{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T22:43:20Z","timestamp":1773355400124,"version":"3.50.1"},"update-to":[{"DOI":"10.12688\/openreseurope.21608.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T00:00:00Z","timestamp":1773014400000}}],"reference-count":47,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T00:00:00Z","timestamp":1773014400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100014013","name":"UK Research and Innovation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014013","id-type":"DOI","asserted-by":"publisher"}]},{"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"}]},{"DOI":"10.13039\/100018693","name":"Horizon Europe Framework Programme","doi-asserted-by":"publisher","award":["101094924"],"award-info":[{"award-number":["101094924"]}],"id":[{"id":"10.13039\/100018693","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Swiss State Secretariat for Education, Research and Innovation","award":["22.00173"],"award-info":[{"award-number":["22.00173"]}]},{"name":"Swiss State Secretariat for Education, Research and Innovation","award":["24.00054"],"award-info":[{"award-number":["24.00054"]}]}],"content-domain":{"domain":["open-research-europe.ec.europa.eu"],"crossmark-restriction":false},"short-container-title":["Open Res Europe"],"abstract":"<ns3:p>\n                    The reference genome of\n                    <ns3:italic>Patella rustica<\/ns3:italic>\n                    Linnaeus, 1758 (Gastropoda, Patellidae) will offer a unique opportunity to understand how intertidal organisms respond to the effects of global warming, contributing to improve our predictions about the impact of climate change on the maintenance and diversification of marine biodiversity. A total of 9 contiguous chromosomal pseudomolecules were assembled from the genome sequence, made up from Oxford Nanopore Technologies (ONT) long-reads, WGS and Chromatin-Conformation-Capture (Hi-C) short-read sequences. This chromosome-level assembly encompasses 719 Mb, composed of 157 contigs and 24 scaffolds, with contig and scaffold N50 values of 8.52 Mb and 83.6 Mb, respectively, and assembly and annotation BUSCO completeness of 97.7% and 96.5%, respectively. The production of this genome assembly and annotation was coordinated and supported by the European Reference Genome Atlas (ERGA) and Biodiversity Genomics Europe project (BGE).\n                  <\/ns3:p>","DOI":"10.12688\/openreseurope.21608.2","type":"journal-article","created":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T05:04:09Z","timestamp":1773032649000},"page":"350","update-policy":"https:\/\/doi.org\/10.12688\/openreseurope.crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["ERGA-BGE Chromosome-Level Genome of Patella rustica Linnaeus, 1758: a Resource to Investigate Responses to Global Warming in the intertidal"],"prefix":"10.12688","volume":"5","author":[{"given":"Rui","family":"Faria","sequence":"first","affiliation":[]},{"given":"Roc\u00edo","family":"Nieto Vilela","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9575-9834","authenticated-orcid":false,"given":"Fernando P","family":"Lima","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1374-4474","authenticated-orcid":false,"given":"Rita","family":"Monteiro","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\/0000-0002-1960-9508","authenticated-orcid":false,"given":"Thomas","family":"Marcussen","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3280-6239","authenticated-orcid":false,"given":"Torsten H","family":"Struck","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2094-5592","authenticated-orcid":false,"given":"Rebekah A","family":"Oomen","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":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2960-5420","authenticated-orcid":false,"given":"Tyler","family":"Alioto","sequence":"additional","affiliation":[]},{"given":"Francisco","family":"C\u00e2mara Ferreira","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\/0000-0003-4098-8829","authenticated-orcid":false,"given":"Fernando","family":"Cruz","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9533-1675","authenticated-orcid":false,"given":"Anna","family":"Lazar","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8843-3596","authenticated-orcid":false,"given":"Leanne","family":"Haggerty","sequence":"additional","affiliation":[]},{"given":"Fergal","family":"Martin","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8293-4816","authenticated-orcid":false,"given":"Tom","family":"Brown","sequence":"additional","affiliation":[]}],"member":"2560","published-online":{"date-parts":[[2026,3,9]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","DOI":"10.1093\/database\/baw093","article-title":"The Ensembl gene annotation system.","volume":"2016","author":"B Aken","year":"2016","journal-title":"Database"},{"key":"ref2","doi-asserted-by":"publisher","DOI":"10.1002\/9780470015902.a0029536","article-title":"Evolutionary processes in marine environments.","volume":"3","author":"P Barry","year":"2024","journal-title":"eLS, Encyclopedia of Life Sciences."