ArticleBMC genomics2017
A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 111 papers.
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Who cites it
111 citing papers in PubMed, 252 citations in OpenAlex.
- Developmental divergence in gene regulation underlies trophic innovation in Lake Victoria cichlids.Proceedings. Biological sciences · 2026Article
- Near telomere-to-telomere genome assembly of the rainbow trout (Oncorhynchus mykiss).Scientific data · 2026Article
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- Ancestral splice variation is a key substrate for rapid diversification in African cichlids.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Sex chromosome identification and genome curation from a single individual with SCINKD.Molecular biology and evolution · 2026Article
- Before the East African Radiation: Sex Chromosome Systems in Basal Haplotilapiine Cichlids.Genome biology and evolution · 2026Article
- Chromosome-level genome assembly of Chirolophis japonicus Herzenstein, 1890 (Stichaeidae, Perciformes).Scientific data · 2026Article
- Divergence at the IRX gene cluster underlies extreme trophic polymorphism in a cichlid fish (Herichthys minckleyi).Communications biology · 2026Article
- Fine mapping and functional annotation of a QTL for resistance to tilapia lake virus in Nile tilapia (Oreochromis niloticus).G3 (Bethesda, Md.) · 2026Article
- Current State of Fish Reference Genome and Pangenome: Methodologies, Sampling Strategies, Quality Assessment and Future Perspectives to Aquaculture Breeding.Marine biotechnology (New York, N.Y.) · 2025Review
- 3D Genome Constrains Breakpoints of Inversions That Can Act as Barriers to Gene Flow in the Stickleback.Molecular ecology · 2025Article
- Haplotype-resolved genomics identifiesiScience · 2025Article
- Intron turnover of slc26a1 and slc26a2 and convergence of intron insertion sites.Scientific reports · 2025Article
- Heat inducible nuclear translocation of Kdm6bb drives temperature dependent sex reversal in Nile tilapia.PLoS genetics · 2025Article
- The origin, evolution, and translocation of sex chromosomes in Silurus catfish mediated by transposons.BMC biology · 2025Article
- Identification of a Novel QTL on LG16 Associated with Acute Salt Tolerance in Red Tilapia (Oreochromis spp.) Using GWAS.Marine biotechnology (New York, N.Y.) · 2025Article
- Towards Reliable Detection of Introgression in the Presence of Among-Species Rate Variation.Systematic biology · 2024Article
- A pheromone receptor in cichlid fish mediates attraction to females but inhibits male parental care.Current biology : CB · 2024Article
- Transcriptomics and gut microbiome analysis of the edible herb Bidens pilosa as a functional feed additive to promote growth and metabolism in tilapia (Oreochromis spp.).BMC genomics · 2024Article
- The regulatory effects of water probiotic supplementation on the blood physiology, reproductive performance, and its related genes in Red Tilapia (Oreochromis niloticus X O. mossambicus).BMC veterinary research · 2024Article
51 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundTilapias 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.
resultsA 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.
conclusionsThis 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.
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