A reference genome and transcriptome of haustorial development in Pedicularis groenlandica reveal diverse trajectories of haustoria-associated gene evolution in parasitic plants

O_LINovel traits frequently evolve by co-opting existing genetic pathways through direct repurposing of existing genes or neofunctionalization of duplicated genes. Parasitism represents a major innovation in plants, where a novel organ--the haustorium--evolved to penetrate hosts and extract water and nutrients. Previous studies hypothesized that haustoria-associated genes primarily evolve from root and pollen-associated pathways. C_LIO_LITo examine evolutionary trajectories of haustoria-associated genes, we generated a chromosome-scale genome of Pedicularis groenlandica (Orobanchaceae) and sampled transcriptomes throughout haustorial development. We examined differential expression of haustoria-associated genes and their paralogs and investigated orthology among haustoria-associated genes in five parasitic plants. C_LIO_LIWe identified 5,635 haustoria-associated genes in P. groenlandica, of which a greater proportion were associated with pollen tubes (67%) than roots (33%), evidenced by being differentially expressed in pollen tubes, nested within pollen tube-associated gene families, or both. Haustoria-associated genes with paralogs that arose after the evolution of parasitism in Orobanchaceae are more likely to be uniquely expressed in haustoria, consistent with neofunctionalization. C_LIO_LIOur results support both pleiotropy and neofunctionalization as mechanisms by which genetic pathways are co-opted for haustorial function. Haustoria-associated genes are highly lineage-specific, highlighting a dynamic and ongoing process of haustorial co-option of genes among parasitic plant lineages. C_LI