Abstract
We present a genome assembly from an individual female Elmis aenea (a riffle beetle; Arthropoda; Insecta; Coleoptera; Elmidae). The genome sequence is 516.5 megabases in span. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 18.06 kilobases in length.
Keywords: Elmis aenea, riffle beetle, genome sequence, chromosomal, Coleoptera
Species taxonomy
Eukaryota; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Elateriformia; Byrrhoidea; Elmidae; Elminae; Elmis; Elmis aenea (Müller, 1806) (NCBI:txid186982).
Background
Elmis aenea ( Figure 1) is a western Palaearctic species found from Portugal to Finland, Russia and Ukraine ( Jäch et al., 2016). It is the commonest elmid beetle in Britain and Ireland, known in most parts except the Shetlands, Uists, Coll and Tiree, and the Isle of Man ( Foster et al., 2020). It is, however, rare in some lowland areas lacking fast-running water, such as the Wash, and in heavily industrialised or lowland urbanised areas such as around Manchester, the Tyne Valley and parts of West Yorkshire ( Hammond, 2017). Whereas it might be considered almost eurythermal in Britain and Ireland, found in any fast-running water, in mainland Europe it reaches 2,400 metres above sea level in Italy ( Olmi, 1976), and is generally considered to be an upland species, but this view has been challenged in Poland ( Buczyński & Buczyńska, 2022). It is, however, most likely to be found in headwaters, often in the absence of other riffle beetle species, and it is occasionally found in subterranean waters ( Knight, 2011). Adults were found in areas with a particle size averaging 103 mm in diameter whereas larvae were found where particle size averaged 77 mm ( Malmqvist & Sjöström, 1984). Elliott (2008) found that about half of adults tested would fly, but flight records are rare in nature, and this tallies with the beetle's absence from the Isle of Man, where the other three common elmid species occur, as originally reported by ( Britten, 1944).
Figure 1. Photograph of Elmis aenea (icElmAene2). Photograph by Udo Schmidt (CC BY-SA 2.0).
Adults and larvae are detritivorous but adult guts may also contain periphytic algae ( Elliott, 2008). Eggs are laid from April to June on aquatic mosses, there being six instars with mostly the fourth one overwintering ( Holland, 1972). The final instar leaves the water to pupate in the following spring, with a new generation of adults emerging that autumn. Adults and larvae can be encountered together through most of the year, except when adults are scarce in January and February. Decline has been reported in association with milder winter temperatures and higher than average rainfall during the cycle of the North Atlantic Oscillation ( Bradley & Ormerod, 2001). Life-table analysis by ( Elliott, 2006) showed that the greatest losses, at 36%, are in immature stages owing to spating. On the other hand, ( Hoffsten, 2003) noted slow recovery following a severe winter in Sweden when precipitation was low.
Elmis aenea is the sole known representative of Elmis in Britain and Ireland. Several other Elmis species, in particular E. maugetii Latreille, can be found in low-lying parts of mainland Europe ( Olmi, 1976). There is a faint possibility that their presence has been overlooked if anywhere in eastern England. The high-quality genome sequence described here is, to our knowledge, the first one reported for the true E. aenea. The genome sequence for E. aenea will aid in understanding the biology, physiology and ecology of the species.
Genome sequence report
The genome was sequenced from one female Elmis aenea collected from Great Staughton, UK (52.27, –0.35). A total of 35-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 89 missing joins or misjoins, reducing the scaffold number by 4.57%, and increasing the scaffold N50 by 0.34%.
The final assembly has a total length of 516.5 Mb in 333 sequence scaffolds with a scaffold N50 of 60.3 Mb ( Table 1). Most (95.3%) of the assembly sequence was assigned to 9 chromosomal-level scaffolds, representing 8 autosomes and the X sex chromosome. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size ( Figure 2– Figure 5; Table 2). The X chromosome was identified based on synteny with Agrypnus murinus (GCA_929113105.1; icAgrMuri1.1). 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 Elmis aenea, icElmAene2.1: 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 516,518,598 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 (73,284,568 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (60,347,194 and 31,928,154 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 endopterygota_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Elmis aenea/dataset/CANTFG01/snail.
Figure 5. Genome assembly of Elmis aenea, icElmAene2.1: Hi-C contact map of the icElmAene2.1 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=FN93Vc1kQT6dWcM8J2qaVw.
