Genomic structural variants constrain and facilitate adaptation in natural populations of Theobroma cacao , the chocolate tree

Significance Genomic structural variants (SVs) are frequent contributors to adaptation and speciation, but our understanding of their overall fitness consequences is limited, with data and analyses primarily available for humans and short-lived domesticated species. Here, we use 31 high-quality genome assemblies to study the evolutionary impact of SVs among natural populations of Theobroma cacao . We find that most SVs are deleterious and thus constrain adaptation. These detrimental effects likely arise as a direct result of impaired gene function and as an indirect result of suppressed recombination. Yet we detect several SVs that may contribute to local adaptation mainly through traits involved in pathogen resistance. Overall, we provide important insight into processes underlying the fitness effects of SVs in natural populations.