Chromosome-level genome assembly of the Vermillion Snapper (Rhomboplites aurorubens)

Chromosome-level genome assembly of the Vermillion Snapper (Rhomboplites aurorubens) | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Data Note Chromosome-level genome assembly of the Vermillion Snapper ( Rhomboplites aurorubens ) Roa-Varón, A., Moulos, P., Harter, S., David, A, Quattrini, A.M., and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4927070/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Vermillion Snapper ( Rhomboplites aurorubens , Lutjanidae) inhabits deep waters (20-300 m) from North America through Brazil, sustaining significant commercial and recreational fisheries. Despite its economic importance, knowledge of its biology is limited. Classified as Vulnerable on the Red List due to overfishing, populations have declined by over 30% in recent generations. We assembled and annotated the first chromosome-scale genome of this species by combining PacBio long reads, Illumina short reads, and Hi-C data. The resulting assembly is 987.5 Mbp, with a scaffold N50 size of 41.3 Mbp, and 135 contigs clustered and ordered onto 24 chromosomes with 34,496 predicted genes. The high-quality assembly and annotation contained 98% complete and single-copy BUSCO genes. This is the most complete, chromosome-level genome assembly of an Atlantic snapper to date. The Vermillion Snapper genome assembly and its supporting data are valuable tools for ecological and comparative genomics studies of snappers and other valuable commercial species within the family. Molecular Genetics Vermillion Snapper Rhomboplites aurorubens Lutjanidae IUCN Vulnerable Chromosome-Level Genome Full Text Additional Declarations The authors declare no competing interests. Supplementary Files FigureS1VermillionSnapperFieldPicturePE2019429.pdf FigureS2SummaryofBasicStatistics.pdf FigureS3HiCcontactandassemblymapbeforecuration.pdf FigureS4BUSCO.pdf TablesS1S5.xlsx Tables (single excel file) Table S1. Mapping parameters used for mapping Rhomboplites aurorubens distribution. Data retrieved from href="https://www.aquamaps.org/">AquaMaps (Kaschener et al., 2019). Table S2. Genome assembly statistics of Vermillion Snapper. All statistics are based on contigs of size >= 500 bp, unless otherwise noted. The overall best results according to telomere sequence content are provided by the HiC-Pro + EndHiC pipeline at the 100k pb bin scale (ticked box). Table S3. Number of paired whole genome sequencing reads and bases aligned on each unpolished genome version. Table S4. Number of paired whole genome sequencing reads and bases aligned on each polished genome version. Table S5. Statistics for Vermillion Snapper assembly, annotation and orthology. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-4927070","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Data Note","associatedPublications":[],"authors":[{"id":341304788,"identity":"1b2cede3-e973-43dc-a53c-836af25e8a80","order_by":0,"name":"Roa-Varón, 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02:22:58","extension":"pdf","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":26908,"visible":true,"origin":"","legend":"","description":"","filename":"FigureS4BUSCO.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4927070/v1/2eb56293111e51f7705011e0.pdf"},{"id":62825866,"identity":"a6d868fe-790d-4f1d-8340-5a4afe162407","added_by":"auto","created_at":"2024-08-20 02:23:02","extension":"xlsx","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":141733,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eTables\u003c/strong\u003e (single excel file)\u003c/p\u003e\n\u003cp\u003eTable S1. Mapping parameters used for mapping \u003cem\u003eRhomboplites aurorubens \u003c/em\u003edistribution. Data retrieved from \u003ca href=\"https://www.aquamaps.org/\"\u003eAquaMaps\u003c/a\u003e (Kaschener et al., 2019).\u003c/p\u003e\n\u003cp\u003eTable S2. Genome assembly statistics of Vermillion Snapper. All statistics are based on contigs of size \u0026gt;= 500 bp, unless otherwise noted. The overall best results according to telomere sequence content are provided by the HiC-Pro + EndHiC pipeline at the 100k pb bin scale (ticked box).\u003c/p\u003e\n\u003cp\u003eTable S3. Number of paired whole genome sequencing reads and bases aligned on each unpolished genome version.\u003c/p\u003e\n\u003cp\u003eTable S4. Number of paired whole genome sequencing reads and bases aligned on each polished genome version.\u003c/p\u003e\n\u003cp\u003eTable S5. Statistics for \u003cem\u003eVermillion Snapper\u003c/em\u003e assembly, annotation and orthology.\u003c/p\u003e","description":"","filename":"TablesS1S5.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-4927070/v1/87b892f6b7f0bca3c49499d5.xlsx"}],"financialInterests":"The authors declare no competing interests.","formattedTitle":"\u003cp\u003eChromosome-level genome assembly of the Vermillion Snapper (\u003cem\u003eRhomboplites aurorubens\u003c/em\u003e)\u003c/p\u003e","fulltext":[],"fulltextSource":"","fullText":"","funders":[{"identity":"60e69f4d-ade3-4fa2-9d7f-2eabf6678984","identifier":"10.13039/100000192","name":"National Oceanic and Atmospheric Administration","awardNumber":"NA18NOS4780166 ","order_by":0}],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"National Oceanic and Atmospheric Administration","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Vermillion Snapper, Rhomboplites aurorubens, Lutjanidae, IUCN Vulnerable, Chromosome-Level Genome","lastPublishedDoi":"10.21203/rs.3.rs-4927070/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4927070/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eVermillion Snapper (\u003cem\u003eRhomboplites aurorubens\u003c/em\u003e, Lutjanidae) inhabits deep waters (20-300 m) from North America through Brazil, sustaining significant commercial and recreational fisheries. Despite its economic importance, knowledge of its biology is limited. Classified as Vulnerable on the Red List due to overfishing, populations have declined by over 30% in recent generations. We assembled and annotated the first chromosome-scale genome of this species by combining PacBio long reads, Illumina short reads, and Hi-C data. The resulting assembly is 987.5 Mbp, with a scaffold N50 size of 41.3 Mbp, and 135 contigs clustered and ordered onto 24 chromosomes with 34,496 predicted genes. The high-quality assembly and annotation contained 98% complete and single-copy BUSCO genes. This is the most complete, chromosome-level genome assembly of an Atlantic snapper to date. The Vermillion Snapper genome assembly and its supporting data are valuable tools for ecological and comparative genomics studies of snappers and other valuable commercial species within the family.\u003c/p\u003e","manuscriptTitle":"Chromosome-level genome assembly of the Vermillion Snapper (Rhomboplites aurorubens)","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-08-20 02:22:53","doi":"10.21203/rs.3.rs-4927070/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"fdc11386-df5b-4b45-81c3-27e7cfeddfa7","owner":[],"postedDate":"August 20th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":36167381,"name":"Molecular Genetics"}],"tags":[],"updatedAt":"2024-08-22T15:01:52+00:00","versionOfRecord":[],"versionCreatedAt":"2024-08-20 02:22:53","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-4927070","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-4927070","identity":"rs-4927070","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}