Next Article in Journal
Inherited Renal Tubulopathies—Challenges and Controversies
Next Article in Special Issue
Evolution of the Human Chromosome 13 Synteny: Evolutionary Rearrangements, Plasticity, Human Disease Genes and Cancer Breakpoints
Previous Article in Journal
High Contiguity de novo Genome Sequence Assembly of Trifoliate Yam (Dioscorea dumetorum) Using Long Read Sequencing
Previous Article in Special Issue
Evolutionary Dynamics of the POTE Gene Family in Human and Nonhuman Primates
Open AccessArticle

Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing

1
Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, Davis, CA 95616, USA
2
Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA 95616, USA
3
UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
4
DNA Technologies Sequencing Core Facility, University of California, Davis, CA 95616, USA
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Genes 2020, 11(3), 276; https://doi.org/10.3390/genes11030276
Received: 8 February 2020 / Revised: 29 February 2020 / Accepted: 29 February 2020 / Published: 4 March 2020
(This article belongs to the Special Issue A Tale of Genes and Genomes)
Recent efforts to comprehensively characterize great ape genetic diversity using short-read sequencing and single-nucleotide variants have led to important discoveries related to selection within species, demographic history, and lineage-specific traits. Structural variants (SVs), including deletions and inversions, comprise a larger proportion of genetic differences between and within species, making them an important yet understudied source of trait divergence. Here, we used a combination of long-read and -range sequencing approaches to characterize the structural variant landscape of two additional Pan troglodytes verus individuals, one of whom carries 13% admixture from Pan troglodytes troglodytes. We performed optical mapping of both individuals followed by nanopore sequencing of one individual. Filtering for larger variants (>10 kbp) and combined with genotyping of SVs using short-read data from the Great Ape Genome Project, we identified 425 deletions and 59 inversions, of which 88 and 36, respectively, were novel. Compared with gene expression in humans, we found a significant enrichment of chimpanzee genes with differential expression in lymphoblastoid cell lines and induced pluripotent stem cells, both within deletions and near inversion breakpoints. We examined chromatin-conformation maps from human and chimpanzee using these same cell types and observed alterations in genomic interactions at SV breakpoints. Finally, we focused on 56 genes impacted by SVs in >90% of chimpanzees and absent in humans and gorillas, which may contribute to chimpanzee-specific features. Sequencing a greater set of individuals from diverse subspecies will be critical to establish the complete landscape of genetic variation in chimpanzees. View Full-Text
Keywords: structural variation; comparative genomics; chimpanzee; nanopore sequencing; optical mapping; chromatin organization; gene regulation; natural selection structural variation; comparative genomics; chimpanzee; nanopore sequencing; optical mapping; chromatin organization; gene regulation; natural selection
Show Figures

Figure 1

MDPI and ACS Style

Soto, D.C.; Shew, C.; Mastoras, M.; Schmidt, J.M.; Sahasrabudhe, R.; Kaya, G.; Andrés, A.M.; Dennis, M.Y. Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing. Genes 2020, 11, 276.

Show more citation formats Show less citations formats
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Search more from Scilit
 
Search
Back to TopTop