},{"key":"ref3","doi-asserted-by":"crossref","first-page":"S81-S90","DOI":"10.1890\/08-0635.1","article-title":"Climate and recruitment of rocky shore intertidal invertebrates in the eastern North Atlantic.","volume":"89","author":"B Broitman","year":"2008","journal-title":"Ecology."},{"key":"ref4","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":"ref5","first-page":"1305-1392","article-title":"R\u00e9vision du genre Patella (Mollusca, Gastropoda).","volume":"182","author":"J Christiaens","year":"1973","journal-title":"Bulletin du Museum National d\u2019Histoire Naturelle, Paris."},{"key":"ref6","first-page":"275-388","article-title":"R\u00e9partition des principales esp\u00e8ces intercotidales de la c\u00f4te atlantique fran\u00e7aise en 1954\u20131955.","volume":"36","author":"D Crisp","year":"1959","journal-title":"Annales de l\u2019Institut Oc\u00e9anographique, Paris."},{"key":"ref7","doi-asserted-by":"publisher","DOI":"10.48546\/WORKFLOWHUB.WORKFLOW.1103.2","article-title":"ERGA-BGE Genome Report ASM analyses (one-asm WGS Illumina PE + HiC).","author":"D De Panis","year":"2024a","journal-title":"WorkflowHub."},{"key":"ref8","doi-asserted-by":"publisher","DOI":"10.48546\/WORKFLOWHUB.WORKFLOW.1096.1","article-title":"ERGA-BGE Genome Report ANNOT analyses.","author":"D De Panis","year":"2024b","journal-title":"WorkflowHub."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"1375-1393","DOI":"10.1111\/mec.15036","article-title":"Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.","volume":"28","author":"R Faria","year":"2019","journal-title":"Molecular Ecology."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"4-15","DOI":"10.1111\/jeb.13615","article-title":"Speciation in marine environments: Diving under the surface.","volume":"34","author":"R Faria","year":"2021","journal-title":"Journal of Evolutionary Biology."},{"key":"ref11","first-page":"37-124","article-title":"R\u00e9partition le long des c\u00f4tes septentrionales de l\u2019Espagne, des principales esp\u00e8ces peuplant les rochers intercotidaux.","volume":"31","author":"E Fischer-Pi\u00e8tte","year":"1955","journal-title":"Annales de l\u2019Institut Oc\u00e9anographique, Paris."},{"key":"ref12","first-page":"135-200","article-title":"Les patelles au long des c\u00f4tes atlantiques Ib\u00e9riques et Nord-Marocaines.","volume":"99","author":"E Fischer-Pi\u00e8tte","year":"1959","journal-title":"Journal of Conchology."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"5-45","DOI":"10.22459\/IREH.07.02.2021.01","article-title":"What have limpets ever done for us? On the past and present provisioning and cultural services of limpets.","volume":"7","author":"L Firth","year":"2021","journal-title":"International Review of Environmental History."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"197-202","DOI":"10.1016\/j.tree.2021.11.005","article-title":"The era of reference genomes in conservation genomics.","volume":"37","author":"G Formenti","year":"2022","journal-title":"Trends in Ecology & Evolution."},{"key":"ref15","doi-asserted-by":"publisher","DOI":"10.48546\/WORKFLOWHUB.WORKFLOW.567.2","article-title":"CLAWS (CNAG\u2019s long-read assembly workflow in Snakemake).","author":"J Gomez-Garrido","year":"2024","journal-title":"WorkflowHub."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"W70-W74","DOI":"10.1093\/nar\/gkn188","article-title":"The Vienna RNA Websuite.","volume":"36","author":"A Gruber","year":"2008","journal-title":"Nucleic Acids Research."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"418","DOI":"10.12688\/wellcomeopenres.20008.1","article-title":"The genome sequence of the common limpet, Patella vulgata (Linnaeus, 1758).","volume":"8","author":"S Hawkins","year":"2023","journal-title":"Wellcome Open Research."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"47","DOI":"10.12688\/wellcomeopenres.20687.1","article-title":"The genome sequence of the black-footed limpet, Patella depressa (Pennant, 1777).","volume":"9","author":"S Hawkins","year":"2024","journal-title":"Wellcome Open Research."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"245-259","DOI":"10.3354\/meps08378","article-title":"Consequences of climate-driven biodiversity changes for ecosystem functioning of north European rocky shores.","volume":"396","author":"S Hawkins","year":"2009","journal-title":"Marine Ecology Progress Series."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"373-404","DOI":"10.1146\/annurev.ecolsys.37.091305.110149","article-title":"Living on the edge of two changing worlds: Forecasting the responses of rocky intertidal ecosystems to climate change.","volume":"37","author":"B Helmuth","year":"2006","journal-title":"Annual Review of Ecology, Evolution, and Systematics."