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Background  Plant parasitism represents an extraordinary interaction among flowering plants: parasitic plants use a specialized organ, the haustorium, to invade the host vascular system to deprive host plants of water and nutrients. Various compounds present in exudates of host plants trigger haustorium development. The two most effective haustorium inducing factors (HIFs) known for the parasitic plant  Triphysaria versicolor  ( T. versicolor ) are peonidin, an antioxidant flavonoid, and 2,6-dimethoxybenzoquinone (DMBQ), an oxidative stress agent. To date, two genes involved in haustorium initiation in  T. versicolor  have been identified:  TvQR1 , a quinone oxidoreductase that generates the active HIF from DMBQ, and  TvPirin , a transcription co-factor that regulates several other DMBQ- responsive and –non-responsive genes. While the expression of these genes in response to DMBQ is well characterized, their expression in response to peonidin is not. In addition, the pattern of polymorphisms in these genes is unknown, even though nucleotide changes in  TvQR1  and  TvPirin  may have contributed to the ability of  T. versicolor  to develop haustoria. To gain insights into these aspects, we investigated their transcriptional responses to HIFs and non-HIF and their natural nucleotide diversity.    Results  Here we show that  TvQR1  and  TvPirin  are transcriptionally upregulated by both DMBQ and peonidin in  T. versicolor  roots. Yet, while  TvQR1  also responded to juglone, a non-HIF quinone with toxicity comparable to that of DMBQ,  TvPirin  did not. We further demonstrate that  TvPirin  encodes a protein shorter than the one previously reported. In the  T. versicolor  natural population of Northern California,  TvQR1  exhibited remarkably higher molecular diversity and more recombination events than  TvPirin , with the highest non-synonymous substitution rate in the substrate recognition and catalytic domain of the TvQR1 protein.    Conclusion  Our results suggest that  TvQR1  and  TvPirin  have most likely evolved highly distinct roles for haustorium formation. Unlike  TvPirin ,  TvQR1  might have been under diversifying selection to maintain a diverse collection of polymorphisms, which might be related to the recognition of an assortment of HIF and non-HIF quinones as substrates for successful haustorial establishment in a wide range of host plants.

The differentially regulated genes TvQR1 and TvPirin of the parasitic plant Triphysaria exhibit distinctive natural allelic diversity