Abstract
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.
Keywords: Andrena bucephala, big-headed mining bee, genome sequence, chromosomal, Hymenoptera
Species taxonomy
Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Hymenoptera; Apocrita; Aculeata; Apoidea; Anthophila; Andrenidae; Andreninae; Andrena; Hoplandrena; Andrena bucephala (Stephens, 1846) (NCBI:txid1542580).
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%.
Figure 1. Photograph of the Andrena bucephala (iyAndBuce1) specimen used for genome sequencing.
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.
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. 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. 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. 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 | ||
|---|---|---|
| Assembly identifier | iyAndBuce1.1 | |
| Species | Andrena bucephala | |
| Specimen | iyAndBuce1 | |
| NCBI taxonomy ID | 1542580 | |
| BioProject | PRJEB55567 | |
| BioSample ID | SAMEA10166816 | |
| Isolate information | iyAndBuce1, female: thorax (DNA sequencing), head Hi-C sequencing), abdomen (RNA sequencing) | |
| Assembly metrics * | Benchmark | |
| Consensus quality (QV) | 63.5 | ≥ 50 |
| k-mer completeness | 100.0% | ≥ 95% |
| BUSCO ** | C:96.7%[S:96.4%,D:0.3%],F:0.9%,M:2.4%,n:5,991 | C ≥ 95% |
| Percentage of assembly mapped to chromosomes | 99.93% | ≥ 95% |
| Sex chromosomes | None | localised homologous pairs |
| Organelles | Mitochondrial genome: 19.57 kb | complete single alleles |
| Raw data accessions | ||
| PacificBiosciences SEQUEL II | ERR10115637 | |
| Hi-C Illumina | ERR10123710 | |
| PolyA RNA-Seq Illumina | ERR10890704 | |
| Genome assembly | ||
| Assembly accession | GCA_947577245.1 | |
| Accession of alternate haplotype | GCA_947577235.1 | |
| Span (Mb) | 379.8 | |
| Number of contigs | 195 | |
| Contig N50 length (Mb) | 8.0 | |
| Number of scaffolds | 13 | |
| Scaffold N50 length (Mb) | 110.2 | |
| Longest scaffold (Mb) | 122.96 | |
| Genome annotation | ||
| Number of protein-coding genes | 12,022 | |
| Number of non-coding genes | 4,153 | |
| Number of gene transcripts | 27,899 | |
* Assembly metric benchmarks are adapted from column VGP-2020 of “Table 1: Proposed standards and metrics for defining genome assembly quality” from ( Rhie et al., 2021).
** BUSCO scores based on the hymenoptera_odb10 BUSCO set using version 5.3.2. C = complete [S = single copy, D = duplicated], F = fragmented, M = missing, n = number of orthologues in comparison. A full set of BUSCO scores is available at https://blobtoolkit.genomehubs.org/view/CANPUK01/dataset/CANPUK01/busco.
Table 2. Chromosomal pseudomolecules in the genome assembly of Andrena bucephala, iyAndBuce1.
| INSDC accession | Chromosome | Length (Mb) | GC% |
|---|---|---|---|
| OX387715.1 | 1 | 122.96 | 41.0 |
| OX387716.1 | 2 | 110.2 | 41.5 |
| OX387717.1 | 3 | 78.17 | 40.5 |
| OX387718.1 | 4 | 34.89 | 40.5 |
| OX387719.1 | 5 | 33.33 | 41.0 |
| OX387720.1 | MT | 0.02 | 20.5 |
The estimated Quality Value (QV) of the final assembly is 63.5 with k-mer completeness of 100.0%, and the assembly has a BUSCO v5.3.2 completeness of 96.7% (single = 96.4%, duplicated = 0.3%), using the hymenoptera_odb10 reference set ( n = 5,991).
Metadata for specimens, barcode results, spectra estimates, sequencing runs, contaminants and pre-curation assembly statistics are given at https://links.tol.sanger.ac.uk/species/1542580.
