Functional genomics of a generalist parasitic plant: Laser microdissection of host-parasite interface reveals host-specific patterns of parasite gene expression

Abstract

BackgroundOrobanchaceae is the only plant family with members representing the full range of parasitic lifestyles plus a free-living lineage sister to all parasitic lineages, Lindenbergia. A generalist member of this family, and an important parasitic plant model, Triphysaria versicolor regularly feeds upon a wide range of host plants. Here, we compare de novo assembled transcriptomes generated from laser micro-dissected tissues at the host-parasite interface to uncover details of the largely uncharacterized interaction between parasitic plants and their hosts.ResultsThe interaction of Triphysaria with the distantly related hosts Zea mays and Medicago truncatula reveals dramatic host-specific gene expression patterns. Relative to above ground tissues, gene families are disproportionally represented at the interface including enrichment for transcription factors and genes of unknown function. Quantitative Real-Time PCR of a T. versicolor β-expansin shows strong differential (120x) upregulation in response to the monocot host Z. mays; a result that is concordant with our read count estimates. Pathogenesis-related proteins, other cell wall modifying enzymes, and orthologs of genes with unknown function (annotated as such in sequenced plant genomes) are among the parasite genes highly expressed by T. versicolor at the parasite-host interface.ConclusionsLaser capture microdissection makes it possible to sample the small region of cells at the epicenter of parasite host interactions. The results of our analysis suggest that T. versicolor’s generalist strategy involves a reliance on overlapping but distinct gene sets, depending upon the host plant it is parasitizing. The massive upregulation of a T. versicolor β-expansin is suggestive of a mechanism for parasite success on grass hosts. In this preliminary study of the interface transcriptomes, we have shown that T. versicolor, and the Orobanchaceae in general, provide excellent opportunities for the characterization of plant genes with unknown functions.

Local Auxin Biosynthesis Mediated by a YUCCA Flavin Monooxygenase Regulates Haustorium Development in the Parasitic Plant Phtheirospermum japonicum

“…Interestingly, the earliest expression modulation occurs with genes related to calmodulin binding and oxidoreductase activity ( Figure 2C), suggesting that calcium and reactive oxygen species (ROS)-related signaling may be triggered in the early stage of development. Indeed, the involvement of ROS in haustorium initiation signaling has been proposed (Kim et al, 1998;Ngo et al, 2013;Matvienko et al, 2001aMatvienko et al, , 2001bHonaas et al, 2013;Bandaranayake et al, 2010;Yang et al, 2015). Consistent with other published studies, our analysis identified homologous genes, which were previously identified as DMBQ-responsive genes in T. versicolor, such as QR2 and Pirin, that are upregulated after DMBQ treatment in P. japonicum, suggesting that gene expression profiles are conserved among Orobanchaceae species during haustorium formation.…”

Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation

“…We thus took these factors into account in our pipeline and carefully evaluated each potential HGT candidate with additional data to identify and reduce potential sources of error. We focus on potentially functional genes acquired by parasitic plants by concentrating our search on extensive transcriptome evidence for members of Orobanchaceae grown on host plants with known genome sequences (30,32,33); in addition to greatly improving the accuracy of HGT identification, it offers the opportunity to identify the expression patterns associated with genes derived from HGT events (28).…”

De Novo Assembly and Characterization of the Transcriptome of the Parasitic Weed Dodder Identifies Genes Associated with Plant Parasitism

“…Genes associated with stress responses were also found to be up-regulated in roots of a root parasite after contact with a host plant (Torres et al, 2005;Honaas et al, 2013). Thus, it can be hypothesized that parasitic plants recruit defense-related genes for host recognition.…”

“…Expansin cell wall modulators were identified as core regulators of parasitism in the root parasites Striga spp. and T. versicolor (O'Malley and Lynn, 2000;Vaughn, 2002;Honaas et al, 2013). However, expansin regulation of plant parasitism might be a more complex phenomenon in the stem parasite Cuscuta spp., as different genes encoding expansins were represented among both the up-regulated and down-regulated genes.…”

“…Recently, de novo assembly and analysis of transcriptomes of root parasites, belonging to family Orobanchaceae, provided important insight into the process of parasitism, showing the association of photosynthesis-related genes and cell wall-modifying b-expansin in the process of parasitism (Wickett et al, 2011;Honaas et al, 2013). To understand the molecular mechanisms underlying dynamic morphological and functional changes in haustoria development, however, detailed transcriptional profiling along developmental stages of parasitism is necessary.…”