Genomic signatures of lineage-specific structural variants in the <i>Pan</i> genus

Abstract Background Structural variants (SVs; ≥ 50 bp) represent a major source of genomic variation and are more likely to influence gene function and phenotypes than small-scale insertions/deletions or single nucleotide variants. Although, many studies have characterized SVs in humans and non-human primates, lineage-specific SVs within the Pan genus remain underexplored. The only species in this genus, chimpanzee (Pan troglodytes) and bonobo (Pan paniscus), exhibit lineage-specific differences for several behavioral and physiological traits. Aim In current study, we sought to identify and characterize lineage-specific structural variants (LSSVs) in the Pan genus using high-quality genome assemblies, thereby providing novel insights into their lineage-specific emergence and potential functional impacts. Methods We detected LSSVs using an assembly-comparison approach that leveraged high-quality genome assemblies of chimpanzee, bonobo, and human. We then mapped their genome-wide distributions and conducted functional enrichment analyses of genes impacted by these variants. Results We observed substantial variation in SV abundance between the two sister species, with the chimpanzee assembly exhibiting nearly a four-fold higher SV count compared with the bonobo lineage. Genome-wide SV distribution maps revealed distinct genomic regions abundant or depleted in SVs, highlighting a marked difference in LSSV distribution across diverse genomic landscapes. Functional enrichment analysis of LSSV-impacted genes highlighted many genes related to body growth, brain function, and neurological disorders in the bonobo lineage, whereas metabolism and transcriptional regulation showed enrichment in the chimpanzee lineage. Additionally, a small subset of the SV-affected genes also corresponded to distinctive behavioral differences between the two lineages, suggesting a potential role in shaping the lineage-specific traits present within the Pan genus.