Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah1,2,
- Miguel Vasconcelos Almeida1,
- Moritz Blumer2,
- Chengwei Ulrika Yuan1,2,
- Bettina Fischer2,
- Kirsten See1,
- Ben Jackson2,
- Richard Zatha3,
- Bosco Rusuwa3,
- George F. Turner4,
- M. Emília Santos5,
- Hannes Svardal6,
- Martin Hemberg7,
- Richard Durbin2 and
- Eric Miska1,2
- 1Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom;
- 2Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom;
- 3Department of Biological Sciences, University of Malawi, P.O. Box 280, Zomba, Malawi;
- 4School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2TH, United Kingdom;
- 5Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom;
- 6Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium;
- 7The Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
Abstract
Pangenome methods have the potential to uncover hitherto undiscovered sequences missing from established reference genomes, making them useful to study evolutionary and speciation processes in diverse organisms. The cichlid fishes of the East African Rift Lakes represent one of nature's most phenotypically diverse vertebrate radiations, but single-nucleotide polymorphism (SNP)–based studies have revealed little sequence difference, with 0.1%–0.25% pairwise divergence between Lake Malawi species. These were based on aligning short reads to a single linear reference genome and ignored the contribution of larger-scale structural variants (SVs). We constructed a pangenome graph that integrates six new and two existing long-read genome assemblies of Lake Malawi haplochromine cichlids. This graph intuitively represents complex and nested variation between the genomes and reveals that the SV landscape is dominated by large insertions, many exclusive to individual assemblies. The graph incorporates a substantial amount of extra sequence across seven species, the total size of which is 33.1% longer than that of a single cichlid genome. Approximately 4.73% to 9.86% of the assembly lengths are estimated as interspecies structural variation between cichlids, suggesting substantial genomic diversity underappreciated in SNP studies. Although coding regions remain highly conserved, our analysis uncovers a significant proportion of SV sequences as transposable element (TE) insertions, especially DNA, LINE, and LTR TEs. These findings underscore that the cichlid genome is shaped both by small-nucleotide mutations and large, TE-derived sequence alterations, both of which merit study to understand their interplay in cichlid evolution.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.279674.124.
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Freely available online through the Genome Research Open Access option.
- Received June 16, 2024.
- Accepted February 6, 2025.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
