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dc.contributor.authorFernández Silva, Iria 
dc.contributor.authorHenderson, James B
dc.contributor.authorRocha, Luiz A
dc.contributor.authorSimison, W. Brian
dc.date.accessioned2022-12-27T12:01:56Z
dc.date.available2022-12-27T12:01:56Z
dc.date.issued2018-01-24
dc.identifier.citationScientific Reports, 8(1): 1498 (2018)spa
dc.identifier.issn20452322
dc.identifier.urihttp://hdl.handle.net/11093/4301
dc.description.abstractThe diversity of DNA sequencing methods and algorithms for genome assemblies presents scientists with a bewildering array of choices. Here, we construct and compare eight candidate assemblies combining overlapping shotgun read data, mate-pair and Chicago libraries and four different genome assemblers to produce a high-quality draft genome of the iconic coral reef Pearlscale Pygmy Angelfish, Centropyge vrolikii (family Pomacanthidae). The best candidate assembly combined all four data types and had a scaffold N50 127.5 times higher than the candidate assembly obtained from shotgun data only. Our best candidate assembly had a scaffold N50 of 8.97 Mb, contig N50 of 189,827, and 97.4% complete for BUSCO v2 (Actinopterygii set) and 95.6% complete for CEGMA matches. These contiguity and accuracy scores are higher than those of any other fish assembly released to date that did not apply linkage map information, including those based on more expensive long-read sequencing data. Our analysis of how different data types improve assembly quality will help others choose the most appropriate de novo genome sequencing strategy based on resources and target applications. Furthermore, the draft genome of the Pearlscale Pygmy angelfish will play an important role in future studies of coral reef fish evolution, diversity and conservationen
dc.description.sponsorshipUC Berkeley | Ref. S10RR029668spa
dc.description.sponsorshipUC Berkeley | Ref. S10RR027303spa
dc.language.isoengspa
dc.publisherScientific Reportsspa
dc.rightsAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.titleWhole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii)en
dc.typearticlespa
dc.rights.accessRightsopenAccessspa
dc.relation.projectIDinfo:eu-repo/grantAgreement/EC/FP7/600391spa
dc.relation.projectIDinfo:eu-repo/grantAgreement/EC/FP7/302957spa
dc.identifier.doi10.1038/s41598-018-19430-x
dc.identifier.editorhttps://www.nature.com/articles/s41598-018-19430-xspa
dc.publisher.departamentoBioquímica, xenética e inmunoloxíaspa
dc.publisher.grupoinvestigacionXenómica e Biomedicinaspa
dc.subject.unesco2409.03 Genética de Poblacionesspa
dc.subject.unesco3105 Peces y Fauna Silvestrespa
dc.date.updated2022-12-27T11:59:38Z
dc.computerCitationpub_title=Scientific Reports|volume=8|journal_number=1|start_pag=1498|end_pag=spa


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    Attribution 4.0 International
    Except where otherwise noted, this item's license is described as Attribution 4.0 International