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"447-460","DOI":"10.1016\/0300-9629(74)90008-5","article-title":"Cellular DNA content of the Mollusca.","volume":"47","author":"R Hinegardner","year":"1974","journal-title":"Comparative Biochemistry and Physiology Part A: Physiology."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"479-485","DOI":"10.1038\/nature09670","article-title":"Climate change and evolutionary adaptation.","volume":"470","author":"A Hoffmann","year":"2011","journal-title":"Nature."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"e51","DOI":"10.1002\/cpbi.51","article-title":"Non-Coding RNA Analysis Using the Rfam Database.","volume":"62","author":"I Kalvari","year":"2018","journal-title":"Current Protocols in Bioinformatics."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"D155-D162","DOI":"10.1093\/nar\/gky1141","article-title":"miRBase: From microRNA sequences to function.","volume":"47","author":"A Kozomara","year":"2019","journal-title":"Nucleic Acids Research."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"126","DOI":"10.12688\/wellcomeopenres.17825.1","article-title":"The genome sequence of the blue-rayed limpet, Patella pellucida Linnaeus, 1758.","volume":"7","author":"M Lawniczak","year":"2022","journal-title":"Wellcome Open Research."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"812-822","DOI":"10.1111\/j.1365-2699.2006.01457.x","article-title":"Recent changes in the distribution of a marine gastropod, Patella rustica Linnaeus, 1758, and their relationship to unusual climatic events.","volume":"33","author":"F Lima","year":"2006","journal-title":"Journal of Biogeography."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"2065-2077","DOI":"10.1111\/j.1365-2486.2007.01424.x","article-title":"Modelling past and present geographical distribution of the marine gastropod Patella rustica as a tool for exploring responses to environmental change.","volume":"13","author":"F Lima","year":"2007","journal-title":"Global Change Biology."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1038\/s44285-024-00027-8","article-title":"Building a Portuguese coalition for biodiversity genomics.","volume":"3","author":"J Marques","year":"2024","journal-title":"NPJ Biodiversity."},{"key":"ref29","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":"ref30","doi-asserted-by":"publisher","first-page":"419","DOI":"10.12688\/wellcomeopenres.24681.1","article-title":"The genome sequence of the China Limpet, Patella ulyssiponensis Gmelin, 1791 (Patellidae).","volume":"10","author":"N Mieszkowska","year":"2025","journal-title":"Wellcome Open Research."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"eaav9963","DOI":"10.1126\/sciadv.aav9963","article-title":"Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast.","volume":"5","author":"H Morales","year":"2019","journal-title":"Science Advances."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"2933-2935","DOI":"10.1093\/bioinformatics\/btt509","article-title":"Infernal 1.1: 100-fold faster RNA homology searches.","volume":"29","author":"E Nawrocki","year":"2013","journal-title":"Bioinformatics."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"219-225","DOI":"10.1007\/s10709-009-9416-y","article-title":"Molecular cytogenetic study of three common Mediterranean limpets, Patella caerulea, P. rustica and P. ulyssiponensis (Archaeogastropoda, Mollusca).","volume":"138","author":"A Petraccioli","year":"2010","journal-title":"Genetica."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"1-40","DOI":"10.1163\/18759866-20191330","article-title":"Speciation with gene flow in marine systems.","volume":"88","author":"G Potkamp","year":"2019","journal-title":"Contributions to Zoology."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"1651-1660","DOI":"10.1017\/S0025315414000976","article-title":"On the reproduction of the Mediterranean keystone limpet Patella rustica: histological overview.","volume":"94","author":"I Prusina","year":"2014","journal-title":"Journal of the Marine Biological Association of the United Kingdom."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"1782-1796","DOI":"10.1111\/j.1365-2699.2010.02330.x","article-title":"Recent changes in the distribution of a marine gastropod, Patella rustica, across the Iberian Atlantic coast did not result in diminished genetic diversity or increased connectivity.","volume":"37","author":"P Ribeiro","year":"2010","journal-title":"Journal of Biogeography."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"912-920","DOI":"10.1242\/jeb.037473","article-title":"The physiology of climate change: How potentials for acclimatization and genetic adaptation will determine \u2018winners\u2019 and \u2018losers\u2019.","volume":"213","author":"G Somero","year":"2010","journal-title":"Journal of Experimental Biology."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"154-169","DOI":"10.1111\/j.1095-8312.2010.01405.x","article-title":"A three-way contact zone between forms of Patella rustica (Mollusca: Patellidae) in the central Mediterranean Sea.","volume":"100","author":"A S\u00e1-Pinto","year":"2010","journal-title":"Biological Journal of the Linnean Society."