| description |
The genus Cuscuta is a group of parasitic plants that are distributedworld-wide. The process of parasitization starts with a Cuscuta plantcoiling around the host stem, and then haustorial organs establish apermanent vascular connection allowing for access to the phloem content. Thehost and the parasite form new cellular connections, suggesting coordinationof developmental and biochemical processes. Simultaneous monitoring of geneexpression in the parasite’s and host’s tissues may shed light on thecomplex events occurring between the parasitic and host cells and may helpto overcome experimental limitation (i.e. how to separate host tissue fromCuscuta tissue at the haustorial connection). An alternative approach is touse bioinformatic analysis to classify sequencing reads as either belongingto the host or to the parasite and to characterize the expression patterns.Owing to the lack of a comprehensive genomic dataset from Cuscuta spp., sucha classification has not been performed previously. We first performed dissection of RNA-Seq reads from an interface regionbetween a non-model parasitic plant and a non-model host plant, Cuscutajaponica and Impatiens balsamina. Without established reference sequences,we classified reads into either of the plants by stepwise similarity searchagainst de novo assembled transcript set of themselves, unigene sets of thesame genus, and cDNA sequences of the same family, and then assembled denovo transcriptomes. We assessed the quality of the classification bymapping a given read to contigs of both plants, achieving amisclassification rate low enough (0.22-0.39%) to be used reliably for theanalysis of differential gene expression. We then applied the readdissection method to RNA-Seq data from the interface between a non-modelparasitic plant and a model host plant, C. japonica and Glycine max.Analysis of gene expression profiles at 5 parasitizing stages revealeddifferentially expressed genes from both C. japonica and G. max, anduncovered coordination of cellular processes between the two plants. We demonstrated that reliable identification of differentially expressedtranscripts in undissected interface region of the parasite-host associationis feasible and informative with respect to differential-expressionpatterns. |