Abstract
We present a genome assembly from an individual male Conomelus anceps (planthopper; Arthropoda; Insecta; Hemiptera; Delphacidae). The genome sequence has a total length of 957.80 megabases. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 21.98 kilobases in length.
Keywords: Conomelus anceps, planthopper, genome sequence, chromosomal, Hemiptera
Species taxonomy
Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Paraneoptera; Hemiptera; Auchenorrhyncha; Fulgoromorpha; Fulgoroidea; Delphacidae; Delphacinae; Conomelus; Conomelus anceps (Germar, 1821) (NCBI:txid491269).
Background
Conomelus anceps (Germar, 1821) ( Figure 1) is a species of planthopper belonging to the family Delphacidae. Its global distribution extends across Europe and parts of Asia, with records from various countries in the Palaearctic region. There are also a few records from North America ( GBIF Secretariat, 2024). Within the United Kingdom, C. anceps is commonly found throughout England, Wales, and southern Scotland, primarily in grassland habitats. They are herbivorous, feeding on the sap of Juncus spp. (rushes) in meadows and woodlands in damp habitats.
Figure 1. Photograph of the Conomelus anceps (ihConAnce5) specimen used for RNA sequencing.
Adults are active from late spring to early autumn, and although small in size (up to 4 mm in length), they can be distinguished by the reddish-brown ground colour and the wings have dark spots on the veins. C. anceps has two wing forms: macropterous (long-winged) and brachypterous (short-winged). The macropterous form can fly and disperse, while the brachypterous form has reduced wings and limited mobility. Both forms are commonly observed, with the brachypterous form often more prevalent in some populations ( British Bugs, no date).
In this data note we present a chromosomally complete genome sequence for Conomelus anceps, based on a specimen from Beinn Eighe National Nature Reserve, Scotland, UK.
Genome sequence report
The genome of an adult male Conomelus anceps was sequenced using Pacific Biosciences single-molecule HiFi long reads, generating a total of 27.17 Gb (gigabases) from 2.22 million reads, providing approximately 28-fold coverage. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data, which produced 119.77 Gb from 793.15 million reads, yielding an approximate coverage of 125-fold. Specimen and sequencing information is summarised in Table 1.
Table 1. Specimen and sequencing data for Conomelus anceps.
| Project information | |||
|---|---|---|---|
| Study title | Conomelus anceps | ||
| Umbrella BioProject | PRJEB58256 | ||
| Species | Conomelus anceps | ||
| BioSample | SAMEA12997853 | ||
| NCBI taxonomy ID | 491269 | ||
| Specimen information | |||
| Technology | ToLID |
BioSample
accession |
Organism part |
| PacBio long read sequencing | ihConAnce4 | SAMEA12997912 | Whole organism |
| Hi-C sequencing | ihConAnce1 | SAMEA12997909 | Whole organism |
| RNA sequencing | ihConAnce5 | SAMEA110451719 | Whole organism |
| Sequencing information | |||
| Platform |
Run
accession |
Read count |
Base
count (Gb) |
| Hi-C Illumina NovaSeq 6000 | ERR10684084 | 7.93e+08 | 119.77 |
| PacBio Sequel IIe | ERR10688630 | 2.22e+06 | 27.17 |
| RNA Illumina NovaSeq 6000 | ERR12642421 | 7.05e+07 | 10.64 |
| RNA Illumina NovaSeq X | ERR12861027 | 5.93e+07 | 8.96 |
Manual assembly curation corrected 75 missing joins or mis-joins and one haplotypic duplications, reducing the scaffold number by 6.83%. The final assembly has a total length of 957.80 Mb in 504 sequence scaffolds with a scaffold N50 of 73.1 Mb ( Table 2). The total count of gaps in the scaffolds is. The snail plot 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 (94.29%) of the assembly sequence was assigned to 12 chromosomal-level scaffolds, representing 11 autosomes and the X sex chromosome. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size ( Figure 5; Table 3). The order and orientation of contigs along Chromosome 6 is uncertain between 31.7 Mb and 42.5 Mb. 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 Conomelus anceps, ihConAnce4.1: metrics.
The BlobToolKit snail plot 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 957,858,181 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 (169,506,832 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (73,089,041 and 42,841,405 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 hemiptera_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CAOJWK01/dataset/CAOJWK01/snail.
Figure 3. Genome assembly of Conomelus anceps, ihConAnce4.1: Blob plot of base coverage against GC proportion for sequences in the assembly.
Sequences are coloured by phylum. Circles are sized in proportion to sequence length. Histograms show the distribution of sequence length sum along each axis. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CAOJWK01/dataset/CAOJWK01/blob.
Figure 4. Genome assembly of Conomelus anceps ihConAnce4.1: BlobToolKit cumulative sequence plot.