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; https://rapid.ensembl.org/Andrena_bucephala_GCA_947577245.1/Info/Index). The resulting annotation includes 27,899 transcribed mRNAs from 12,022 protein-coding and 4,153 non-coding genes.
Methods
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.
Protocols developed by the Wellcome Sanger Institute (WSI) Tree of Life core laboratory have been deposited on protocols.io ( Denton et al., 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). Sheared DNA was purified by solid-phase reversible immobilisation ( Strickland et al., 2023): in brief, the method employs a 1.8X ratio of AMPure PB beads to sample to eliminate shorter fragments and concentrate the DNA. 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 iyAndBuce1 in the Tree of Life Laboratory at the WSI using the RNA Extraction: Automated MagMax™ mirVana protocol ( do Amaral et al., 2023). The RNA concentration was assessed using a Nanodrop spectrophotometer and a Qubit Fluorometer using the Qubit RNA Broad-Range Assay kit. Analysis of the integrity of the RNA was done using the Agilent RNA 6000 Pico Kit and Eukaryotic Total RNA assay.
Sequencing
Pacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers’ instructions. Poly(A) RNA-Seq libraries were constructed using the NEB Ultra II RNA Library Prep kit. DNA and RNA sequencing was performed by the Scientific Operations core at the WSI on Pacific Biosciences SEQUEL II (HiFi) and Illumina NovaSeq 6000 (RNA-Seq) instruments. Hi-C data were also generated from head tissue of iyAndBuce1 using the Arima2 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 and corrected 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., 2023), 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.
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 was done using Nextflow ( Di Tommaso et al., 2017) DSL2 pipelines “sanger-tol/readmapping” ( Surana et al., 2023a) and “sanger-tol/genomenote” ( Surana et al., 2023b). The genome was analysed within the BlobToolKit environment ( Challis et al., 2020) and BUSCO scores ( Manni et al., 2021; Simão et al., 2015) were calculated.
Table 3 contains a list of relevant software tool versions and sources.
Table 3. Software tools: versions and sources.
| Software tool | Version | Source |
|---|---|---|
| BlobToolKit | 4.1.7 | https://github.com/blobtoolkit/blobtoolkit |
| BUSCO | 5.3.2 | https://gitlab.com/ezlab/busco |
| Hifiasm | 0.16.1-r375 | https://github.com/chhylp123/hifiasm |
| HiGlass | 1.11.6 | https://github.com/higlass/higlass |
| Merqury | MerquryFK | https://github.com/thegenemyers/MERQURY.FK |
| MitoHiFi | 2.3 | https://github.com/marcelauliano/MitoHiFi |
| PretextView | 0.2 | https://github.com/wtsi-hpag/PretextView |
| purge_dups | 1.2.3 | https://github.com/dfguan/purge_dups |
| sanger-tol/genomenote | v1.0 | https://github.com/sanger-tol/genomenote |
| sanger-tol/readmapping | 1.1.0 | https://github.com/sanger-tol/readmapping/tree/1.1.0 |
| YaHS | yahs-1.1.91eebc2 | https://github.com/c-zhou/yahs |
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 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
• Legality of collection, transfer and use (national and international)
Each transfer of samples is further undertaken according to a Research Collaboration Agreement or Material Transfer Agreement entered into by the Darwin Tree of Life Partner, Genome Research Limited (operating as the Wellcome Sanger Institute), and in some circumstances other Darwin Tree of Life collaborators.
Funding Statement
This work was supported by Wellcome through core funding to the Wellcome Sanger Institute (206194) and the Darwin Tree of Life Discretionary Award (218328).
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
[version 1; peer review: 2 approved]
Data availability
European Nucleotide Archive: Andrena bucephala. Accession number PRJEB55567; https://identifiers.org/ena.embl/PRJEB55567 ( Wellcome Sanger Institute, 2022). The genome sequence is released openly for reuse. The Andrena bucephala 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.
