We present a genome assembly from an individual male specimen of the small dung beetle, Aphodius sticticus (Arthropoda; Insecta; Coleoptera; Scarabaeidae). The genome sequence has a total length of 628.40 megabases. Most of the assembly (98.96%) is scaffolded into 11 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 20.8 kilobases in length.

Department of Biology University of Oxford Oxford England UK

Department of Zoology University of South Bohemia České Budějovice Czech Republic

Zobrazit více v PubMed

Abdennur N, Mirny LA: Cooler: scalable storage for Hi-C data and other genomically labeled arrays. PubMed DOI PMC

Allio R, Schomaker-Bastos A, Romiguier J, et al. : MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics. PubMed DOI PMC

Altschul SF, Gish W, Miller W, et al. : Basic local alignment search tool. PubMed DOI

Bateman A, Martin MJ, Orchard S, et al. : UniProt: the universal protein knowledgebase in 2023. PubMed DOI PMC

Bates A, Clayton-Lucey I, Howard C: Sanger Tree of Life HMW DNA fragmentation: diagenode Megaruptor DOI

Beasley J, Uhl R, Forrest LL, et al. : DNA barcoding SOPs for the Darwin Tree of Life project. DOI

British Scarabs: Dwellers – Aphodiines.2025; [Accessed 28 January 2025]. Reference Source

Buchfink B, Reuter K, Drost HG: Sensitive protein alignments at Tree-of-Life scale using DIAMOND. PubMed DOI PMC

Challis R, Kumar S, Sotero-Caio C, et al. : Genomes on a Tree (GoaT): a versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic Tree of Life [version 1; peer review: 2 approved]. PubMed DOI PMC

Challis R, Richards E, Rajan J, et al. : BlobToolKit – interactive quality assessment of genome assemblies. PubMed DOI PMC

Cheng H, Concepcion GT, Feng X, et al. : Haplotype-resolved PubMed DOI PMC

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]. PubMed DOI PMC

da Veiga Leprevost F, Grüning BA, Alves Aflitos S, et al. : BioContainers: an open-source and community-driven framework for software standardization. PubMed DOI PMC

Danecek P, Bonfield JK, Liddle J, et al. : Twelve years of SAMtools and BCFtools. PubMed DOI PMC

Denton A, Oatley G, Cornwell C, et al. : Sanger Tree of Life sample homogenisation: PowerMash. DOI

Denton A, Yatsenko H, Jay J, et al. : Sanger Tree of Life wet laboratory protocol collection V.1. DOI

Diesh C, Stevens GJ, Xie P, et al. : JBrowse 2: a modular genome browser with views of synteny and structural variation. PubMed DOI PMC

Duff AG: Checklist of Beetles of the British Isles. 3rd Edition. Iver: Pemberley Books,2018. Reference Source

Ewels P, Magnusson M, Lundin S, et al. : MultiQC: summarize analysis results for multiple tools and samples in a single report. PubMed DOI PMC

Ewels PA, Peltzer A, Fillinger S, et al. : The nf-core framework for community-curated bioinformatics pipelines. PubMed DOI

Formenti G, Abueg L, Brajuka A, et al. : Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs. PubMed DOI PMC

GBIF Secretariat:

Grüning B, Dale R, Sjödin A, et al. : Bioconda: sustainable and comprehensive software distribution for the life sciences. PubMed DOI PMC

Guan D, McCarthy SA, Wood J, et al. : Identifying and removing haplotypic duplication in primary genome assemblies. PubMed DOI PMC

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. PubMed DOI PMC

Jay J, Yatsenko H, Narváez-Gómez JP, et al. : Sanger Tree of Life sample preparation: triage and dissection. DOI

Kerpedjiev P, Abdennur N, Lekschas F, et al. : HiGlass: web-based visual exploration and analysis of genome interaction maps. PubMed DOI PMC

Kurtzer GM, Sochat V, Bauer MW: Singularity: scientific containers for mobility of compute. PubMed DOI PMC

Li H: Minimap2: pairwise alignment for nucleotide sequences. PubMed DOI PMC

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. PubMed DOI PMC

Merkel D: Docker: lightweight Linux containers for consistent development and deployment. DOI

NBN Atlas Partnership:

Oatley G, Denton A, Howard C: Sanger Tree of Life HMW DNA extraction: automated MagAttract v.2. DOI

Oatley G, Sampaio F, Howard C: Sanger Tree of Life fragmented DNA clean up: automated SPRI. DOI

Pointon DL, Eagles W, Sims Y, et al. : sanger-tol/treeval v1.0.0 – Ancient Atlantis. 2023. 10.5281/zenodo.10047654 DOI

Quinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. PubMed DOI PMC

Rao SSP, Huntley MH, Durand NC, et al. : A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. PubMed DOI PMC

Rhie A, McCarthy SA, Fedrigo O, et al. : Towards complete and error-free genome assemblies of all vertebrate species. PubMed DOI PMC

Rhie A, Walenz BP, Koren S, et al. : Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. PubMed DOI PMC

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: 2 approved]. PubMed DOI PMC

Uliano-Silva M, Ferreira JGRN, Krasheninnikova K, et al. : MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads. PubMed DOI PMC

Vasimuddin M, Misra S, Li H, et al. : Efficient architecture-aware acceleration of BWA-MEM for multicore systems.In: DOI

Zhou C, McCarthy SA, Durbin R: YaHS: yet another Hi-C scaffolding tool. PubMed DOI PMC