The grey line shows cumulative length for all sequences. Coloured lines show cumulative lengths of sequences assigned to each phylum using the buscogenes taxrule. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CAOJWK01/dataset/CAOJWK01/cumulative.
Figure 5. Genome assembly of Conomelus anceps ihConAnce4.1: Hi-C contact map of the ihConAnce4.1 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=FTonhwL0SLi-C0cN5GqwoQ.
Table 2. Genome assembly data for Conomelus anceps, ihConAnce4.1.
| Genome assembly | ||
|---|---|---|
| Assembly name | ihConAnce4.1 | |
| Assembly accession | GCA_948455865.1 | |
|
Accession of alternate
haplotype |
GCA_948455875.1 | |
| Span (Mb) | 957.80 | |
| Number of contigs | 2,253 | |
| Contig N50 length (Mb) | 1.1 | |
| Number of scaffolds | 504 | |
| Scaffold N50 length (Mb) | 73.1 | |
| Longest scaffold (Mb) | 169.51 | |
| Assembly metrics * | Benchmark | |
| Consensus quality (QV) | 59.2 | ≥ 50 |
| k-mer completeness | 100.0% | ≥ 95% |
| BUSCO ** | C:98.2%[S:96.4%,D:1.8%],
F:0.9%,M:0.9%,n:2,510 |
C ≥ 95% |
| Percentage of assembly
mapped to chromosomes |
94.29% | ≥ 95% |
| Sex chromosomes | X | localised homologous pairs |
| Organelles | Mitochondrial genome: 21.98 kb | complete single alleles |
* 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 hemiptera_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/CAOJWK01/dataset/CAOJWK01/busco.
Table 3. Chromosomal pseudomolecules in the genome assembly of Conomelus anceps, ihConAnce4.
| INSDC accession | Name | Length (Mb) | GC% |
|---|---|---|---|
| OX418216.1 | 1 | 169.51 | 34.5 |
| OX418217.1 | 2 | 114.62 | 34.5 |
| OX418218.1 | 3 | 93.62 | 34.5 |
| OX418219.1 | 4 | 74.37 | 34.5 |
| OX418220.1 | 5 | 73.09 | 34.5 |
| OX418221.1 | 6 | 68.83 | 36.0 |
| OX418223.1 | 7 | 57.1 | 34.0 |
| OX418224.1 | 8 | 55.53 | 34.0 |
| OX418225.1 | 9 | 49.77 | 34.0 |
| OX418226.1 | 10 | 42.84 | 34.0 |
| OX418227.1 | 11 | 35.43 | 34.5 |
| OX418222.1 | X | 68.52 | 34.5 |
| OX418228.1 | MT | 0.02 | 20.5 |
The estimated Quality Value (QV) of the final assembly is 59.2 with k-mer completeness of 100.0%, and the assembly has a BUSCO v5.3.2 completeness of 98.2% (single = 96.4%, duplicated = 1.8%), using the hemiptera_odb10 reference set ( n = 2,510).
Metadata for specimens, BOLD barcode results, spectra estimates, sequencing runs, contaminants and pre-curation assembly statistics are given at https://links.tol.sanger.ac.uk/species/491269.
Methods
Sample acquisition
Adult specimens of Conomelus anceps were hand-collected from Beinn Eighe National Nature Reserve, Scotland, UK (latitude 57.63, longitude –5.35) on 2021-08-04. The specimens were collected by Stephen Moran (Highland Biological Recording Group) and Andy Griffiths (Wellcome Sanger Institute), identified by Stephen Moran, and preserved by flash freezing. The genome was assembled from PacBio HiFi data generated from one specimen (specimen ID SAN0001820, ToLID ihConAnce4). Another specimen (specimen ID SAN0001817, ToLID ihConAnce1) was used for Hi-C sequencing.
The specimen used for RNA sequencing (specimen ID Ox001994, ToLID ihConAnce5) was an adult specimen collected from Wytham Woods, Oxfordshire, UK (latitude 51.77, longitude –1.34) on 2021-12-16, using a sweep net. The specimen was collected and identified by Liam Crowley (University of Oxford) and preserved on dry ice. The image in Figure 1 shows this specimen.
The initial identification was verified by an additional DNA barcoding process according to the framework developed by Twyford et al. (2024). A small sample was dissected from the specimens and stored in ethanol, while the remaining parts of the specimen were shipped on dry ice to the Wellcome Sanger Institute (WSI). The tissue was lysed, the COI marker region was amplified by PCR, and amplicons were sequenced and compared to the BOLD database, confirming the species identification ( Crowley et al., 2023). Following whole genome sequence generation, the relevant DNA barcode region was also used alongside the initial barcoding data for sample tracking at the WSI ( Twyford et al., 2024). The standard operating procedures for Darwin Tree of Life barcoding have been deposited on protocols.io ( Beasley et al., 2023).
