Utilizing a comparative approach to assess genome evolution during diploidization in Artemisia tridentata, a keystone species of western North America

Abstract Premise Polyploidization is often followed by diploidization. Diploidization is generally studied using synthetic polyploid lines and/or crop plants, but rarely using extant diploids or nonmodel plants such as Artemisia tridentata . This threatened western North American keystone species has a large genome compared to congeneric Artemisia species; dominated by diploid and tetraploid cytotypes, with multiple origins of tetraploids with genome size reduction. Methods The genome of an A. tridentata sample was resequenced to study genome evolution and compared to that of A. annua , a diploid congener. Three diploid genomes of A. tridentata were compared to test for multiple diploidization events. Results The A. tridentata genome had many chromosomal rearrangements relative to that of A. annua , while large‐scale synteny of A. tridentata chromosome 3 and A. annua chromosome 4 was conserved. The three A. tridentata genomes had similar sizes (4.19–4.2 Gbp), heterozygosity (2.24–2.25%), and sequence (98.73–99.15% similarity) across scaffolds, and in k ‐mer analyses, similar patterns of diploid heterozygous k ‐mers (AB = 41%, 47%, and 47%), triploid heterozygous k ‐mers (AAB = 18–21%), and tetraploid k ‐mers (AABB = 13–17%). Biallelic SNPs were evenly distributed across scaffolds for all individuals. Comparisons of transposable element (TE) content revealed differential enrichment of TE clades. Conclusions Our findings suggest population‐level TE differentiation after a shared polyploidization‐to‐diploidization event(s) and exemplify the complex processes of genome evolution. This research approached provides new resources for exploration of abiotic stress response, especially the roles of TEs in response pathways.