This is an open access work distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Pleuronectiformes; Solea solea; chromosomal; common sole; genome sequence
Abstract :
[en] We present a genome assembly from an individual female Solea solea (Linnaeus, 1758) (the common sole; Chordata; Actinopteri; Pleuronectiformes; Soleidae). The genome sequence spans 643.80 megabases. Most of the assembly (97.81%) is scaffolded into 21 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.03 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,646 protein-coding genes.
Disciplines :
Zoology
Author, co-author :
Geslain, Enora ; Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
Volckaert, Filip A M ; Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
Mc Cartney, Ann M; Genomics Institute, University of California Santa Cruz, Santa Cruz, California, USA
Formenti, Giulio ; The Vertebrate Genome Laboratory, The Rockefeller University, New York, New York, USA ; Department of Biology, University of Florence, Sesto Fiorentino, Italy
Mouton, Alice ; Université de Liège - ULiège > Département des sciences et gestion de l'environnement (Arlon Campus Environnement) > Socio-économie, Environnement et Développement (SEED) ; Leibniz Institut für Zoo und Wildtierforschung, Berlin, Germany
Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team
Wellcome Sanger Institute Scientific Operations: Sequencing Operations
Wellcome Sanger Institute Tree of Life Core Informatics team
Tree of Life Core Informatics collective
Language :
English
Title :
The genome sequence of the common sole, Solea solea (Linnaeus, 1758).
Abdennur N Mirny LA: Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2020;36(1):311–316. 31290943 10.1093/bioinformatics/btz540 8205516
Aken BL Ayling S Barrell D et al.: The ensembl gene annotation system. Database (Oxford). 2016;2016: baw093. 27337980 10.1093/database/baw093 4919035
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. 32243090 10.1111/1755-0998.13160 7497042
Challis R Richards E Rajan J et al.: BlobToolKit – interactive quality assessment of genome assemblies. G3 (Bethesda). 2020;10(4):1361–1374. 32071071 10.1534/g3.119.400908 7144090
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. 33526886 10.1038/s41592-020-01056-5 7961889
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. 28379341 10.1093/bioinformatics/btx192 5870671
Denton A Yatsenko H Jay J et al.: Sanger Tree of Life wet laboratory protocol collection V.1. protocols.io. 2023. 10.17504/protocols.io.8epv5xxy6g1b/v1
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. 37069644 10.1186/s13059-023-02914-z 10108523
Diopere E Vandamme SG Hablützel PI et al.: Seascape genetics of a flatfish reveals local selection under high levels of gene flow. ICES J Mar Sci. 2018;75(2):675–689. 10.1093/icesjms/fsx160
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
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. 27312411 10.1093/bioinformatics/btw354 5039924
Ewels PA Peltzer A Fillinger S et al.: The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020;38(3):276–278. 32055031 10.1038/s41587-020-0439-x
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. 35799367 10.1093/bioinformatics/btac460 9438950
Froese R Pauly D: FishBase.2024. https://fishbase.de/ Reference Source
Gibson RN Nash RDM Geffen AJ (eds.) et al.: Flatfishes. Wiley.2014. 10.1002/9781118501153
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. 29967506 10.1038/s41592-018-0046-7 11070151
Guan D McCarthy SA Wood J et al.: Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics. 2020;36(9):2896–2898. 31971576 10.1093/bioinformatics/btaa025 7203741
Harry E: PretextView (Paired REad TEXTure Viewer): a desktop application for viewing pretext contact maps.2022. https://github.com/wtsi-hpag/PretextView Reference Source
Howe K Chow W Collins J et al.: Significantly improving the quality of genome assemblies through curation. GigaScience. 2021;10(1): giaa153. 33420778 10.1093/gigascience/giaa153 7794651
ICES: Sole Solea solea.2006. https://www.ices.dk/about-ICES/projects/EU-RFP/EU%20Repository/ICES%20FIshMap/ICES%20FishMap%20species%20factsheet-sole.pdf Reference Source
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
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. 30143029 10.1186/s13059-018-1486-1 6109259
Kurtzer GM Sochat V Bauer MW: Singularity: scientific containers for mobility of compute. PLoS One. 2017;12(5): e0177459. 28494014 10.1371/journal.pone.0177459 5426675
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. 34320186 10.1093/molbev/msab199 8476166
Merkel D: Docker: lightweight Linux containers for consistent development and deployment. Linux J. 2014;2014(239): 2. [Accessed 2 April 2024]. https://dl.acm.org/doi/10.5555/2600239.2600241 Reference Source
Narváez-Gómez JP Mbye H Oatley G et al.: Sanger Tree of Life sample homogenisation: covaris cryoPREP ® automated dry pulverizer V.1. protocols.io. 2023. 10.17504/protocols.io.eq2lyjp5qlx9/v1
Pauly D Zeller D Palomares MLD (eds.): Sea around us: concepts, design and data.2020. https://www.seaaroundus.org/ Reference Source
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. 25497547 10.1016/j.cell.2014.11.021 5635824
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. 33911273 10.1038/s41586-021-03451-0 8081667
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. 32928274 10.1186/s13059-020-02134-9 7488777
Rijnsdorp AD Boute PG Tiano JC et al.: Electrotrawling can improve the sustainability of the bottom trawl fishery for sole: a review of the evidence. Rev Fish Biol Fisher. 2024;34(3):959–993. 10.1007/s11160-024-09867-x
Sheerin E Sampaio F Oatley G et al.: Sanger Tree of Life HMW DNA extraction: automated MagAttract v.1. protocols.io. 2023. 10.17504/protocols.io.x54v9p2z1g3e/v1
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
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
Surana P Muffato M Sadasivan Baby C: sanger-tol/genomenote (v1.0.dev). Zenodo. 2023b. 10.5281/zenodo.6785935
Todorovic M Sampaio F Howard C: Sanger Tree of Life HMW DNA fragmentation: diagenode Megaruptor ®3 for PacBio HiFi. protocols.io. 2023. 10.17504/protocols.io.8epv5x2zjg1b/v1
Tous P Sidibe A Mbye E et al.: Solea solea. The IUCN Red List of threatened species. 2015;2015: e.T198739A15595369, [Accessed 17 October 2024]. 10.2305/IUCN.UK.2015-4.RLTS.T198739A15595369.en
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. 37464285 10.1186/s12859-023-05385-y 10354987
UniProt Consortium: UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 2019;47(D1):D506–D515. 30395287 10.1093/nar/gky1049 6323992
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
Zhou C McCarthy SA Durbin R: YaHS: yet another Hi-C scaffolding tool. Bioinformatics. 2023;39(1): btac808. 36525368 10.1093/bioinformatics/btac808 9848053