Table 1. Genome data for Elmis aenea, icElmAene2.1.
| Project accession data | ||
|---|---|---|
| Assembly identifier | icElmAene2.1 | |
| Species | Elmis aenea | |
| Specimen | icElmAene2 | |
| NCBI taxonomy ID | 186982 | |
| BioProject | PRJEB57664 | |
| BioSample ID | SAMEA7521014 | |
| Isolate information | icElmAene2, female: whole organism (DNA sequencing); icElmAene3, whole organism (Hi-C scaffolding) | |
| Assembly metrics * | Benchmark | |
| Consensus quality (QV) | 58.1 | ≥ 50 |
| k-mer completeness | 99.99% | ≥ 95% |
| BUSCO ** | C:99.1%[S:98.2%,D:0.9%],
F:0.5%,M:0.4%,n:2,124 |
C ≥ 95% |
| Percentage of assembly mapped to chromosomes | 95.3% | ≥ 95% |
| Sex chromosomes | X chromosome | localised homologous pairs |
| Organelles | Mitochondrial genome assembled. | complete single alleles |
| Raw data accessions | ||
| PacificBiosciences SEQUEL II | ERR10499354 | |
| Hi-C Illumina | ERR10501012 | |
| Genome assembly | ||
| Assembly accession | GCA_947652605.1 | |
| Accession of alternate haplotype | GCA_947652985.1 | |
| Span (Mb) | 516.5 | |
| Number of contigs | 1187 | |
| Contig N50 length (Mb) | 0.9 | |
| Number of scaffolds | 333 | |
| Scaffold N50 length (Mb) | 60.3 | |
| Longest scaffold (Mb) | 73.3 | |
* 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 endopterygota_odb10 BUSCO set using v5.3.2. 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/Elmis%20aenea/dataset/CANTFG01/busco.
Figure 3. Genome assembly of Elmis aenea, icElmAene2.1: 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/Elmis%20aenea/dataset/CANTFG01/blob.
Figure 4. Genome assembly of Elmis aenea, icElmAene2.1: 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/Elmis aenea/dataset/CANTFG01/cumulative.
Table 2. Chromosomal pseudomolecules in the genome assembly of Elmis aenea, icElmAene 2.
| INSDC accession | Chromosome | Length (Mb) | GC% |
|---|---|---|---|
| OX393576.1 | 1 | 73.28 | 31.5 |
| OX393577.1 | 2 | 71.35 | 31.5 |
| OX393578.1 | 3 | 62.65 | 31.5 |
| OX393579.1 | 4 | 60.35 | 32.0 |
| OX393580.1 | 5 | 55.9 | 31.5 |
| OX393581.1 | 6 | 55.28 | 31.5 |
| OX393582.1 | 7 | 47.42 | 32.0 |
| OX393583.1 | 8 | 34.12 | 33.0 |
| OX393584.1 | X | 31.93 | 31.5 |
| OX393585.1 | MT | 0.02 | 27.0 |
The estimated Quality Value (QV) of the final assembly is 58.1 with k-mer completeness of 99.99%, and the assembly has a BUSCO v5.3.2 completeness of 99.1% (single = 98.2%, duplicated = 0.9%), using the endopterygota_odb10 reference set ( n = 2,124).
Metadata for specimens, spectral estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/species/186982.
Methods
Sample acquisition and nucleic acid extraction
The specimen used for genome sequencing was a female Elmis aenea (specimen ID NHMUK014361123, individual icElmAene2), collected from freshwater in Great Staughton, UK (latitude 52.27, longitude –0.35) on 2019-03-11 using a kick-net. The specimen used for Hi-C scaffolding was icElmAene3, which was collected from freshwater in Dover Beck, Caythorpe, UK (latitude 53.01, longitude –0.99) on 2019-03-19. The specimens were collected and identified by John Findlay (Environment Agency), and were snap-frozen on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI). The icElmAene2 sample was weighed and dissected on dry ice. Tissue from the whole organism was cryogenically disrupted to a fine powder using a Covaris cryoPREP Automated Dry Pulveriser, receiving multiple impacts. High molecular weight (HMW) DNA was extracted using the Qiagen MagAttract HMW DNA extraction kit. 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.
Sequencing
Pacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers’ instructions. DNA sequencing was performed by the Scientific Operations core at the WSI on a Pacific Biosciences SEQUEL II (HiFi) instrument. Hi-C data were also generated from tissue of icElmAene3 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). One round of polishing was performed by aligning 10X Genomics read data to the assembly with Long Ranger ALIGN, calling variants with FreeBayes ( Garrison & Marth, 2012). 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 using the gEVAL system ( Chow et al., 2016) as described previously ( Howe et al., 2021). Manual curation was performed using gEVAL, 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 | 4.1.5 | https://github.com/blobtoolkit/blobtoolkit |
| BUSCO | 5.3.2 | https://gitlab.com/ezlab/busco |
| gEVAL | N/A | https://geval.org.uk/ |
| 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 | 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 | 1.1a.2 | https://github.com/c-zhou/yahs |
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: Elmis aenea (riffle beetle). Accession number PRJEB57664; https://identifiers.org/ena.embl/PRJEB57664. ( Wellcome Sanger Institute, 2022)
The genome sequence is released openly for reuse. The Elmis aenea 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 available 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.
