ArticleGigaScience2019
Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes.
Article in GigaScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed, 117 citations in OpenAlex.
- Near-complete genomes for nine haplochromine cichlid fishes reveal a novel centromeric satellite structure organised around a pair of inverted elements.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2026Article
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- Same Sex Chromosomes With Independent Origins in Haplochromine Cichlids.Genome biology and evolution · 2026Article
- A T2T Genome of the Lobed-Lip Iguazu Joana (Crenicichla tuca) Reveals Intrachromosomal Rearrangements and Trans-species Polymorphism in Cichlid Fishes.Genome biology and evolution · 2026Article
- Chromosome-level genome assembly of Trichiurus japonicus resolves species boundaries and evolutionary history of cutlassfishes in Northwest Pacific.BMC genomics · 2026Article
- A comparative brain atlas in the Mexican cavefish identifies widespread changes in cellular composition and gene expression.bioRxiv : the preprint server for biology · 2026Article
- Before the East African Radiation: Sex Chromosome Systems in Basal Haplotilapiine Cichlids.Genome biology and evolution · 2026Article
- Article
- A Chromosome Inversion Creates a Supergene for Sex and Colour in Lake Malawi Cichlids.Molecular ecology · 2025Article
- Rapid Divergence of Visual Systems and Signaling Traits to Contrasting Light Regimes During Early Speciation of African Crater Lake Cichlid Fish.Molecular biology and evolution · 2025Article
- Article
- Introgression dynamics of sex-linked chromosomal inversions shape the Malawi cichlid radiation.Science (New York, N.Y.) · 2025Article
- Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements.Genome research · 2025Article
- Large inversions in Lake Malawi cichlids are associated with habitat preference, lineage, and sex determination.bioRxiv : the preprint server for biology · 2025Article
- Article
- Diversity of Sex Chromosomes in Vertebrates: Six Novel Sex Chromosomes in Basal Haplochromines (Teleostei: Cichlidae).Genome biology and evolution · 2024Article
- Ancient and Recent Hybridization in the Oreochromis Cichlid Fishes.Molecular biology and evolution · 2024Article
- Spatially resolved cell atlas of the teleost telencephalon and deep homology of the vertebrate forebrain.Communications biology · 2024Article
- Turnover of sex chromosomes in the Lake Tanganyika cichlid tribe Tropheini (Teleostei: Cichlidae).Scientific reports · 2024Article
- Article
2 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundAfrican cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome-scale genome assemblies to elucidate the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages.
resultsWe re-anchored our recent assembly of the Nile tilapia (Oreochromis niloticus) genome using a new high-density genetic map. We also developed a new de novo genome assembly of the Lake Malawi cichlid, Metriaclima zebra, using high-coverage Pacific Biosciences sequencing, and anchored contigs to linkage groups (LGs) using 4 different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes. Large intra-chromosomal structural differences (∼2-28 megabase pairs) among species are common, while inter-chromosomal differences are rare (<10 megabase pairs total). Placement of the centromeres within the chromosome-scale assemblies identifies large structural differences that explain many of the karyotype differences among species. Structural differences are also associated with unique patterns of recombination on sex chromosomes. Structural differences on LG9, LG11, and LG20 are associated with reduced recombination, indicative of inversions between the rock- and sand-dwelling clades of Lake Malawi cichlids. M. zebra has a larger number of recent transposable element insertions compared with O. niloticus, suggesting that several transposable element families have a higher rate of insertion in the haplochromine cichlid lineage.
conclusionThis study identifies novel structural variation among East African cichlid genomes and provides a new set of genomic resources to support research on the mechanisms driving cichlid adaptation and speciation.
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