Soto, Daniela C;
Shew, Colin;
Mastoras, Mira;
Schmidt, Joshua M;
Sahasrabudhe, Ruta;
Kaya, Gulhan;
Andrés, Aida M;
(2020)
Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing.
Genes
, 11
(3)
, Article 276. 10.3390/genes11030276.
Preview |
Text
Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing. .pdf - Published Version Download (1MB) | Preview |
Abstract
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.
| Type: | Article |
|---|---|
| Title: | Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing |
| Location: | Switzerland |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.3390/genes11030276 |
| Publisher version: | https://doi.org/10.3390/genes11030276 |
| Language: | English |
| Additional information: | Copyright © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license, (http://creativecommons.org/licenses/by/4.0/). |
| Keywords: | Structural variation; comparative genomics; chimpanzee; nanopore sequencing; optical mapping; chromatin organization; gene regulation; natural selection |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10176937 |
Archive Staff Only
 |
View Item |