Author information
Members of the Natural History Museum Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.4790042.
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 programme are listed here: https://doi.org/10.5281/zenodo.4783585.
Members of Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective are listed here: https://doi.org/10.5281/zenodo.4790455.
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]
- 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]
- 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]
- Bradley DC, Ormerod SJ: Community persistence among stream invertebrates tracks the North Atlantic Oscillation. J Anim Ecol. 2001;70(6):987–996. 10.1046/j.0021-8790.2001.00551.x [DOI] [Google Scholar]
- Britten H: The Coleoptera of the Isle of Man. The North Western Naturalist. 1944;158–164. [Google Scholar]
- Buczyński P, Buczyńska E: Czy Elmis aenea (Müll.) (Coleoptera: Elmidae) to faktycznie gatunek górski w Polsce? Uwagi o jej występowaniu górami i pogórzami. Przegląd Przyrodniczy. 2022;33:94–99. Reference Source [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]
- Chow W, Brugger K, Caccamo M, et al. : gEVAL — a web-based browser for evaluating genome assemblies. Bioinformatics. 2016;32(16):2508–2510. 10.1093/bioinformatics/btw159 [DOI] [PMC free article] [PubMed] [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]
- Elliott JM: Critical periods in the life cycle and the effects of a severe spate vary markedly between four species of elmid beetles in a small stream. Freshw Biol. 2006;51(8):1527–1542. 10.1111/j.1365-2427.2006.01587.x [DOI] [Google Scholar]
- Elliott JM: The Ecology of Riffle Beetles (Coleoptera: Elmidae). Freshw Rev. 2008;1(2):189–203. 10.1608/FRJ-1.2.4 [DOI] [Google Scholar]
- Foster GN, Bilton DT, Hammond M, et al. : Atlas of water beetles of Britain and Ireland - smaller families of Polyphaga.Telford: FSC Publications,2020. Reference Source [Google Scholar]
- Garrison E, Marth G: Haplotype-based variant detection from short-read sequencing.2012. 10.48550/arXiv.1207.3907 [DOI] [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]
- Hammond MR: The water beetles of Yorkshire.Yorkshire & Humber Ecological Data Trust,2017. Reference Source
- Harry E: PretextView (Paired REad TEXTure Viewer): A desktop application for viewing pretext contact maps.2022; [Accessed 19 October 2022]. Reference Source
- Hoffsten PO: Effects of an extraordinarily harsh winter on macroinvertebrates and fish in boreal streams. Arch Hydrobiol. 2003;157:505–523. 10.1127/0003-9136/2003/0157-0505 [DOI] [Google Scholar]
- Holland DG: A key to the larvae, pupae and adults of the British species of Elminthidae.Scientific Publication-Freshwater Biological Association,1972. Reference Source [Google Scholar]
- 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]
- Jäch MA, Kodada J, Brojer MA, et al. : World Catalogue of Insects. 14. Coleoptera: Elmidae and Protelmidae.Leiden: Koninklijke Brill NV,2016. Reference Source [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]
- Knight LRFD: The aquatic macro-invertebrate fauna of Swildon’s Hole, Mendip Hills, Somerset, UK. Cave and Karst Science. 2011;38:81–92. Reference Source [Google Scholar]
- Malmqvist B, Sjöström P: The microdistribution of three beetle species inhabiting a south Swedish stream riffle. Acta Hydrobiologia, Krakow. 1984;25/26:409–414. [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]
- Olmi M: Coleoptera Dryopidae-Elminthidae. Fauna d’Italia 12.Bologna: Calderini,1976. [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]
- Surana P, Muffato M, Qi G: sanger-tol/readmapping: sanger-tol/readmapping v1.1.0 - Hebridean Black (1.1.0). Zenodo. 2023a. 10.5281/zenodo.7755665 [DOI] [Google Scholar]
- Surana P, Muffato M, Sadasivan Baby C: sanger-tol/genomenote (v1.0.dev). Zenodo. 2023b. 10.5281/zenodo.6785935 [DOI] [Google Scholar]
- Uliano-Silva M, Ferreira JGRN, 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]
- Vasimuddin M, Misra S, Li H, et al. : Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems.In: 2019 IEEE Int Parallel Distrib Process Symp (IPDPS). IEEE,2019;314–324. 10.1109/IPDPS.2019.00041 [DOI] [Google Scholar]
- Wellcome Sanger Institute: The genome sequence of a riffle beetle, Elmis aenea (Müller, 1806). European Nucleotide Archive.[dataset], accession number PRJEB57664,2022.
- 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]