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"1-15","DOI":"10.1016\/j.marenvres.2012.04.003","article-title":"Energy homeostasis as an integrative tool for assessing limits of environmental stress tolerance in aquatic invertebrates.","volume":"79","author":"I Sokolova","year":"2012","journal-title":"Marine Environmental Research."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"68-75","DOI":"10.1016\/j.jembe.2012.09.005","article-title":"Fate of a climate-driven colonisation: Demography of newly established populations of the limpet Patella rustica Linnaeus, 1758, in northern Portugal.","volume":"438","author":"L Sousa","year":"2012","journal-title":"Journal of Experimental Marine Biology and Ecology."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"5025-5041","DOI":"10.1111\/j.1365-294X.2011.05307.x","article-title":"Climate-driven genetic divergence of limpets with different life histories across a southeast African marine biogeographic disjunction: Different processes, same outcome.","volume":"20","author":"P Teske","year":"2011","journal-title":"Molecular Ecology."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"545-559","DOI":"10.1016\/j.tig.2023.04.003","article-title":"How genomics can help biodiversity conservation.","volume":"39","author":"K Theissinger","year":"2023","journal-title":"Trends in Genetics."},{"key":"ref43","doi-asserted-by":"publisher","DOI":"10.1016\/j.biocon.2024.110394","article-title":"Effects of climate change on marine coastal ecosystems: A review to guide research and management.","volume":"289","author":"E Tr\u00e9garot","year":"2024","journal-title":"Biological Conservation."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"D506-D515","DOI":"10.1093\/nar\/gky1049","article-title":"UniProt: A worldwide hub of protein knowledge.","volume":"47","year":"2019","journal-title":"Nucleic Acids Research."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"153-162","DOI":"10.1007\/s00227-004-1540-2","article-title":"Patella aspera and P. ulyssiponensis: Genetic evidence of speciation in the north-east Atlantic.","volume":"147","author":"L Weber","year":"2005","journal-title":"Marine Biology."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"297-309","DOI":"10.1002\/evl3.66","article-title":"Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow.","volume":"2","author":"A Westram","year":"2018","journal-title":"Evolution Letters."},{"key":"ref47","first-page":"42-51","article-title":"Reproduction of Patella rustica (Mollusca, Gastropoda) in the gulf of Annaba (Algeria, Mediterranean South Western).","volume":"10","author":"B Zegaoula","year":"2016","journal-title":"Advances in Environmental Biology."}],"container-title":["Open Research Europe"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-350\/v2\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-350\/v2\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-350\/v2\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T11:54:09Z","timestamp":1773316449000},"score":1,"resource":{"primary":{"URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-350\/v2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,9]]},"references-count":47,"URL":"https:\/\/doi.org\/10.12688\/openreseurope.21608.2","relation":{"has-version":[{"id-type":"doi","id":"10.12688\/openreseurope.21608.1","asserted-by":"subject"}],"has-review":[{"id-type":"doi","id":"10.21956\/openreseurope.24968.r70969","asserted-by":"subject"},{"id-type":"doi","id":"10.21956\/openreseurope.24968.r70969","asserted-by":"object"}]},"ISSN":["2732-5121"],"issn-type":[{"value":"2732-5121","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,9]]},"assertion":[{"value":"Indexed","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-350\/v2#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.21956\/openreseurope.23376.r64050, Jacob A Tennessen, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, 24 Nov 2025, version 1, 1 approved, 1 approved with reservations","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-350\/v1#referee-response-64050","order":0,"name":"referee-response-64050","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Thomas Brown<\/b>; \n<i>Posted: 03 Feb 2026<\/i>; \n<b>Review: <\/b>This is a nicely assembled and annotated genome that will be a useful resource for the mollusk genomics community. Assembly and annotation methods are appropriately described, albeit with minimal details. &nbsp; The genome is from an outbred diploid individual, and it would be nice to see more details on how heterozygous sites and more complex structural polymorphisms were handled. Presumably they were arbitrarily collapsed and it says haplotigs were removed. Is there an estimate of genome-wide heterozygosity (e.g. from alignment of the short reads