Author information
Members of the University of Oxford and Wytham Woods Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.7125292.
Members of the Darwin Tree of Life Barcoding collective are listed here: https://doi.org/10.5281/zenodo.4893703.
Members of the Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team are listed here: https://doi.org/10.5281/zenodo.10066175.
Members of Wellcome Sanger Institute Scientific Operations: Sequencing Operations are listed here: https://doi.org/10.5281/zenodo.10043364.
Members of the Wellcome Sanger Institute Tree of Life Core Informatics team are listed here: https://doi.org/10.5281/zenodo.10066637.
Members of the Tree of Life Core Informatics collective are listed here: https://doi.org/10.5281/zenodo.5013541.
Members of the Darwin Tree of Life Consortium are listed here: https://doi.org/10.5281/zenodo.4783558.
References
- Abdennur N, Mirny LA: Cooler: Scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2020;36(1):311–316. 10.1093/bioinformatics/btz540 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Aken BL, Ayling S, Barrell D, et al. : The Ensembl gene annotation system. Database (Oxford). 2016;2016: baw093. 10.1093/database/baw093 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Allio R, Schomaker‐Bastos A, Romiguier J, et al. : MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics. Mol Ecol Resour. 2020;20(4):892–905. 10.1111/1755-0998.13160 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bates A, Clayton-Lucey I, Howard C: Sanger Tree of Life HMW DNA Fragmentation: Diagenode Megaruptor ®3 for LI PacBio. protocols.io. 2023. 10.17504/protocols.io.81wgbxzq3lpk/v1 [DOI] [Google Scholar]
- Bernt M, Donath A, Jühling F, et al. : MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 2013;69(2):313–319. 10.1016/j.ympev.2012.08.023 [DOI] [PubMed] [Google Scholar]
- Challis R, Richards E, Rajan J, et al. : BlobToolKit - interactive quality assessment of genome assemblies. G3 (Bethesda). 2020;10(4):1361–1374. 10.1534/g3.119.400908 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cheng H, Concepcion GT, Feng X, et al. : Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 2021;18(2):170–175. 10.1038/s41592-020-01056-5 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Denton A, Oatley G, Cornwell C, et al. : Sanger Tree of Life Sample Homogenisation: PowerMash. protocols.io. 2023a. 10.17504/protocols.io.5qpvo3r19v4o/v1 [DOI] [Google Scholar]
- Denton A, Yatsenko H, Jay J, et al. : Sanger Tree of Life Wet Laboratory Protocol Collection V.1. protocols.io. 2023b. 10.17504/protocols.io.8epv5xxy6g1b/v1 [DOI] [Google Scholar]
- Di Tommaso P, Chatzou M, Floden EW, et al. : Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017;35(4):316–319. 10.1038/nbt.3820 [DOI] [PubMed] [Google Scholar]
- do Amaral RJV, Bates A, Denton A, et al. : Sanger Tree of Life RNA Extraction: Automated MagMax TM mirVana. protocols.io. 2023. 10.17504/protocols.io.6qpvr36n3vmk/v1 [DOI] [Google Scholar]
- Falk S: A review of the scarce and threatened flies of Great Britain. Nature Conservancy Council,1991. Reference Source [Google Scholar]
- Falk S, Lewington R: Field Guide to the Bees of Great Britain and Ireland. London: Bloomsbury,2019. [Google Scholar]
- Guan D, McCarthy SA, Wood J, et al. : Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics. 2020;36(9):2896–2898. 10.1093/bioinformatics/btaa025 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Harry E: PretextView (Paired REad TEXTure Viewer): A desktop application for viewing pretext contact maps.2022; [Accessed 19 October 2022]. Reference Source