Nucleic acid extraction
The workflow for high molecular weight (HMW) DNA extraction at the WSI Tree of Life Core Laboratory includes a sequence of core procedures: sample preparation and homogenisation, DNA extraction, fragmentation and purification. Detailed protocols are available on protocols.io ( Denton et al., 2023b). The ihConAnce4 sample was weighed and dissected on dry ice ( Jay et al., 2023) and tissue from the whole organism 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). The DNA was sheared into an average fragment size of 12–20 kb in a Megaruptor 3 system ( Bates et al., 2023). Sheared DNA was purified by solid-phase reversible immobilisation, using AMPure PB beads to eliminate shorter fragments and concentrate the DNA ( Strickland et al., 2023). The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer using the Qubit dsDNA High Sensitivity Assay kit. Fragment size distribution was evaluated by running the sample on the FemtoPulse system.
RNA was extracted from whole organism tissue of ihConAnce5 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 IIe (HiFi) and Illumina NovaSeq X (RNA-Seq) instruments.
Hi-C data were generated from the whole organism tissue of ihConAnce1, using the Arima-HiC v2 kit. In brief, frozen tissue (–80°C) was fixed, and the DNA crosslinked using a TC buffer containing formaldehyde. The crosslinked DNA was then digested using a restriction enzyme master mix. The 5’-overhangs were then filled in and labelled with a biotinylated nucleotide and proximally ligated. The biotinylated DNA construct was fragmented to a fragment size of 400 to 600 bp using a Covaris E220 sonicator. The DNA was then enriched, barcoded, and amplified using the NEBNext Ultra II DNA Library Prep Kit, following manufacturers’ instructions. The Hi-C sequencing was performed using paired-end sequencing with a read length of 150 bp on an Illumina NovaSeq 6000 instrument.
Genome assembly, curation and evaluation
Assembly
The HiFi reads were first assembled using Hifiasm ( Cheng et al., 2021) with the --primary option. Haplotypic duplications were identified and removed using purge_dups ( Guan et al., 2020). The Hi-C reads were mapped to the primary contigs using bwa-mem2 ( Vasimuddin et al., 2019). The contigs were further scaffolded using the provided Hi-C data ( Rao et al., 2014) in YaHS ( Zhou et al., 2023) using the --break option. The scaffolded assemblies were evaluated using Gfastats ( Formenti et al., 2022), BUSCO ( Manni et al., 2021) and MERQURY.FK ( Rhie et al., 2020).
The mitochondrial genome was assembled using MitoHiFi ( Uliano-Silva et al., 2023), which runs MitoFinder ( Allio et al., 2020) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.
Assembly curation
The assembly was decontaminated using the Assembly Screen for Cobionts and Contaminants (ASCC) pipeline (article in preparation). Manual curation was primarily conducted using PretextView ( Harry, 2022), with additional insights provided by JBrowse2 ( Diesh et al., 2023) and HiGlass ( Kerpedjiev et al., 2018). Scaffolds were visually inspected and corrected as described by Howe et al. (2021). Any identified contamination, missed joins, and mis-joins were corrected, and duplicate sequences were tagged and removed. The process is documented at https://gitlab.com/wtsi-grit/rapid-curation (article in preparation).
Evaluation of the final assembly
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 the “sanger-tol/readmapping” ( Surana et al., 2023a) and “sanger-tol/genomenote” ( Surana et al., 2023b) pipelines. The genome readmapping pipelines were developed using the nf-core tooling ( Ewels et al., 2020), use MultiQC ( Ewels et al., 2016), and make extensive use of the Conda package manager, the Bioconda initiative ( Grüning et al., 2018), the Biocontainers infrastructure ( da Veiga Leprevost et al., 2017), and the Docker ( Merkel, 2014) and Singularity ( Kurtzer et al., 2017) containerisation solutions. The genome was also analysed within the BlobToolKit environment ( Challis et al., 2020) and BUSCO scores ( Manni et al., 2021) were calculated.
Table 4 contains a list of relevant software tool versions and sources.
Table 4. Software tools: versions and sources.
| Software tool | Version | Source |
|---|---|---|
| BlobToolKit | 4.2.1 | https://github.com/blobtoolkit/blobtoolkit |
| BUSCO | 5.3.2 | https://gitlab.com/ezlab/busco |
| bwa-mem2 | 2.2.1 | https://github.com/bwa-mem2/bwa-mem2 |
| Cooler | 0.8.11 | https://github.com/open2c/cooler |
| Gfastats | 1.3.6 | https://github.com/vgl-hub/gfastats |
| Hifiasm | 0.16.1-r375 | https://github.com/chhylp123/hifiasm |
| HiGlass | 1.11.6 | https://github.com/higlass/higlass |
| Merqury.FK | d00d98157618f4e8d1a9
190026b19b471055b22e |
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 |
| Singularity | 3.9.0 | https://github.com/sylabs/singularity |
| YaHS | 1.2a | 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, <a href=https://doi.org/10.35802/206194>https://doi.org/10.35802/206194</a>] and the Darwin Tree of Life Discretionary Award [218328, <a href=https://doi.org/10.35802/218328>https://doi.org/10.35802/218328 </a>].