to the final assembly)? Is it possible that some contigs\/scaffolds are allelic copies of each other? As much as possible, any retained sequences from the other haplotype were removed both during the purge-dups and manual curation steps. An analysis of any heterozygosity levels or regions is not considered part of this data note. &nbsp; The authors mention the genomes of five other Patella species. These should be cited in this paper (if no publication exists, then link to their accessions on ENA or https:\/\/beta.ensembl.org). The utility of this genome will largely be found in the context of those congener genomes: comparative work will allow errors to be identified and corrected, while also revealing informative evolutionary patterns. It would be interesting to see such comparative work included here, though I understand if such analysis is beyond the scope of the funded project.  \n<b>Response: <\/b>Thank you for the suggestion. We have included the citations for 4 papers where the genomes have been published in a corresponding article. For the 5th genome, we have included the genbank accession. &nbsp; Change (Hoffmann, 2011) to (Hoffmann &amp; Sgr&ograve;, 2011) Thank you for noticing the error - we have corrected the citation in the text","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-350\/v2#referee-comment-5060","order":1,"name":"referee-comment-5060","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/openreseurope.23376.r64049, Yasuto ISHII, Tohoku University, Sendai, 11 Dec 2025, version 1, 1 approved, 1 approved with reservations","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-350\/v1#referee-response-64049","order":2,"name":"referee-response-64049","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"<b>Thomas Brown<\/b>; \n<i>Posted: 03 Feb 2026<\/i>; \n<b>GENERAL COMMENTS<\/b> The present study released a genome assembly of Patella rustica. The assembly have high continuity and completeness, so thereby it should be valuable genetic resource. Also, the authors provided a high-quality gene annotation which is also a promising genetic resource. The assembly and annotation are available from a public database. Collectively, the assembly and annotation should promote further genomic research in Patella snails and other related species. Yet, this manuscript does not contain fundamental information, such as details of pre-Hi-C scaffolding assembly and how much sequences were anchored on the Hi-C scaffolds. Also, some fruitful analyses, including repeat masking, are lack in the current version. I listed some minor comments and suggestions below.  \n<b>Thank you for the suggestions. We have added to the text following the guidelines of the reviewer: &nbsp;<\/b>  \n<b>COMMENTS Title and abstract: ERGA-BGE is not a common abbreviation. The full name should be addressed in the abstract. Also, I suggest that the word &quot;chromosome-level assembly&quot; should be included in the title to be appealing to readers. If the word limit is not strict, sequencing methods (e.g., the use of long-read, read type [ONT+Hi-C+short-read]) and BUSCO values should be noted in the abstract. This information ensures the validity of the assembly. Furthermore, the taxonomic information (e.g., family, class; I\u2019m not familiar with limpets, so not sure what rank is useful) is helpful for readers to reach this article.<\/b> Thank you for the suggestions. We have added \u201cChromosome-Level\u201d to the title, further details of the class and family (Gastropoda, Patellidae), as well as the sequencing recipe and the project and consortia to the abstract.&nbsp; &nbsp;  \n<b>In the introduction, while the authors stated that the species is serve as a &quot;sentinel&quot;, the reason why this species particularly has such a character.<\/b> We would like to clarify that this is not a particular attribute of our focal species and that the term was not coined by us. We only use it in the introduction to refer to other intertidal species, in the sense that they can inform us about environmental change, for instance, via shifts in their distribution ranges as a consequence of global warming (as mentioned in the introduction and supported by references). We hope that this is clear in the main text and no further changes are needed. &nbsp;  \n<b>Add appropriate reference(s) for the following sentence: &quot;Several studies have documented recent changes in its distribution, particularly the bridging of a historical distribution gap in northwestern Iberia.