The genome sequence of the short-fringed mining bee, Andrena dorsata (Kirby, 1802)

We present a genome assembly from an individual female Andrena dorsata (the short-fringed mining bee; Arthropoda; Insecta; Hymenoptera; Andrenidae). The genome sequence is 277.3 megabases in span. Most of the assembly is scaffolded into 3 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.11 kilobases in length. Gene annotation of this assembly on Ensembl identified 10,916 protein coding genes.


Background
The short-fringed mining bee (Andrena dorsata) is a small (8-9 mm body length (Warzecha et al., 2016)) groundnesting solitary bee found in western Europe that is especially common in south-eastern England, with scattered records further north and in south and north Wales (NBN Atlas Partnership, 2021).As with other mining bees, females dig a nest burrow and provision each egg with pollen collected from nearby flowers.A. dorsata is a bivoltine species (Warzecha et al., 2016), with one generation in spring (peaking in April in the UK) and another in summer (peaking in July), and the more southerly distribution may reflect the need for warmer temperatures to facilitate production of two generations in a year.Whilst some members of the genus Andrena are communal, with many females nesting independently but in close proximity, A. dorsata is a true solitary bee (Wcislo & Fewell, 2017).The conservation status of A. dorsata is currently unclear, as this species, like some 56.7% of all European bee species is classified as 'Data deficient' by the ICUN (Nieto et al., 2014;Potts et al., 2016).
Karyotype information for bees is sparse, with only around 200 of the estimated 18,00-20,000 bee species having been investigated (Cunha et al., 2021), and members of the genus Andrena are at the low end of the bee chromosome scale, with a diploid chromosome number (2n) of 6, with the full bee range spanning 6 to 58 chromosomes.This A. dorsata genome, together with those of other bee species, will be useful for the identification of the processes that have so radically altered chromosome number in bees, and for the characterisation of the genome-level processes underlying increased GC content in this and other members of the genus (Sless et al., 2022): the three chromosomes of A. dorsata range in GC content from 42.5-43%, whereas the honeybee (Apis mellifera, 2n = 32) genome average is 10% lower at 34% (Wallberg et al., 2019).

Genome sequence report
The genome was sequenced from one female Andrena dorsata (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 40-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 85-fold coverage in 10X Genomics read clouds were generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 20 missing joins or mis-joins and removed 2 haplotypic duplications, reducing the assembly length by 1.27% and the scaffold number by 3.68%, and increasing the scaffold N50 by 2.3%. The final assembly has a total length of 277.3 Mb in 157 sequence scaffolds with a scaffold N50 of 88.5 Mb (Table 1).Most (97.03%) of the assembly sequence was assigned to 3 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/1411666.

Sample acquisition and nucleic acid extraction
A female Andrena dorsata (specimen ID Ox000751, ToLID iyAndDors1) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.33) on 2020-08-04 by netting.The specimen was   collected and identified by Steven Falk (independent researcher) and preserved on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The iyAndDors1 sample was weighed and dissected on dry ice with head tissue set aside for Hi-C sequencing.Thorax tissue was disrupted using a Nippi Powermasher fitted with a BioMasher pestle.High molecular weight (HMW) DNA was extracted using the Qiagen MagAttract HMW DNA extraction kit.Low molecular weight DNA was removed from a 20 ng aliquot of extracted DNA using the 0.8X AMpure XP purification kit prior to 10X Chromium sequencing; a minimum of 50 ng DNA was submitted for 10X sequencing.HMW DNA was sheared into an average fragment size of 12-20 kb in a Megaruptor 3 system with speed setting 30.Sheared DNA was purified by solid-phase reversible immobilisation using AMPure PB beads with a 1.8X ratio of beads to sample to remove the shorter fragments and concentrate the DNA sample.The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer and Qubit dsDNA High Sensitivity Assay kit.Fragment size distribution was evaluated by running the sample on the FemtoPulse system.
RNA was extracted from abdomen tissue of iyAndDors2 in the Tree of Life Laboratory at the WSI using TRIzol, according to the manufacturer's instructions.RNA was then eluted in 50 μl RNAse-free water and its concentration assessed using a Nanodrop spectrophotometer and Qubit Fluorometer using the Qubit RNA Broad-Range (BR) Assay kit.Analysis of the integrity of the RNA was done using Agilent RNA 6000 Pico Kit and Eukaryotic Total RNA assay.

Sequencing
Pacific Biosciences HiFi circular consensus and 10X Genomics read cloud DNA sequencing libraries were constructed according to the manufacturers' instructions.DNA sequencing was performed by the Scientific Operations core at the WSI on Pacific Biosciences SEQUEL II (HiFi) and Illumina NovaSeq 6000 (10X) instruments.Hi-C data were also generated from head tissue of iyAndDors1 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.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 assembly, curation and evaluation
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 Table 3 contains a list of relevant software tool versions and sources.

Genome annotation
The Ensembl gene annotation system (Aken et al., 2016) was used to generate annotation for the Andrena dorsata assembly (GCA_929108735.1).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 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

Manee M Manee
King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia The study presents a comprehensive genome assembly of the short-fringed mining bee, Andrena dorsata.The assembly has a high consensus quality value (QV) of 53.5 and a k-mer completeness of 99.99%.BUSCO analysis indicates 96.8% completeness for hymenoptera_odb10 reference genes.I am pleased with the current form of the study.

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: bioinformatics, genomics, and evolutionary biology 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 dorsata, iyAndDors1.1: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 277,337,111 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 (110,492,342 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (88,484,888 and 70,131,001 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/iyAndDors1.1/dataset/CAKMYH01/snail.

Figure 3 .
Figure 3. Genome assembly of Andrena dorsata, iyAndDors1.1: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/iyAndDors1.1/dataset/CAKMYH01/blob.

Figure 4 .
Figure 4. Genome assembly of Andrena dorsata, iyAndDors1.1: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/iyAndDors1.1/dataset/CAKMYH01/ cumulative.

Figure 5 .
Figure 5. Genome assembly of Andrena dorsata, iyAndDors1.1:Hi-C contact map of the iyAndDors1.1 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=AD908eZZTU2AuDnxO0UBbA.

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. YesAre

have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
Reviewer Report 22 July 2024 https://doi.org/10.21956/wellcomeopenres.21882.r88318© 2024 Manee M. 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.