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

Novel 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. To 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. We 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. Our 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.