A high-resolution map of small-scale inversions in the gibbon genome
- Ludovica Mercuri1,
- Donato Palmisano1,
- Alberto L'Abbate2,
- Pietro D'Addabbo1,
- Francesco Montinaro1,3,
- Claudia Rita Catacchio1,
- Patrick Hasenfeld4,
- Mario Ventura1,
- Jan O. Korbel4,
- Ashley D. Sanders5,6,7,
- Flavia Angela Maria Maggiolini1,8 and
- Francesca Antonacci1
- 1Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Bari 70125, Italy;
- 2IBIOM, Institute of Biomembranes, Bioenergetics, and Molecular Biotechnology, Bari 70125, Italy;
- 3Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia;
- 4European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany;
- 5Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115 Berlin, Germany;
- 6Berlin Institute of Health (BIH), 10178 Berlin, Germany;
- 7Charité-Universitätsmedizin, 10117 Berlin, Germany;
- 8Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-Centro di Ricerca Viticoltura ed Enologia (CREA-VE), Turi 70010, Italy
Abstract
Gibbons are the most speciose family of living apes, characterized by a diverse chromosome number and rapid rate of large-scale rearrangements. Here we performed single-cell template strand sequencing (Strand-seq), molecular cytogenetics, and deep in silico analysis of a southern white-cheeked gibbon genome, providing the first comprehensive map of 238 previously hidden small-scale inversions. We determined that more than half are gibbon specific, at least fivefold higher than shown for other primate lineage-specific inversions, with a significantly high number of small heterozygous inversions, suggesting that accelerated evolution of inversions may have played a role in the high sympatric diversity of gibbons. Although the precise mechanisms underlying these inversions are not yet understood, it is clear that segmental duplication–mediated NAHR only accounts for a small fraction of events. Several genomic features, including gene density and repeat (e.g., LINE-1) content, might render these regions more break-prone and susceptible to inversion formation. In the attempt to characterize interspecific variation between southern and northern white-cheeked gibbons, we identify several large assembly errors in the current GGSC Nleu3.0/nomLeu3 reference genome comprising more than 49 megabases of DNA. Finally, we provide a list of 182 candidate genes potentially involved in gibbon diversification and speciation.
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.276960.122.
- Received May 24, 2022.
- Accepted September 20, 2022.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