&nbsp;<\/b> Thank you for the suggestion. We added \u201c(Fischer-Pi&egrave;tte and Gaillard, 1959; Lima et al., 2006)\u201d at the end of the sentence. And added the first reference to the final list. &nbsp;  \n<b>&nbsp;How did you detect the sex?: &quot;female sample of Patella rustica was sampled&quot;<\/b> The sex of the individual was determined macroscopically as they are easily distinguishable by gonad coloration: females have green or brown gonads, while males present a pinkish-cream color (based on previous work describing the reproductive cycles of the species, with some examples in Zegaoula 2016 and Prusina 2014). We added the following information in one of the subsequent sections of the same section with the new text underlined:&nbsp; After dissection and sexing (based on gonad colouration) by Roc&iacute;o Nieto Vilela, the specimen's tissues (mollusc foot, gonad, head, hepatopancreas and other somatic tissue)&nbsp; &nbsp; Refs Zegaoula, B., Beldi, H., Draredja, B., &amp; Soltani, N. (2016). Reproduction of Patella rustica (Mollusca, Gastropoda) in the gulf of Annaba (Algeria, Mediterranean South Western). Advances in Environmental Biology, 10(11), 42-51. Prusina, I., Ezgeta-Bali\u0107, D., Ljubimir, S., Dobroslavi\u0107, T., &amp; Glamuzina, B. (2014). On the reproduction of the Mediterranean keystone limpet Patella rustica: histological overview. Journal of the Marine Biological Association of the United Kingdom, 94(8), 1651-1660. &nbsp;  \n<b>I suggest that you should do the genome size estimation by yourself. In my opinion, articles should be self-contained if possible.: &quot;the estimation based on reads kmer profiling is 726 Mb&quot;<\/b> We performed genome size estimation using the sequenced genomic DNA, estimating the size based on total coverage and ratio of heterozygous - homozygous kmers. To add context in the manuscript, we have added the range of genome sizes identified by Hinegardner, however performing genome size calculation from scratch is not within the scope of this study. &nbsp; \n<b>I cannot grasp the meaning of this sentence. Does it mean that the estimation is for the haploid genome?: &quot;This is a diploid genome with a haploid number of 9 chromosomes (2n=18)<\/b> &quot; We apologise for the confusion and have explicitly stated that the size estimates correspond to the haploid genome size. &nbsp;  \n<b>To be clear, did you perform genome annotation without repeat masking? One intriguing feature of molluscan genomes are the evolution of repeat elements. If you can do it, it should be a valuable resource. Also, while I\u2019m not familiar with the gene annotation pipeline, generally repeat masking improves the quality of gene annotations.<\/b> The gene annotation pipeline used did not make use of masked repetitive elements, however soft- and hard-masked versions of the genome assembly are available via the Ensembl download site alongside the annotation files. &nbsp;  \n<b>In Table 2, you reported the proportion of contaminations is 0.05 (lack of &quot;%&quot;?) but the number of contaminated transcripts is zero. It looks weird. The proportion should be 0.00%; otherwise, the number of contaminated transcripts is wrong.<\/b> Thank you for noticing our typo - which came from 5 and % sharing a key - this has been corrected in the table. &nbsp;  \n<b>More details of the assembly should be reported, including the statistics of the assembly before Hi-C scaffolding. Moreover, according to Fig. 3, the sequences look to be anchored on nine mega-scaffolds, but it is not clear due to the lack of the mention in the main text. If so, the number of mega-scaffolds is matched with the haploid number of chromosomes of this species (documented in the method section); this information is noteworthy. It is also unclear how much sequences are anchored on the mega-scaffolds.<\/b> We have added details as to the choice of assembler in the methods section and the amount of sequence removed by the purge-dups step in creating the assembly for a single haplotype. We have furthermore added the total proportion of the assembly anchored to the pseudo-chromosomal molecules to the results section.","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-350\/v2#referee-comment-5061","order":3,"name":"referee-comment-5061","label":"Referee Comment","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.21956\/openreseurope.24968.r70969, Craig Wilding, University College Dublin, Dublin, 12 Mar 2026, version 2, indexed","URL":"https:\/\/open-research-europe.ec.europa.eu\/articles\/5-350\/v2#referee-response-70969","order":4,"name":"referee-response-70969","label":"Referee Report","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. RF and FPL received support from Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia through a CEECInd contracts (https:\/\/doi.org\/10.54499\/2020.00275.CEECIND\/CP1601\/CP1649\/CT0001, https:\/\/doi.org\/10.54499\/2020.00275.CEECIND\/CP1601\/CT0002 and   https:\/\/doi.org\/10.54499\/CEECIND\/03185\/2018\/CP1546\/CP1648\/CT0004) and through the project INVCONTINUUM (https:\/\/doi.org\/10.54499\/PTDC\/BIA-EVL\/1614\/2021) and OceanLog (PTDC\/BIA-BMA\/4848\/2021). RNV received support from the EU under the Horizon 2020  program (project ANERIS, ref. 101094924). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","order":5,"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"}]}}