{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,10]],"date-time":"2026-02-10T18:39:39Z","timestamp":1770748779626,"version":"3.50.0"},"update-to":[{"DOI":"10.12688\/openreseurope.21671.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,2,10]],"date-time":"2026-02-10T00:00:00Z","timestamp":1770681600000}}],"reference-count":15,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2026,2,10]],"date-time":"2026-02-10T00:00:00Z","timestamp":1770681600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100018693","name":"Horizon Europe Framework Programme","doi-asserted-by":"publisher","award":["101059492"],"award-info":[{"award-number":["101059492"]}],"id":[{"id":"10.13039\/100018693","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Swiss State Secretariat for Education, Research and Innovation","award":["22.00173, 24.00054"],"award-info":[{"award-number":["22.00173, 24.00054"]}]},{"DOI":"10.13039\/501100004329","name":"Slovenian Research and Innovation Agency","doi-asserted-by":"crossref","award":["P1-0236"],"award-info":[{"award-number":["P1-0236"]}],"id":[{"id":"10.13039\/501100004329","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100014013","name":"UK Research and Innovation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100014013","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["open-research-europe.ec.europa.eu"],"crossmark-restriction":false},"short-container-title":["Open Res Europe"],"abstract":"<ns3:p>\n                    The\n                    <ns3:italic>Leviellus thorelli<\/ns3:italic>\n                    reference genome provides the first high-quality genomic resource for\n                    <ns3:italic>Zygiellidae<\/ns3:italic>\n                    , a family of orb-weaving spiders with a dynamic systematic history and distinct for constructing webs with a characteristic spiral-free sector. As part of the European Reference Genome Atlas (ERGA), we generated a chromosome-level assembly for\n                    <ns3:italic>L. thorelli<\/ns3:italic>\n                    that is organized into 13 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 2.20 Gb and is composed of 939 contigs and 130 scaffolds, with contig and scaffold N50 values of 5.4 Mb and 167.1 Mb, respectively. This genome represents a valuable addition to the growing collection of spider genomes. With\n                    <ns3:italic>Zygiellidae<\/ns3:italic>\n                    now included among the available genomes of true orb-weavers, this is a key resource for comparative studies into the genomic basis of orb web and silk evolution.\n                  <\/ns3:p>","DOI":"10.12688\/openreseurope.21671.2","type":"journal-article","created":{"date-parts":[[2026,2,10]],"date-time":"2026-02-10T09:59:07Z","timestamp":1770717547000},"page":"365","update-policy":"https:\/\/doi.org\/10.12688\/openreseurope.crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["ERGA-BGE reference genome of Leviellus thorelli, a common orb-weaving spider representing the Zygiellidae family"],"prefix":"10.12688","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4882-4282","authenticated-orcid":false,"given":"Matjaz","family":"Gregori\u010d","sequence":"first","affiliation":[]},{"given":"Elena","family":"Bu\u017ean","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1284-3115","authenticated-orcid":false,"given":"Astrid","family":"B\u00f6hne","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1374-4474","authenticated-orcid":false,"given":"Rita","family":"Monteiro","sequence":"additional","affiliation":[]},{"given":"Rosa","family":"Fern\u00e1ndez","sequence":"additional","affiliation":[]},{"given":"Nuria","family":"Escudero","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4063-7159","authenticated-orcid":false,"given":"Marta","family":"Gut","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8631-8778","authenticated-orcid":false,"given":"Laura","family":"Aguilera","sequence":"additional","affiliation":[]},{"given":"Francisco","family":"C\u00e2mara Ferreira","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4098-8829","authenticated-orcid":false,"given":"Fernando","family":"Cruz","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6409-8009","authenticated-orcid":false,"given":"J\u00e8ssica","family":"G\u00f3mez-Garrido","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2960-5420","authenticated-orcid":false,"given":"Tyler","family":"S. Alioto","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6589-6635","authenticated-orcid":false,"given":"Chiara","family":"Bortoluzzi","sequence":"additional","affiliation":[]}],"member":"2560","published-online":{"date-parts":[[2026,2,10]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"24","DOI":"10.12688\/wellcomeopenres.18658.1","article-title":"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].","volume":"8","author":"R Challis","year":"2023","journal-title":"Wellcome Open Res."},{"key":"ref2","article-title":"CLAWS (CNAG\u2019s long-read assembly workflow in snakemake) [Computer software].","author":"J Gomez-Garrido","year":"2024"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"225-243","DOI":"10.1111\/zoj.12281","article-title":"Phylogenetic position and composition of Zygiellinae and Caerostris, with new insight into orb-web evolution and gigantism.","volume":"175","author":"M Gregori\u010d","year":"2015","journal-title":"Zool. J. Linnean Soc."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"2896-2898","DOI":"10.1093\/bioinformatics\/btaa025","article-title":"Identifying and removing haplotypic duplication in primary genome assemblies.","volume":"36","author":"D Guan","year":"2020","journal-title":"Bioinformatics."