- Howe K, Chow W, Collins J, et al. : Significantly improving the quality of genome assemblies through curation. GigaScience. Oxford University Press,2021;10(1): giaa153. 10.1093/gigascience/giaa153 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jay J, Yatsenko H, Narváez-Gómez JP, et al. : Sanger Tree of Life Sample Preparation: Triage and Dissection. protocols.io. 2023. 10.17504/protocols.io.x54v9prmqg3e/v1 [DOI] [Google Scholar]
- Kerpedjiev P, Abdennur N, Lekschas F, et al. : HiGlass: Web-based visual exploration and analysis of genome interaction maps. Genome Biol. 2018;19(1): 125. 10.1186/s13059-018-1486-1 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Manni M, Berkeley MR, Seppey M, et al. : BUSCO update: Novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol. 2021;38(10):4647–4654. 10.1093/molbev/msab199 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Oatley G, Denton A, Howard C: Sanger Tree of Life HMW DNA Extraction: Automated MagAttract v.2. protocols.io. 2023. 10.17504/protocols.io.kxygx3y4dg8j/v1 [DOI] [Google Scholar]
- O’Toole C, Raw A: Bees of the world. New York: Blandford Press,1991. [Google Scholar]
- Perkins RCL: Notes on the collection of British Hymenoptera (Aculeata) formed by F. Smith. Entomologist’s Monthly Magazine. 1917;53:71–76. [Google Scholar]
- Rao SSP, Huntley MH, Durand NC, et al. : A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159(7):1665–1680. 10.1016/j.cell.2014.11.021 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rhie A, McCarthy SA, Fedrigo O, et al. : Towards complete and error-free genome assemblies of all vertebrate species. Nature. 2021;592(7856):737–746. 10.1038/s41586-021-03451-0 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rhie A, Walenz BP, Koren S, et al. : Merqury: Reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 2020;21(1): 245. 10.1186/s13059-020-02134-9 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Simão FA, Waterhouse RM, Ioannidis P, et al. : BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31(19):3210–3212. 10.1093/bioinformatics/btv351 [DOI] [PubMed] [Google Scholar]
- Strickland M, Cornwell C, Howard C: Sanger Tree of Life Fragmented DNA clean up: Manual SPRI. protocols.io. 2023. 10.17504/protocols.io.kxygx3y1dg8j/v1 [DOI] [Google Scholar]
- Surana P, Muffato M, Qi G: sanger-tol/readmapping: sanger-tol/readmapping v1.1.0 - Hebridean Black (1.1.0). Zenodo. 2023a; (Accessed: 17 April 2023). 10.5281/zenodo.7755669 [DOI] [Google Scholar]
- Surana P, Muffato M, Sadasivan Baby C: sanger-tol/genomenote (v1.0.dev). Zenodo. 2023b; (Accessed: 17 April 2023). 10.5281/zenodo.6785935 [DOI] [Google Scholar]
- Uliano-Silva M, Ferreira GJRN, Krasheninnikova K, et al. : MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio High Fidelity reads. BMC Bioinformatics. 2023;24(1): 288. 10.1186/s12859-023-05385-y [DOI] [PMC free article] [PubMed] [Google Scholar]
- UniProt Consortium: UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 2019;47(D1):D506–D515. 10.1093/nar/gky1049 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Vasimuddin Md, Misra S, Li H, et al. : Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. In: 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS). IEEE,2019;314–324. 10.1109/IPDPS.2019.00041 [DOI] [Google Scholar]
- Wellcome Sanger Institute: The genome sequence of the big-headed mining bee, Andrena bucephala (Stephens, 1846). European Nucleotide Archive, [dataset], accession number PRJEB55567.2022.
- Wood TJ, Roberts SPM: An assessment of historical and contemporary diet breadth in polylectic Andrena bee species. Biol Conserv. 2017;215:72–80. 10.1016/j.biocon.2017.09.009 [DOI] [Google Scholar]
- Zhou C, McCarthy SA, Durbin R: YaHS: yet another Hi-C scaffolding tool. Bioinformatics. 2023;39(1): btac808. 10.1093/bioinformatics/btac808 [DOI] [PMC free article] [PubMed] [Google Scholar]