{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T05:10:19Z","timestamp":1772169019506,"version":"3.50.1"},"update-to":[{"DOI":"10.12688\/openreseurope.20841.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,1,27]],"date-time":"2026-01-27T00:00:00Z","timestamp":1769472000000}}],"reference-count":12,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2026,1,27]],"date-time":"2026-01-27T00:00:00Z","timestamp":1769472000000},"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":"Agence nationale de la recherche","award":["ANR-10-INBS-09-08"],"award-info":[{"award-number":["ANR-10-INBS-09-08"]}]},{"name":"Agence nationale de la recherche","award":["ANR-22-EXAT-0003-SEQ-Sea"],"award-info":[{"award-number":["ANR-22-EXAT-0003-SEQ-Sea"]}]},{"DOI":"10.13039\/100014013","name":"UK Research and Innovation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100014013","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Swiss State Secretariat for Education, Research and Innovation","award":["22.00173, 24.00054"],"award-info":[{"award-number":["22.00173, 24.00054"]}]}],"content-domain":{"domain":["open-research-europe.ec.europa.eu"],"crossmark-restriction":false},"short-container-title":["Open Res Europe"],"abstract":"<ns3:p>\n                    <ns3:italic>Holothuria sanctori<\/ns3:italic>\n                    is a common species of sea cucumber found in the Mediterranean Sea and the Northeast Atlantic Ocean. It typically inhabits shallow rocky and sandy seabeds, where it plays a key ecological role as a sediment engineer processing organic matter ts and thereby contributing to nutrient cycling. As an edible species,\n                    <ns3:italic>H. sanctori<\/ns3:italic>\n                    is harvested in several countries. Although it is currently listed as a species of \"Least Concern\" on the IUCN Red List, the absence of a regulatory framework to prevent overexploitation poses a risk of population decline. Given its ecological significance and economic value\n                    <ns3:italic>, H. sanctori<\/ns3:italic>\n                    has become a focal point in both marine conservation and aquaculture research. The entirety of the genome sequence was assembled into 23 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 1.2 Gb, composed of 135 contigs and 46 scaffolds, with contig and scaffold N50 values of 19.9 Mb and 50.7 Mb, respectively.\n                  <\/ns3:p>","DOI":"10.12688\/openreseurope.20841.2","type":"journal-article","created":{"date-parts":[[2026,1,27]],"date-time":"2026-01-27T10:09:08Z","timestamp":1769508548000},"page":"297","update-policy":"https:\/\/doi.org\/10.12688\/openreseurope.crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["ERGA-BGE reference genome of Holothuria (Platyperona) sanctori: a sea cucumber from the Mediterranean Sea"],"prefix":"10.12688","volume":"5","author":[{"given":"Katerina","family":"Vasileiadou","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4102-9331","authenticated-orcid":false,"given":"Thanos","family":"Dailianis","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8482-460X","authenticated-orcid":false,"given":"Grigorios","family":"Skouradakis","sequence":"additional","affiliation":[]},{"given":"Emmanouela","family":"Vernadou","sequence":"additional","affiliation":[]},{"given":"Danae","family":"Karakasi","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":[]},{"given":"Tereza","family":"Manousaki","sequence":"additional","affiliation":[]},{"name":"Genoscope Sequencing Team","sequence":"additional","affiliation":[]},{"given":"Alice","family":"Moussy","sequence":"additional","affiliation":[]},{"given":"Corinne","family":"Cruaud","sequence":"additional","affiliation":[]},{"given":"Karine","family":"Labadie","sequence":"additional","affiliation":[]},{"given":"Lola","family":"Demirdjian","sequence":"additional","affiliation":[]},{"given":"Adama","family":"Ndar","sequence":"additional","affiliation":[]},{"given":"Patrick","family":"Wincker","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3161-8367","authenticated-orcid":false,"given":"Pedro","family":"H Oliveira","sequence":"additional","affiliation":[]},{"given":"Jean-Marc","family":"Aury","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":[[2026,1,27]]},"reference":[{"key":"ref-2","doi-asserted-by":"publisher","first-page":"899-906","DOI":"10.1016\/j.ympev.2010.08.019","article-title":"Molecular systematics of the genus Holothuria in the Mediterranean and Northeastern Atlantic and a molecular clock for the diversification of the Holothuriidae (Echinodermata: Holothuroidea).","volume":"57","author":"G Borrero-P\u00e9rez","year":"2010","journal-title":"Mol Phylogenet Evol."},{"key":"ref-3","doi-asserted-by":"publisher","first-page":"119-127","DOI":"10.1016\/j.bse.2016.06.005","article-title":"Chemical characterization of saponins contained in the body wall and the Cuvierian tubules of the sea cucumber Holothuria (Platyperona) sanctori (Delle Chiaje, 1823).","volume":"68","author":"G Caulier","year":"2016","journal-title":"Biochem Syst Ecol."