{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:37:55Z","timestamp":1772138275988,"version":"3.50.1"},"reference-count":61,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2024,4,8]],"date-time":"2024-04-08T00:00:00Z","timestamp":1712534400000},"content-version":"vor","delay-in-days":7,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,4,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The intertidal gastropod Littorina saxatilis is a model system to study speciation and local adaptation. The repeated occurrence of distinct ecotypes showing different levels of genetic divergence makes L. saxatilis particularly suited to study different stages of the speciation continuum in the same lineage. A major finding is the presence of several large chromosomal inversions associated with the divergence of ecotypes and, specifically, the species offers a system to study the role of inversions in this divergence. The genome of L. saxatilis is 1.35\u2005Gb and composed of 17 chromosomes. The first reference genome of the species was assembled using Illumina data, was highly fragmented (N50 of 44\u2005kb), and was quite incomplete, with a BUSCO completeness of 80.1% on the Metazoan dataset. A linkage map of one full-sibling family enabled the placement of 587\u2005Mbp of the genome into 17 linkage groups corresponding to the haploid number of chromosomes, but the fragmented nature of this reference genome limited the understanding of the interplay between divergent selection and gene flow during ecotype formation. Here, we present a newly generated reference genome that is highly contiguous, with a N50 of 67\u2005Mb and 90.4% of the total assembly length placed in 17 super-scaffolds. It is also highly complete with a BUSCO completeness of 94.1% of the Metazoa dataset. This new reference will allow for investigations into the genomic regions implicated in ecotype formation as well as better characterization of the inversions and their role in speciation.<\/jats:p>","DOI":"10.1093\/gbe\/evae076","type":"journal-article","created":{"date-parts":[[2024,4,5]],"date-time":"2024-04-05T11:59:05Z","timestamp":1712318345000},"source":"Crossref","is-referenced-by-count":4,"title":["Chromosome-scale Genome Assembly of the Rough Periwinkle\n                    <i>Littorina saxatilis<\/i>"],"prefix":"10.1093","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0428-439X","authenticated-orcid":false,"given":"Aur\u00e9lien","family":"De Jode","sequence":"first","affiliation":[{"name":"Department of Marine Sciences, Tj\u00e4rn\u00f6 Marine Laboratory, University of Gothenburg , SE 45296 Str\u00f6mstad , Sweden"},{"name":"Department of Biological Sciences, University of Alabama , Tuscaloosa, AL , USA"},{"name":"Dauphin Island Sea Lab , Dauphin Island, AL , USA"}]},{"given":"Rui","family":"Faria","sequence":"additional","affiliation":[{"name":"CIBIO, Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos, InBIO Laborat\u00f3rio Associado, Campus de Vair\u00e3o, Universidade do Porto , 4485-661 Vair\u00e3o , Portugal"},{"name":"BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vair\u00e3o , 4485-661 Vair\u00e3o , Portugal"},{"name":"Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield , Sheffield S10 2TN , UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7554-5991","authenticated-orcid":false,"given":"Giulio","family":"Formenti","sequence":"additional","affiliation":[{"name":"The Vertebrate Genome Laboratory, The Rockefeller University , New York, NY 10065 , USA"}]},{"given":"Ying","family":"Sims","sequence":"additional","affiliation":[{"name":"Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus , Hinxton CB10 1SA , UK"}]},{"given":"Timothy P","family":"Smith","sequence":"additional","affiliation":[{"name":"USDA Agricultural Research Service, U.S. Meat Animal Research Center , Clay Center, NE 68933 , USA"}]},{"given":"Alan","family":"Tracey","sequence":"additional","affiliation":[{"name":"Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus , Hinxton CB10 1SA , UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7545-2162","authenticated-orcid":false,"given":"Jonathan M D","family":"Wood","sequence":"additional","affiliation":[{"name":"Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus , Hinxton CB10 1SA , UK"}]},{"given":"Zuzanna B","family":"Zagrodzka","sequence":"additional","affiliation":[{"name":"Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield , Sheffield S10 2TN , UK"}]},{"given":"Kerstin","family":"Johannesson","sequence":"additional","affiliation":[{"name":"Department of Marine Sciences, Tj\u00e4rn\u00f6 Marine Laboratory, University of Gothenburg , SE 45296 Str\u00f6mstad , Sweden"}]},{"given":"Roger K","family":"Butlin","sequence":"additional","affiliation":[{"name":"Department of Marine Sciences, Tj\u00e4rn\u00f6 Marine Laboratory, University of Gothenburg , SE 45296 Str\u00f6mstad , Sweden"},{"name":"Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield , Sheffield S10 2TN , UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7160-2290","authenticated-orcid":false,"given":"Erica H","family":"Leder","sequence":"additional","affiliation":[{"name":"Department of Marine Sciences, Tj\u00e4rn\u00f6 Marine Laboratory, University of Gothenburg , SE 45296 Str\u00f6mstad , Sweden"},{"name":"Natural History Museum, University of Oslo , Oslo , Norway"}]}],"member":"286","published-online":{"date-parts":[[2024,4,8]]},"reference":[{"issue":"12","key":"2024042911480605600_evae076-B1","doi-asserted-by":"crossref","first-page":"1691","DOI":"10.1093\/bioinformatics\/btr174","article-title":"BamTools: a C++ API and toolkit for analyzing and managing BAM files","volume":"27","author":"Barnett","year":"2011","journal-title":"Bioinformatics"},{"issue":"3","key":"2024042911480605600_evae076-B2","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1007\/BF00137320","article-title":"On the karyology of trematodes of the genus Microphallus and their intermediate gastropod host, Littorina saxatilis I. 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