A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions

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dc.contributor.authorConte, Matthew A.
dc.contributor.authorGammerdinger, William J.
dc.contributor.authorBartie, Kerry L.
dc.contributor.authorPenman, David J.
dc.contributor.authorKocher, Thomas D.
dc.date.accessioned2021-07-21T19:10:13Z
dc.date.available2021-07-21T19:10:13Z
dc.date.issued2017-05-02
dc.description.abstractTilapias 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. 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 recent vasa gene 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. 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_US
dc.description.urihttps://doi.org/10.1186/s12864-017-3723-5
dc.identifierhttps://doi.org/10.13016/poxu-2dtv
dc.identifier.citationConte, M.A., Gammerdinger, W.J., Bartie, K.L. et al. A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions. BMC Genomics 18, 341 (2017).en_US
dc.identifier.urihttp://hdl.handle.net/1903/27557
dc.language.isoen_USen_US
dc.publisherSpringer Natureen_US
dc.relation.isAvailableAtCollege of Computer, Mathematical & Physical Sciencesen_us
dc.relation.isAvailableAtDigital Repository at the University of Marylanden_us
dc.relation.isAvailableAtBiologyen_us
dc.relation.isAvailableAtUniversity of Maryland (College Park, MD)en_us
dc.subjectGenome assemblyen_US
dc.subjectPacific Biosciences SMRT sequencingen_US
dc.subjectTransposable elementsen_US
dc.subjectGene duplicationen_US
dc.subjectSex chromosomeen_US
dc.subjectSex determinationen_US
dc.subjectAquacultureen_US
dc.subjectTilapiaen_US
dc.titleA high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regionsen_US
dc.typeArticleen_US

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