Abstract Yellow starthistle ( Centaurea solstitialis ) is a highly invasive species that has been a model system for the potential contribution of evolution to invader traits. Here, we report the construction of a chromosome-scale reference genome for C. solstitialis using a combination of PacBio HiFi and Dovetail Omni-C technologies, and functional gene annotation with RNAseq. We validate the reference genome using a restriction site-associated DNA (RAD)-based genetic map from an F2 mapping population. We find that syntenic comparisons to other taxa in the Asteraceae reveal a chromosomal fusion in the lineage of C. solstitialis , and widespread fission in globe artichoke ( Cynara cardunculus ). Using a QTL analysis from the mapping population (derived from a cross between native and invading parents) we identify 13 QTL underpinning size traits that are associated with adaptation in the invaded range, including a putative large-scale chromosomal inversion that has a pleiotropic and overdominant effect on key invader traits.

Chromosome-scale reference genome and RAD-based genetic map of yellow starthistle (<i>Centaurea solstitialis</i>) reveal putative structural variation and QTLs associated with invader traits

Chromosome-scale reference genome and RAD-based genetic map of yellow starthistle (Centaurea solstitialis) reveal putative structural variation and QTLs associated with invader traits