Hämälä T, Wafula EK, Guiltinan MJ, Ralph PE, dePamphilis CW, Tiffin P.

Proc Natl Acad Sci U S A. 2021 Aug 31;118(35):e2102914118. doi:10.1073/pnas.2102914118

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

31 × 2 haplotype assemblies using Illumina and 10x Genomics linked reads. dN/dS (interspecies) and πN/πS (intraspecies) values in SVs are higher than expectation and vary according the type of SV and the proximity to the SV's breakpoints. Genes with allele-specific expression were over-represented at heterozygous inversions. Genetic load is higher at inversions, as expected if they suppress recombination.