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: Conomelus anceps. Accession number PRJEB58256; https://identifiers.org/ena.embl/PRJEB58256 ( Wellcome Sanger Institute, 2023). The genome sequence is released openly for reuse. The Conomelus anceps 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 and Table 2.
Author information
Members of the University of Oxford and Wytham Woods Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.12157525.
Members of the Natural History Museum Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.12159242.
Members of the Darwin Tree of Life Barcoding collective are listed here: https://doi.org/10.5281/zenodo.12158331
Members of the Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team are listed here: https://doi.org/10.5281/zenodo.12162482.
Members of Wellcome Sanger Institute Scientific Operations: Sequencing Operations are listed here: https://doi.org/10.5281/zenodo.12165051.
Members of the Wellcome Sanger Institute Tree of Life Core Informatics team are listed here: https://doi.org/10.5281/zenodo.12160324.
Members of the Tree of Life Core Informatics collective are listed here: https://doi.org/10.5281/zenodo.12205391.
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]
- 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]
- Beasley J, Uhl R, Forrest LL, et al. : DNA barcoding SOPs for the Darwin Tree of Life project. protocols.io. 2023; [Accessed 25 June 2024]. 10.17504/protocols.io.261ged91jv47/v1 [DOI] [Google Scholar]
- British Bugs: Conomelus anceps Family: Delphacidae. [no date]; [Accessed 7 September 2024]. Reference Source
- 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]
- Crowley L, Allen H, Barnes I, et al. : A sampling strategy for genome sequencing the British terrestrial arthropod fauna [version 1; peer review: 2 approved]. Wellcome Open Res. 2023;8:123. 10.12688/wellcomeopenres.18925.1 [DOI] [PMC free article] [PubMed] [Google Scholar]
- da Veiga Leprevost F, Grüning BA, Alves Aflitos S, et al. : BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017;33(16):2580–2582. 10.1093/bioinformatics/btx192 [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]
- Diesh C, Stevens GJ, Xie P, et al. : JBrowse 2: a modular genome browser with views of synteny and structural variation. Genome Biol. 2023;24(1): 74. 10.1186/s13059-023-02914-z [DOI] [PMC free article] [PubMed] [Google Scholar]
- do Amaral RJV, Denton A, Yatsenko H, et al. : Sanger Tree of Life RNA extraction: automated MagMax ™ mirVana. protocols.io. 2023. 10.17504/protocols.io.6qpvr36n3vmk/v1 [DOI] [Google Scholar]
- Ewels P, Magnusson M, Lundin S, et al. : MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32(19):3047–3048. 10.1093/bioinformatics/btw354 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ewels PA, Peltzer A, Fillinger S, et al. : The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020;38(3):276–278. 10.1038/s41587-020-0439-x [DOI] [PubMed] [Google Scholar]
- Formenti G, Abueg L, Brajuka A, et al. : Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs. Bioinformatics. 2022;38(17):4214–4216. 10.1093/bioinformatics/btac460 [DOI] [PMC free article] [PubMed] [Google Scholar]
- GBIF Secretariat: Conomelus anceps (Germar, 1821). GBIF Backbone Taxonomy. 2024; [Accessed 7 September 2024]. Reference Source
- Grüning B, Dale R, Sjödin A, et al. : Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018;15(7):475–476. 10.1038/s41592-018-0046-7 [DOI] [PMC free article] [PubMed] [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. Reference Source
- Howe K, Chow W, Collins J, et al. : Significantly improving the quality of genome assemblies through curation. GigaScience. 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]
- Kurtzer GM, Sochat V, Bauer MW: Singularity: scientific containers for mobility of compute. PLoS One. 2017;12(5): e0177459. 10.1371/journal.pone.0177459 [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]
- Merkel D: Docker: lightweight Linux containers for consistent development and deployment. Linux J. 2014;2014(239): 2, [Accessed 2 April 2024]. Reference Source [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]
- 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]
- 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. 10.5281/zenodo.7755669 [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]
- Twyford AD, Beasley J, Barnes I, et al. : A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life project [version 1; peer review: awaiting peer review]. Wellcome Open Res. 2024;9:339. 10.12688/wellcomeopenres.21143.1 [DOI] [PMC free article] [PubMed] [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 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 planthopper, Conomelus anceps (Germar, 1821). European Nucleotide Archive, [dataset], accession number PRJEB58256,2023.
- 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]