},{"key":"ref-4","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":"ref-5","doi-asserted-by":"publisher","first-page":"170-175","DOI":"10.1038\/s41592-020-01056-5","article-title":"Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm.","volume":"18","author":"H Cheng","year":"2021","journal-title":"Nat Methods."},{"key":"ref-7","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":"ref-10","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":"ref-11","doi-asserted-by":"publisher","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":"ref-12","first-page":"351-357","article-title":"Observations on some biological characteristics of Holothuria polii and Holothuria sanctori from Mediterranean Egypt.","volume":"6","author":"R Moussa","year":"2018","journal-title":"Int J Fish Aquat Stud."},{"key":"ref-13","doi-asserted-by":"publisher","first-page":"741-752","DOI":"10.3989\/scimar.03543.15B","article-title":"Reproductive biology of the sea cucumber Holothuria sanctori (Echinodermata: Holothuroidea).","volume":"76","author":"P Navarro","year":"2012","journal-title":"Sci Mar."},{"key":"ref-16","doi-asserted-by":"publisher","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":"ref-18","doi-asserted-by":"publisher","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."},{"key":"ref-19","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac808","article-title":"YaHS: Yet another Hi-C Scaffolding tool.","volume":"39","author":"C Zhou","year":"2023","journal-title":"Bioinformatics."}],"updated-by":[{"DOI":"10.12688\/openreseurope.20841.3","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,2,3]],"date-time":"2026-02-03T00:00:00Z","timestamp":1770076800000}}],"container-title":["Open Research Europe"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-297\/v2\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-297\/v2\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-297\/v2\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,27]],"date-time":"2026-01-27T10:09:10Z","timestamp":1769508550000},"score":1,"resource":{"primary":{"URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-297\/v2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1,27]]},"references-count":12,"URL":"https:\/\/doi.org\/10.12688\/openreseurope.20841.2","relation":{"has-version":[{"id-type":"doi","id":"10.12688\/openreseurope.20841.1","asserted-by":"subject"}],"is-version-of":[{"id-type":"doi","id":"10.12688\/openreseurope.20841.3","asserted-by":"object"}]},"ISSN":["2732-5121"],"issn-type":[{"value":"2732-5121","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,1,27]]},"assertion":[{"value":"Indexed","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-297\/v2#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/openreseurope.22549.r64816, Poppy Hesketh-Best, IGTP Institut Germans Trias i Pujol, Barcelona, 29 Dec 2025, version 1, indexed","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-297\/v1#referee-response-64816","order":0,"name":"referee-response-64816","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 their comments. We have addressed all of them as following:&nbsp;  1. We slightly changed the text of the Data availability section regarding the annotation by stating that, while the RNA-seq data are available, the annotation is not yet and will be made available in the Ensembl website.&nbsp;  2. We added in the Genome assembly methods section that a bacterial contig and&nbsp; a substantial number of duplications were removed in the assembly step.&nbsp;","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-297\/v2#referee-comment-4966","order":1,"name":"referee-comment-4966","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/openreseurope.22549.r64808, Estelle Proux-W\u00e9ra, Stockholm University, stockholm, 30 Dec 2025, version 1, indexed","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-297\/v1#referee-response-64808","order":2,"name":"referee-response-64808","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 their comments. We have addressed all of them as following:&nbsp; 1.&nbsp;Following reviewer 1, we added to the Genome assembly methods section additional information about the&nbsp;removal of a bacterial contig and a substantial number of duplications during the assembly step.","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-297\/v2#referee-comment-4967","order":3,"name":"referee-comment-4967","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. This work was supported by the Genoscope, the Commissariat \u00e0 l'\u00c9nergie Atomique et aux \u00c9nergies Alternatives (CEA), France G\u00e9nomique (ANR-10-INBS-09-08), and the exploratory research programme \u2018ATLASea: Atlas of marine genomes and its targeted project SEQ-Sea (ANR-22-EXAT-0003-SEQ-Sea). 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"}]}}