggested that they may confer a degree of natural enemy escape (Hamilton, 1971;Rosenheim, 1990). Such aggregated nesting may represent an early step in the evolution of true sociality.
This Andrena fulva genome assembly will prove invaluable in the development of genetic markers to investigate relatedness among aggregated individuals. While a large number of females in the related Andrena jacobi commonly mate with male nest-mates pre-emergence (Paxton & Tengö, 1996;Paxton et al., 1996), this seems not to be the case in A. fulva, in which males tend to emerge before females (Paxton, 1991).

Genome sequence report
The genome was sequenced from one female Andrena fulva ( Figure 1) collected from Wytham Farm, Oxfordshire, UK (51.79, -1.32). A total of 46-fold coverage in Pacific Biosciences single-molecule HiFi long reads was generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 14 missing joins or mis-joins and removed one haplotypic duplication, reducing the assembly length by 0.22% and the scaffold number by 3.94%, and increasing the scaffold N50 by 113.54%.
The final assembly has a total length of 461.7 Mb in 317 sequence scaffolds with a scaffold N50 of 47.5 Mb (Table 1). Most (80.24%) of the assembly sequence was assigned to 7 chromosomal-level scaffolds. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 2- Figure 5; Table 2). While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited. The mitochondrial genome was also assembled and can be found as a contig within the multifasta file of the genome submission.
Metadata for specimens, spectral estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/species/1411667.

Sample acquisition and nucleic acid extraction
A female Andrena fulva (specimen number Ox001244, individual iyAndFulv1) was collected from Wytham Farm,

Genome annotation
Number of protein-coding genes 12,011 Number of non-coding genes 6,025 Number of gene transcripts 28,635 * Assembly metric benchmarks are adapted from column VGP-2020 of "   Illumina NovaSeq 6000 (RNA-Seq) instruments. Hi-C data were also generated from head tissue of iyAndFulv1 using the Arimav2 kit and sequenced on the Illumina NovaSeq 6000 instrument.

Genome assembly, curation and evaluation
Assembly was carried out with Hifiasm (Cheng et al., 2021) and haplotypic duplication was identified and removed with purge_dups (Guan et al., 2020). The assembly was then scaffolded with Hi-C data (Rao et al., 2014) using YaHS (Zhou et al., 2023). The assembly was checked for contamination as described previously (Howe et al., 2021). Manual curation was performed using HiGlass (Kerpedjiev et al., 2018) and Pretext (Harry, 2022). The mitochondrial genome was assembled using MitoHiFi (Uliano-Silva et al., 2022), which runs MitoFinder (Allio et al., 2020) or MITOS (Bernt et al., 2013) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.

Genome annotation
The Ensembl gene annotation system (Aken et al., 2016) was used to generate annotation for the Andrena fulva assembly (GCA_946251845.1). Annotation was created primarily through alignment of transcriptomic data to the genome, with gap filling via protein-to-genome alignments of a select set of proteins from UniProt (UniProt Consortium, 2019).

Wellcome Sanger Institute -Legal and Governance
The materials that have contributed to this genome note have been supplied by a Darwin Tree of Life Partner. Life Partner agrees they will meet the legal and ethical requirements and standards set out within this document in respect of all samples acquired for, and supplied to, the Darwin Tree of Life Project.
Further, the Wellcome Sanger Institute employs a process whereby due diligence is carried out proportionate to the nature of the materials themselves, and the circumstances under which they have been/are to be collected and provided for use. The purpose of this is to address and mitigate any potential legal and/or ethical implications of receipt and use of the materials as part of the research project, and to ensure that in doing so we align with best practice wherever possible.
The overarching areas of consideration are: • Ethical review of provenance and sourcing of the material    The genome sequence is released openly for reuse. The Andrena fulva 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. Raw data and assembly accession identifiers are reported in Table 1.