A High Quality Assembly of the Nile Tilapia (Oreochromis niloticus) Genome Provides Insights into the Structure of Two Sex Determination Regions

Tilapias are the second most farmed fishes and an important source of protein around the world. Here we report a high-quality assembly of the tilapia genome to support research on traits relevant to aquaculture. We sequenced a homozygous clonal XX female tilapia (Oreochromis niloticus) to 44x coverage using PacBio sequencing. We developed 37 candidate assemblies using two different algorithms and a variety of parameter settings. We evaluated the quality of these assemblies using likelihood scores calculated from complementary datasets across several genomic scales. Principal component analysis was used to select an assembly with a contig NG50 of 3.3Mb. We used physical and genetic maps to anchor this assembly to linkage groups (LGs) and to identify 34 likely misassemblies. Each putative misassembly showed a signature consisting of high sequence variation in the aligned PacBio reads, as well as low physical coverage in a complementary 40kb-insert Illumina library. The sites of these misassemblies contained long (>50kbp) stretches of several different complex transposable element nested repeats. Several border large centromeric satellite repeats, which have now been partially assembled for the first time. The overall repeat landscape of the tilapia genome, particularly recent transposable element insertions, is now well represented. The final assembly has a contig NG50 of 3.1Mb, a total size of 1.01Gbp, and 868.6Mbp of anchored LGs. Finally, the new assembly provides insights into the structure of an ~9Mbp XY sex-determination region on LG1 in O. niloticus, and a large (~50Mbp) WZ sex-determination region on LG3 in the related species O. aureus.