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



January 28, 2021

Structural variation, including deletions and inversions, accounts for a large proportion of the genetic differences observed between and within great ape species, making them an important source of trait divergence. We used nanopore sequencing and optical mapping to characterize the structural variant landscape of two Pan troglodytes verus individuals. Filtering for variants >10 kbp, we identified 425 deletions and 59 inversions, of which 88 and 36 were novel. Compared to humans, we found an enrichment of chimpanzee genes differentially expressed both within deletions and near inversion breakpoints, as well as alterations in genomic interactions from chromatin-conformation maps. Finally, we focused on 56 genes impacted by structural variants present in chimpanzees but absent in humans and gorillas, which may contribute to chimpanzee-specific traits.


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