Please use this identifier to cite or link to this item: http://hdl.handle.net/1893/25411
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dc.contributor.authorConte, Matthew Aen_UK
dc.contributor.authorGammerdinger, William Jen_UK
dc.contributor.authorBartie, Kerryen_UK
dc.contributor.authorPenman, Daviden_UK
dc.contributor.authorKocher, Thomas Den_UK
dc.date.accessioned2017-05-30T22:37:24Z-
dc.date.available2017-05-30T22:37:24Z-
dc.date.issued2017-05-02en_UK
dc.identifier.other341en_UK
dc.identifier.urihttp://hdl.handle.net/1893/25411-
dc.description.abstractBackground  Tilapias are the second most farmed fishes in the world and a sustainable source of food. Like many other fish, tilapias are sexually dimorphic and sex is a commercially important trait in these fish. In this study, we developed a significantly improved assembly of the tilapia genome using the latest genome sequencing methods and show how it improves the characterization of two sex determination regions in two tilapia species.  Results  A homozygous clonal XX female Nile tilapia (Oreochromis niloticus) was sequenced to 44X coverage using Pacific Biosciences (PacBio) SMRT sequencing. Dozens of candidate de novo assemblies were generated and an optimal assembly (contig NG50 of 3.3Mbp) was selected using principal component analysis of likelihood scores calculated from several paired-end sequencing libraries. Comparison of the new assembly to the previous O. niloticus genome assembly reveals that recently duplicated portions of the genome are now well represented. The overall number of genes in the new assembly increased by 27.3%, including a 67% increase in pseudogenes. The new tilapia genome assembly correctly represents two recentvasagene duplication events that have been verified with BAC sequencing. At total of 146Mbp of additional transposable element sequence are now assembled, a large proportion of which are recent insertions. Large centromeric satellite repeats are assembled and annotated in cichlid fish for the first time. Finally, the new assembly identifies the long-range structure of both a ~9Mbp XY sex determination region on LG1 in O. niloticus, and a ~50Mbp WZ sex determination region on LG3 in the related species O. aureus.  Conclusions  This study highlights the use of long read sequencing to correctly assemble recent duplications and to characterize repeat-filled regions of the genome. The study serves as an example of the need for high quality genome assemblies and provides a framework for identifying sex determining genes in tilapia and related fish species.en_UK
dc.language.isoenen_UK
dc.publisherBioMed Centralen_UK
dc.relationConte MA, Gammerdinger WJ, Bartie K, Penman D & Kocher TD (2017) A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions. BMC Genomics, 18 (1), Art. No.: 341. https://doi.org/10.1186/s12864-017-3723-5en_UK
dc.rights© The Author(s). 2017 This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.en_UK
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_UK
dc.subjectGenome assemblyen_UK
dc.subjectPacific Biosciences SMRT sequencingen_UK
dc.subjectTransposable elementsen_UK
dc.subjectGene duplicationen_UK
dc.subjectSex chromosomeen_UK
dc.subjectSex determinationen_UK
dc.subjectAquaculture Tilapiaen_UK
dc.titleA high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regionsen_UK
dc.typeJournal Articleen_UK
dc.identifier.doi10.1186/s12864-017-3723-5en_UK
dc.identifier.pmid28464822en_UK
dc.citation.jtitleBMC Genomicsen_UK
dc.citation.issn1471-2164en_UK
dc.citation.volume18en_UK
dc.citation.issue1en_UK
dc.citation.publicationstatusPublisheden_UK
dc.citation.peerreviewedRefereeden_UK
dc.type.statusVoR - Version of Recorden_UK
dc.citation.date02/05/2017en_UK
dc.contributor.affiliationUniversity of Marylanden_UK
dc.contributor.affiliationUniversity of Marylanden_UK
dc.contributor.affiliationInstitute of Aquacultureen_UK
dc.contributor.affiliationInstitute of Aquacultureen_UK
dc.contributor.affiliationUniversity of Marylanden_UK
dc.identifier.isiWOS:000400625600005en_UK
dc.identifier.scopusid2-s2.0-85018278685en_UK
dc.identifier.wtid528199en_UK
dc.contributor.orcid0000-0003-3037-5295en_UK
dc.contributor.orcid0000-0001-8608-6631en_UK
dc.date.accepted2017-04-25en_UK
dcterms.dateAccepted2017-04-25en_UK
dc.date.filedepositdate2017-05-30en_UK
rioxxterms.apcnot requireden_UK
rioxxterms.typeJournal Article/Reviewen_UK
rioxxterms.versionVoRen_UK
local.rioxx.authorConte, Matthew A|en_UK
local.rioxx.authorGammerdinger, William J|en_UK
local.rioxx.authorBartie, Kerry|0000-0003-3037-5295en_UK
local.rioxx.authorPenman, David|0000-0001-8608-6631en_UK
local.rioxx.authorKocher, Thomas D|en_UK
local.rioxx.projectInternal Project|University of Stirling|https://isni.org/isni/0000000122484331en_UK
local.rioxx.freetoreaddate2017-05-30en_UK
local.rioxx.licencehttp://creativecommons.org/licenses/by/4.0/|2017-05-30|en_UK
local.rioxx.filenameConte_etal_BMCGenomics_2017.pdfen_UK
local.rioxx.filecount1en_UK
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