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"797-818","DOI":"10.1071\/IS23050","article-title":"Genitalic morphology and phylogenomic placement of the Australian spider Paraplectanoides crassipes Keyserling, 1886 (Araneae, Araneidae) with a discussion on the classification of the family Araneidae.","volume":"37","author":"G Hormiga","year":"2023","journal-title":"Invertebr. Syst."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1186\/s13059-024-03252-4","article-title":"NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads.","volume":"25","author":"J Hu","year":"2024","journal-title":"Genome Biol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"2019-2012","DOI":"10.1101\/2019.12.19.882506","article-title":"HyPo: super fast & accurate polisher for long read genome assemblies.","author":"R Kundu","year":"2019","journal-title":"bioRxiv."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"964-971","DOI":"10.1093\/sysbio\/syad021","article-title":"Increasing information content and diagnosability in family-level classifications.","volume":"72","author":"M Kuntner","year":"2023","journal-title":"Syst. Biol."},{"key":"ref9","first-page":"267-290","article-title":"The orb-weaver genus Zygiella (Araneae: Araneidae).","volume":"146","author":"H Levi","year":"1974","journal-title":"Bull. Mus. Comp. Zool."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"4647-4654","DOI":"10.1093\/molbev\/msab199","article-title":"BUSCO update: Novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes.","volume":"38","author":"M Manni","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1038\/d41586-023-02229-w","article-title":"Biodiversity: an atlas of European reference genomes.","volume":"619","author":"C Mazzoni","year":"2023","journal-title":"Nature."},{"key":"ref12","doi-asserted-by":"publisher","DOI":"10.24436\/1","article-title":"Spiders of Europe. Version 10.2025.","author":"W Nentwig","year":"2025"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1186\/s13059-020-02134-9","article-title":"Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies.","volume":"21","author":"A Rhie","year":"2020","journal-title":"Genome Biol."},{"key":"ref14","doi-asserted-by":"publisher","year":"2025","journal-title":"World Spider Catalog. Version 26.","DOI":"10.24436\/2"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"2024-2010","DOI":"10.1101\/2024.10.23.619857","article-title":"Oatk: a de novo assembly tool for complex plant organelle genomes.","author":"C Zhou","year":"2024","journal-title":"bioRxiv."}],"container-title":["Open Research Europe"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-365\/v2\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-365\/v2\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-365\/v2\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,10]],"date-time":"2026-02-10T09:59:09Z","timestamp":1770717549000},"score":1,"resource":{"primary":{"URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-365\/v2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,10]]},"references-count":15,"URL":"https:\/\/doi.org\/10.12688\/openreseurope.21671.2","relation":{"has-version":[{"id-type":"doi","id":"10.12688\/openreseurope.21671.1","asserted-by":"subject"}]},"ISSN":["2732-5121"],"issn-type":[{"value":"2732-5121","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,10]]},"assertion":[{"value":"Indexed","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-365\/v2#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/openreseurope.23443.r65094, Zhisheng Zhang, Southwest University, Chongqing, 02 Jan 2026, version 1, indexed","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-365\/v1#referee-response-65094","order":0,"name":"referee-response-65094","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Chiara Bortoluzzi<\/b>; \n<i>Posted: 05 Jan 2026<\/i>; We thank the reviewer for approving the Genome Report of \n<i>Leviellus thorelli<\/i>.","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-365\/v2#referee-comment-4965","order":1,"name":"referee-comment-4965","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/openreseurope.23443.r67343, Guilherme Gainett, Harvard Medical School. Boston Children's Hospital, Boston, 29 Jan 2026, version 1, indexed","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-365\/v1#referee-response-67343","order":2,"name":"referee-response-67343","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Chiara Bortoluzzi<\/b>; \n<i>Posted: 30 Jan 2026<\/i>; We thank the reviewer for their comments. We have addressed all comments as follow:  We have updated the reference, which is indeed published and not in press. We updated the 'Genetic information' section to clarify the concept of 'ancestral taxa' and the 12 chromosomes.&nbsp; We did not add any additional information on the contamination analyses, because are very well described in the EAR reported in the Genome Report. We replaced the word 'thorax' throughout the manuscript as suggested by the reviewer.&nbsp;","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-365\/v2#referee-comment-5048","order":3,"name":"referee-comment-5048","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"Biodiversity Genomics Europe (Grant no.101059492) is funded by Horizon Europe under the Biodiversity, Circular Economy and Environment call (REA.B.3); co-funded by the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract numbers 22.00173 and 24.00054; and by the UK Research and Innovation (UKRI) under the Department for Business, Energy and Industrial Strategy\u2019s Horizon Europe Guarantee Scheme. Matja\u017e Gregori\u010d received funding from the Slovenian Research and Innovation Agency (Research Core Funding No. P1-0236). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":4,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}