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

摘要: Tilapias are the second most farmed fishes in world and a sustainable source of food. Like many other fish, tilapias sexually dimorphic sex is commercially important trait these fish. In this study, we developed significantly improved assembly tilapia genome using latest sequencing methods show how it improves characterization two determination regions species. A homozygous clonal XX female Nile (Oreochromis niloticus) was sequenced to 44X coverage Pacific Biosciences (PacBio) SMRT sequencing. Dozens candidate de novo assemblies were generated an optimal (contig NG50 3.3Mbp) selected principal component analysis likelihood scores calculated from several paired-end libraries. Comparison new previous O. niloticus reveals that recently duplicated portions now well represented. The overall number genes increased by 27.3%, including 67% increase pseudogenes. correctly represents recent vasa gene duplication events have been verified with BAC At total 146Mbp additional transposable element sequence assembled, large proportion which insertions. Large centromeric satellite repeats assembled annotated cichlid fish for first time. Finally, identifies long-range structure both ~9Mbp XY region on LG1 niloticus, ~50Mbp WZ LG3 related species aureus. This study highlights use long read assemble duplications characterize repeat-filled genome. serves as example need high quality provides framework identifying determining