A pangenome-based approach reveals genes associated with polyploidy and apomixis in Eragrostis curvula

Eragrostis curvula is a forage grass species in which multiple cytotypes coexist and shifts between sexual and apomictic reproduction are common. This study investigates genetic variation among these cytotypes in relation to ploidy levels and reproductive modes. To this end, a panel of accessions was assembled to capture the species' intraspecific diversity. The panel was used to construct a whole-genome sequencing-based linear pangenome by iteratively mapping Illumina short reads and de novo assembling unmapped reads, thereby expanding the available reference genome and improving the representation of the species' gene pool. The panel and the resulting pangenome were then used for gene content detection, functional annotation, and variant calling. Using this approach, extensive variation in gene content was observed among E. curvula accessions, with polyploid cytotypes containing a higher fraction of newly assembled pangenome sequences than diploids. In addition, candidate genes associated with polyploidization and apomixis were identified. Polyploid-associated genes were mainly associated with cell-cycle regulation and DNA replication, whereas apomixis-associated genes were mainly associated with post-transcriptional regulation. Moreover, phylogenetic relationships among cytotypes were inferred, and allele-frequency distributions revealed ploidy-associated differences among accessions. Thus, this work identified candidate genes associated with polyploidy and apomictic reproduction, highlighting ploidy-associated changes in gene content and post-transcriptional regulatory processes and providing insights into how polyploidization and reproductive shifts have shaped genome evolution in this agamic grass species.