Supporting data for "Exploring polymorphic interspecies structural variants in Eucalyptus: Unravelling Their Role in Reproductive Isolation and Adaptive Divergence."

Structural variants (SVs) play a significant role in speciation and adaptation in many species, yet few studies have explored the prevalence and impact of different categories of SVs. We conducted a comparative analysis of long-read assembled reference genomes of closely related <i>Eucalyptus</i> species to identify candidate SVs potentially influencing speciation and adaptation. Interspecies SVs can be either fixed differences, or polymorphic in one or both species. To describe SV patterns, we employed short-read whole-genome sequencing on over 600 individuals of <i>E. melliodora</i> and <i>E. sideroxylon</i>, along with recent high quality genome assemblies. We aligned reads and genotyped interspecies SVs predicted between species reference genomes. Our results revealed that 49,756 of 58,025 and 39,536 of 47,064 interspecies SVs could be typed with short reads, in <i>E. melliodora</i> and <i>E. sideroxylon</i> respectively. Focusing on inversions and translocations, symmetric SVs which are readily genotyped within both populations, 24 were found to be structural divergences, 2,623 structural polymorphisms, and 928 shared structural polymorphisms. We assessed the functional significance of fixed interspecies SVs by examining differences in estimated recombination rates and genetic differentiation between species, revealing a complex history of natural selection. Shared structural polymorphisms displayed enrichment of potentially adaptive genes. Understanding how different classes of genetic mutations contribute to genetic diversity and reproductive barriers is essential for understanding how organisms enhance fitness, adapt to changing environments, and diversify. Our findings reveal the prevalence of interspecies SVs and elucidate their role in genetic differentiation, adaptive evolution, and species divergence within and between populations.