Comparative Transcriptome Analyses of Parasitic Plants Reveal Core Parasite Genes and Possible Origin of the Haustorium

Parasitic plants are plants that attach to a host plant from which parasites withdraw nutrients through a modified root structure called the haustorium. Multiple stages of parasite growth and development were studied by a transcriptome sequencing approach in three species of Orobanchaceae. A de novo assembly approach combined the reads into unigenes, whose expression in each stage was determined by read mapping. Differentially expressed (DE) features were identified by DESeq in R, followed by K-means clustering to identify sets of coexpressed genes with abundant expression in haustoria, as well as genes upregulated in response to haustorial inducing factors (HIFs), which we identify as putative “parasitism genes”. DAVID enrichment analysis showed that “parasitism genes” were enriched for proteases with a gene ontology biological process in proteolysis.  Gene family phylogenies of these putative parasite genes showed that most of them derived from gene duplication within the Lamiales order.  Lineage-specific selection processes via a relaxation in purifying selection may be important drivers of parasite evolution. Comparative gene expression analyses revealed from tissue clustering, as well as the gene expression shifts from tomato to parasitic Orobanchaceae, provides evidence for the origin of haustorium primarily as a modified root, but with additional genes co-opted from flowers and other sources.