A high-resolution map of small-scale inversions in the gibbon genome
- Ludovica Mercuri1,
- Donato Palmisano1,
- Alberto L'Abbate2,
- Pietro D'Addabbo1,
- Francesco Montinaro3,
- Claudia Rita Catacchio1,
- Patrick Hasenfeld4,
- Mario Ventura1,
- Jan O. Korbel4,
- Ashley D. Sanders5,
- Flavia Angela Maria Maggiolini6 and
- Francesca Antonacci1,7
- 1 Universita' degli Studi di Bari Aldo Moro;
- 2 IBIOM, Institute of Biomembranes and Bioenergetics;
- 3 Universita' degli Studi di Bari Aldo Moro, Estonian Biocentre, Institute of Genomics, University of Tartu;
- 4 European Molecular Biology Laboratory (EMBL);
- 5 Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine in the Helmholtz Association, Berlin Institute of Health (BIH), Charite-Universitatsmedizin Berlin;
- 6 Universita' degli Studi di Bari Aldo Moro, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-Centro di Ricerca Viticoltura ed Enologia (CREA-VE)
Abstract
Gibbons are the most speciose family of living apes, characterized by a strikingly 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 5-fold higher than shown for other primate lineage specific inversions, with a significant 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. LINE1) 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 over 49 megabases of DNA. Finally, we provide a list of 182 candidate genes potentially involved in gibbons diversification and speciation.
- Received May 24, 2022.
- Accepted September 20, 2022.
- Published by Cold Spring Harbor Laboratory Press
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