The genome sequence of Erebia montana Berg-Mohrenfalter (Lepidoptera: Nymphalidae)

. 2025 ; 10 () : 449. [epub] 20250818

Status PubMed-not-MEDLINE Jazyk angličtina Země Anglie, Velká Británie Médium electronic-ecollection

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid41312298

Grantová podpora
Wellcome Trust - United Kingdom

We present a genome assembly from a female specimen of Erebia montana (Arthropoda; Insecta; Lepidoptera; Nymphalidae). The assembly contains two haplotypes with total lengths of 597.21 megabases and 499.88 megabases. Most of haplotype 1 (98.25%) is scaffolded into 24 chromosomal pseudomolecules, including the W, Z 1, and Z 2 sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.2 kilobases.

Zobrazit více v PubMed

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

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

Cheng H, Jarvis ED, Fedrigo O, et al. : Haplotype-resolved assembly of diploid genomes without parental data. PubMed DOI PMC

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

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

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

Howard C, Denton A, Jackson B, et al. : On the path to reference genomes for all biodiversity: lessons learned and laboratory protocols created in the sanger Tree of Life core laboratory over the first 2000 species. DOI

Howe K, Chow W, Collins J, et al. : Significantly improving the quality of genome assemblies through curation. PubMed DOI PMC

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

Kleckova I, Konvicka M, Klecka J: Thermoregulation and microhabitat use in mountain butterflies of the genus PubMed DOI

Kriventseva EV, Kuznetsov D, Tegenfeldt F, et al. : OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs. 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

Ranallo-Benavidez TR, Jaron KS, Schatz MC: GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. 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

Sonderegger P: Die Erebien Der Schweiz. Brügg bei Biel: P. Sonderegger;2005.

Tolman T, Lewington R: The most complete guide to the butterflies of Britain & Europe. London: HarperCollins Publishers;2008.

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

Wright CJ, Stevens L, Mackintosh A, et al. : Comparative genomics reveals the dynamics of chromosome evolution in Lepidoptera. PubMed DOI PMC

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

Najít záznam

Citační ukazatele

Pouze přihlášení uživatelé

Možnosti archivace

Nahrávání dat ...