Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee
- Mario Ventura1,2,
- Claudia R. Catacchio1,2,
- Can Alkan1,3,
- Tomas Marques-Bonet1,4,
- Saba Sajjadian1,
- Tina A. Graves5,
- Fereydoun Hormozdiari6,
- Arcadi Navarro4,7,8,
- Maika Malig1,
- Carl Baker1,
- Choli Lee1,
- Emily H. Turner1,
- Lin Chen1,
- Jeffrey M. Kidd1,9,
- Nicoletta Archidiacono2,
- Jay Shendure1,
- Richard K. Wilson5 and
- Evan E. Eichler1,3,10
- 1Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA;
- 2Department of Genetics and Microbiology, University of Bari, Bari 70126, Italy;
- 3Howard Hughes Medical Institute, Seattle, Washington 98195, USA;
- 4IBE, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona 08003, Catalonia, Spain;
- 5Washington University Genome Sequencing Center, School of Medicine, St. Louis, Missouri 63108, USA;
- 6School of Computing Science, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada;
- 7Population Genomics Node (GNV8), National Institute for Bioinformatics (INB), Barcelona 08003, Catalonia, Spain;
- 8Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra, Barcelona 08003, Catalonia, Spain;
- 9Department of Genetics, Stanford University, Stanford, California 94305, USA
Abstract
Structural variation has played an important role in the evolutionary restructuring of human and great ape genomes. Recent analyses have suggested that the genomes of chimpanzee and human have been particularly enriched for this form of genetic variation. Here, we set out to assess the extent of structural variation in the gorilla lineage by generating 10-fold genomic sequence coverage from a western lowland gorilla and integrating these data into a physical and cytogenetic framework of structural variation. We discovered and validated over 7665 structural changes within the gorilla lineage, including sequence resolution of inversions, deletions, duplications, and mobile element insertions. A comparison with human and other ape genomes shows that the gorilla genome has been subjected to the highest rate of segmental duplication. We show that both the gorilla and chimpanzee genomes have experienced independent yet convergent patterns of structural mutation that have not occurred in humans, including the formation of subtelomeric heterochromatic caps, the hyperexpansion of segmental duplications, and bursts of retroviral integrations. Our analysis suggests that the chimpanzee and gorilla genomes are structurally more derived than either orangutan or human genomes.
Footnotes
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↵10 Corresponding author.
E-mail eee{at}gs.washington.edu.
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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 http://www.genome.org/cgi/doi/10.1101/gr.124461.111.
- Received April 7, 2011.
- Accepted June 13, 2011.
- Copyright © 2011 by Cold Spring Harbor Laboratory Press
