The genome sequence of the big-headed mining bee, Andrena bucephala (Stephens, 1846)

We present a genome assembly from an individual female Andrena bucephala (the Big-headed Mining Bee; Arthropoda; Insecta; Hymenoptera; Andrenidae). The genome sequence is 379.8 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.57 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,022 protein coding genes.


Background
The Big-headed Mining Bee, Andrena bucephala, is a mid-sized (forewing length 7-10 mm) mining bee in the family Andrenidae.It occurs widely across Europe, although it is generally scarce and locally distributed.This is true in the UK also where it occurs locally across southern England and Wales, and it is designated as 'Nationally Scarce A' (Falk, 1991).Females have a sparse covering of hairs with denser clumps of pale hairs on the sides of the thorax, margins of the tergites and scopa, with yellow hairs on the hind tibiae.The metasoma is narrow and rounded, the facial foveae are pale, and the wings are distinctly tinted yellow.Males have large, square heads with long mandibles lacking a subapical tooth or emargination.
A. bucephala occurs in a wide range of habitats, including open deciduous woodland, calcareous grassland, scrub and gardens.It is univoltine, with a flight period from April to June.Whilst it is a solitary species, it nests in compact aggregations sharing a communal, single nest entrance (Perkins, 1917).Often nests occur in a steep bank or rabbit burrows, lasting for multiple years and may contain more than 200 females (O'Toole & Raw, 1991).It visits the flowers of a range of species, although pollen is mainly collected from common hawthorn, Crataegus monogyna, and field maple, Acer campestre (Falk & Lewington, 2019;Wood & Roberts, 2017).
The complete genome sequence for this species will facilitate studies into the evolution of sociality, reproductive systems and Hymenopteran taxonomy.

Genome sequence report
The genome was sequenced from one female Andrena bucephala (Figure 1) collected from Dry Sandford Pit Nature Reserve, Oxfordshire, UK (51.7, -1.32).A total of 51-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 102 missing joins or mis-joins and removed 2 haplotypic duplications, reducing the assembly length by 0.16% and the scaffold number by 85.26%, and increasing the scaffold N50 by 543.48%.
The final assembly has a total length of 379.8 Mb in 13 sequence scaffolds with a scaffold N50 of 110.2 Mb (Table 1).The snailplot in Figure 2 provides a summary of the assembly statistics, while the distribution of assembly scaffolds on GC proportion and coverage is shown in Figure 3.The cumulative assembly plot in Figure 4 shows curves for subsets of scaffolds assigned to different phyla.Most (99.93%) of the assembly sequence was assigned to 5 chromosomal-level scaffolds.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (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.

Genome annotation report
The Andrena bucephala genome assembly (GCA_947577245.1)was annotated by the European Bioinformatics Institute (EBI) using the Ensembl rapid annotation pipeline (Table 1; h t t p s : / / r a p i d .e n s e m b l .o rg / A n d r e n a _ bu c e p h a l a _ G C A _ 947577245.1/Info/Index).The resulting annotation includes 27,899 transcribed mRNAs from 12,022 protein-coding and 4,153 non-coding genes.

Sample acquisition and nucleic acid extraction
A female Andrena bucephala (specimen ID Ox001341, ToLID iyAndBuce1) was netted at Dry Sandford Pit Nature Reserve, Oxfordshire, UK (latitude 51.7, longitude -1.32) on 2021-05-10.The specimen was collected and identified by Liam Crowley (University of Oxford) and preserved on dry ice.and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.
A Hi-C map for the final assembly was produced using bwa-mem2 (Vasimuddin et al., 2019) in the Cooler file format (Abdennur & Mirny, 2020).To assess the assembly metrics, the k-mer completeness and QV consensus quality values were calculated in Merqury (Rhie et al., 2020).This work Table 3 contains a list of relevant software tool versions and sources.

Genome annotation
The EBI used Ensembl Genebuild (Aken et al., 2016) to generate annotation for the Andrena bucephala assembly (GCA_ 947577245.1).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.The submission of materials by a Darwin Tree of Life Partner is subject to the 'Darwin Tree of Life Project Sampling Code of Practice', which can be found in full on the Darwin Tree of Life website here.By agreeing with and signing up to the Sampling Code of Practice, the Darwin Tree of Life

Software tool Version
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 This short and concise data note presents the genome assembly, annotation and preliminary content analysis for a species of mining bee (Andrenidae).It is clearly written, and adequately justifies the rationale for generating the data, and describes the currently standard benchmarks for assembly quality and content.The data are valuable and should be instrumental both in comparative studies of bee genomes and research on this specific species of bee.
My only observation is that the authors might want to deposit an annotated version of the specific scripts and commands used throughout their assembly and analytical pipelines, and also during the curation process, both to allow for full replicability of the study, but also (and perhaps, more important) to provide other researchers with a template they can use to analyse their own datasets.Such custom code is often hosted at sites like Zenodo or GitHub, which ideally allow version control, support updates and documentation.
Is the rationale for creating the dataset(s) clearly described?

