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McGirr JA, Martin CH. Ecological divergence in sympatry causes gene misexpression in hybrids. Mol Ecol 2020; 29:2707-2721. [PMID: 32557903 DOI: 10.1111/mec.15512] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/21/2020] [Accepted: 06/01/2020] [Indexed: 12/17/2022]
Abstract
Ecological speciation occurs when reproductive isolation evolves as a byproduct of adaptive divergence between populations. Selection favouring gene regulatory divergence between species could result in transgressive levels of gene expression in F1 hybrids that may lower hybrid fitness. We combined 58 resequenced genomes with 124 transcriptomes to identify patterns of hybrid gene misexpression that may be driven by adaptive regulatory divergence within a young radiation of Cyprinodon pupfishes, which consists of a dietary generalist and two trophic specialists-a molluscivore and a scale-eater. We found more differential gene expression between closely related sympatric specialists than between allopatric generalist populations separated by 1,000 km. Intriguingly, 9.6% of genes that were differentially expressed between sympatric species were also misexpressed in F1 hybrids. A subset of these genes were in highly differentiated genomic regions and enriched for functions important for trophic specialization, including head, muscle and brain development. These regions also included genes that showed evidence of hard selective sweeps and were significantly associated with oral jaw length-the most rapidly diversifying skeletal trait in this radiation. Our results indicate that divergent ecological selection in sympatry can contribute to hybrid gene misexpression which may act as a reproductive barrier between nascent species.
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Affiliation(s)
- Joseph A McGirr
- Department of Biology, University of North Carolina, Chapel Hill, NC
| | - Christopher H Martin
- Department of Biology, University of North Carolina, Chapel Hill, NC.,Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA
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Melo US, Schöpflin R, Acuna-Hidalgo R, Mensah MA, Fischer-Zirnsak B, Holtgrewe M, Klever MK, Türkmen S, Heinrich V, Pluym ID, Matoso E, Bernardo de Sousa S, Louro P, Hülsemann W, Cohen M, Dufke A, Latos-Bieleńska A, Vingron M, Kalscheuer V, Quintero-Rivera F, Spielmann M, Mundlos S. Hi-C Identifies Complex Genomic Rearrangements and TAD-Shuffling in Developmental Diseases. Am J Hum Genet 2020; 106:872-884. [PMID: 32470376 PMCID: PMC7273525 DOI: 10.1016/j.ajhg.2020.04.016] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 04/29/2020] [Indexed: 12/15/2022] Open
Abstract
Genome-wide analysis methods, such as array comparative genomic hybridization (CGH) and whole-genome sequencing (WGS), have greatly advanced the identification of structural variants (SVs) in the human genome. However, even with standard high-throughput sequencing techniques, complex rearrangements with multiple breakpoints are often difficult to resolve, and predicting their effects on gene expression and phenotype remains a challenge. Here, we address these problems by using high-throughput chromosome conformation capture (Hi-C) generated from cultured cells of nine individuals with developmental disorders (DDs). Three individuals had previously been identified as harboring duplications at the SOX9 locus and six had been identified with translocations. Hi-C resolved the positions of the duplications and was instructive in interpreting their distinct pathogenic effects, including the formation of new topologically associating domains (neo-TADs). Hi-C was very sensitive in detecting translocations, and it revealed previously unrecognized complex rearrangements at the breakpoints. In several cases, we observed the formation of fused-TADs promoting ectopic enhancer-promoter interactions that were likely to be involved in the disease pathology. In summary, we show that Hi-C is a sensible method for the detection of complex SVs in a clinical setting. The results help interpret the possible pathogenic effects of the SVs in individuals with DDs.
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Affiliation(s)
- Uirá Souto Melo
- Max Planck Institute for Molecular Genetics, RG Development and Disease, 13353 Berlin, Germany; Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Robert Schöpflin
- Max Planck Institute for Molecular Genetics, RG Development and Disease, 13353 Berlin, Germany; Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Rocio Acuna-Hidalgo
- Max Planck Institute for Molecular Genetics, RG Development and Disease, 13353 Berlin, Germany; Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Martin Atta Mensah
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Björn Fischer-Zirnsak
- Max Planck Institute for Molecular Genetics, RG Development and Disease, 13353 Berlin, Germany; Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Manuel Holtgrewe
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Berlin Institute of Health (BIH), Core Unit Bioinformatics, 10117 Berlin, Germany
| | - Marius-Konstantin Klever
- Max Planck Institute for Molecular Genetics, RG Development and Disease, 13353 Berlin, Germany; Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Seval Türkmen
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Verena Heinrich
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, 13353 Berlin, Germany
| | - Ilina Datkhaeva Pluym
- Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Eunice Matoso
- Medical Genetics Unit, Centro Hospitalar e Universitário de Coimbra, 3000-075 Coimbra, Portugal; Center of Investigation on Environment Genetics and Oncobiology (iCBR-CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
| | | | - Pedro Louro
- Medical Genetics Unit, Centro Hospitalar e Universitário de Coimbra, 3000-075 Coimbra, Portugal; Familial Risk Clinic, Instituto Português de Oncologia de Lisboa Francisco Gentil, 1099-023 Lisboa, Portugal; Faculty of Health Sciences, Universidade da Beira Interior, 6201-001 Covilhã, Portugal
| | - Wiebke Hülsemann
- Handchirurgie Kinderkrankenhaus Wilhelmstift, 22149 Hamburg, Germany
| | - Monika Cohen
- kbo-Kinderzentrum München, 81377 München, Germany
| | - Andreas Dufke
- Institut für Medizinische Genetik und Angewandte Genomik, 72076 Tübingen, Germany
| | - Anna Latos-Bieleńska
- Department of Medical Genetics, University of Medical Sciences in Poznan, 60-806 Poznan, Poland; Centers for Medical Genetics GENESIS, Grudzieniec st, 60-601 Poznan, Poland
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, 13353 Berlin, Germany
| | - Vera Kalscheuer
- Max Planck Institute for Molecular Genetics, RG Development and Disease, 13353 Berlin, Germany
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, Human Molecular Genomics Group, 13353 Berlin, Germany; Institut für Humangenetik Lübeck, Universität zu Lübeck, 23538 Lübeck, Germany.
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, RG Development and Disease, 13353 Berlin, Germany; Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, 13353 Berlin, Germany.
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