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

Area of Science:

• Genomics
• Evolutionary Biology
• Comparative Genomics

Background:

• Great ape genetic diversity studies often focus on single-nucleotide variants, overlooking structural variants (SVs).
• SVs, such as deletions and inversions, represent a significant source of genetic differences and trait divergence between and within species.
• Understanding SVs is crucial for a comprehensive view of great ape evolution and unique characteristics.

Purpose of the Study:

• To characterize the structural variant landscape in *Pan troglodytes verus* using advanced sequencing techniques.
• To identify novel deletions and inversions and assess their impact on gene expression and genomic interactions.
• To pinpoint genes affected by SVs that may underlie chimpanzee-specific traits.

Main Methods:

• Employed long-read and long-range sequencing (optical mapping, nanopore sequencing) for SV characterization.
• Integrated short-read data for SV genotyping and identified variants larger than 10 kbp.
• Analyzed gene expression and chromatin conformation data in human and chimpanzee cell lines.

Main Results:

• Identified 425 deletions and 59 inversions, with 88 deletions and 36 inversions being novel.
• Found significant enrichment of differentially expressed chimpanzee genes within deletions and near inversion breakpoints.
• Observed altered genomic interactions at SV breakpoints and identified 56 genes impacted by SVs in most chimpanzees but absent in humans and gorillas.

Conclusions:

• Structural variants play a substantial role in great ape genetic diversity and trait evolution.
• This research provides a deeper understanding of the structural variant landscape in chimpanzees and its functional consequences.
• Further sequencing of diverse chimpanzee subspecies is essential for a complete genetic variation map.