Paulo Cseri Ricardo
Departamento de Genética e Biologia Evolutiva -Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil The article presents data on the assembly of the genome of the bee species Andrena bucephala, which is widely distributed throughout Europe.The main result is a final assembly comprising 379.8 Mb, distributed across 13 scaffolds, with five scaffolds accounting for 99.93% of the assembled sequence, in addition to a 19.57Kb mitogenome.The assembly metrics indicate high quality (QV) and completeness (k-mer completeness and BUSCO).The methods employed were appropriate, utilizing HiFi long reads in conjunction with a Hi-C map to achieve chromosome-scale scaffolds.The protocols are well-described or referenced to ensure reproducibility.Overall, the manuscript is written clearly and objectively, presenting highly relevant information for research on the evolution of hymenopteran species, particularly bees.I believe it is suitable for indexing in its current format.
Is the rationale for creating the dataset(s) clearly described?Yes Are the protocols appropriate and is the work technically sound?Yes

Are sufficient details of methods and materials provided to allow replication by others? Yes
Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.
Reviewer Expertise: transcriptomics, genomics, and evolution of bee species I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

Figure 2 .
Figure 2. Genome assembly of Andrena bucephala, iyAndBuce1.1:metrics.The BlobToolKit Snailplot shows N50 metrics and BUSCO gene completeness.The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 379,790,978 bp assembly.The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold present in the assembly (122,962,308 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (110,195,567 and 34,891,842 bp), respectively.The pale grey spiral shows the cumulative scaffold count on a log scale with white scale lines showing successive orders of magnitude.The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot.A summary of complete, fragmented, duplicated and missing BUSCO genes in the hymenoptera_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CANPUK01/dataset/CANPUK01/snail.

Figure 3 .
Figure 3. Genome assembly of Andrena bucephala, iyAndBuce1.1:BlobToolKit GC-coverage plot.Scaffolds are coloured by phylum.Circles are sized in proportion to scaffold length.Histograms show the distribution of scaffold length sum along each axis.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CANPUK01/dataset/CANPUK01/blob.

Figure 4 .
Figure 4. Genome assembly of Andrena bucephala, iyAndBuce1.1:BlobToolKit cumulative sequence plot.The grey line shows cumulative length for all scaffolds.Coloured lines show cumulative lengths of scaffolds assigned to each phylum using the buscogenes taxrule.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CANPUK01/dataset/CANPUK01/cumulative.

Figure 5 .
Figure 5. Genome assembly of Andrena bucephala, iyAndBuce1.1:Hi-C contact map of the iyAndBuce1.1 assembly, visualised using HiGlass.Chromosomes are shown in order of size from left to right and top to bottom.An interactive version of this figure may be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=ZfRikMozSyiKke1P8NWdfA.

Table 1 . Genome data for Andrena bucephala, iyAndBuce1.1. Project accession data
(Jay et al., 2023)d by the Wellcome Sanger Institute (WSI) Tree of Life core laboratory have been deposited on protocols.io(Dentonetal., 2023b).The workflow for high molecular weight (HMW) DNA extraction at the WSI includes a sequence of core procedures: sample preparation; sample homogenisation, DNA extraction, fragmentation, and clean-up.In sample preparation, the iyAndBuce1 sample was weighed and dissected on dry ice(Jay et al., 2023).Tissue from the thorax was homogenised using a PowerMasher II tissue disruptor(Denton et al., 2023a).HMW DNA was extracted in the WSI Scientific Operations core using the Automated MagAttract v2 protocol(Oatley et al., 2023).HMW DNA was sheared into an average fragment size of 12-20 kb in a Megaruptor 3 system with speed setting 31(Bates et al., 2023).

Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of methods and materials provided to allow replication by others? Partly Are the datasets clearly presented in a useable and accessible format? Yes Competing Interests:
No competing interests were disclosed.

have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
This is an open access peer review report distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.