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

Genes
Daniela C SotoMegan Y Dennis

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 deletion...Continue Reading

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Citations

Oct 30, 2020·International Journal of Molecular Sciences·Denisa ŠimoníkováEva Hřibová
Dec 16, 2020·Bioinformatics·Alaina Shumate, Steven L Salzberg
Jun 3, 2021·Genes·Mario Ventura, Francesca Antonacci
Aug 31, 2021·Frontiers in Genetics·Aisha YousafHua Chen

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Datasets Mentioned

BETA
PRJEB36949
GM20543
AG18359

Methods Mentioned

BETA
genotyping
Hi-C
electrophoresis
Assay
Chip
RNA-seq
Illumina

Software Mentioned

smap
BWA MEM
Juicebox
DAVID
Sniffles
voom
limma
TopDom
ONT
liftOver Browser

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