title: A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads.
abstract: BACKGROUND
  The genus Cuscuta is a group of parasitic plants that are distributed world-wide. The process of parasitization starts with a Cuscuta plant coiling around the host stem. The parasite's haustorial organs then establish a vascular connection allowing for access to the phloem content. The host and the parasite form new cellular connections, suggesting coordination of developmental and biochemical processes. Simultaneous monitoring of gene expression in the parasite's and host's tissues may shed light on the complex events occurring between the parasitic and host cells and may help to overcome experimental limitations (i.e. how to separate host tissue from Cuscuta tissue at the haustorial connection). A novel approach is to use bioinformatic analysis to classify sequencing reads as either belonging to the host or to the parasite and to characterize the expression patterns. Owing to the lack of a comprehensive genomic dataset from Cuscuta spp., such a classification has not been performed previously.
  
  
  RESULTS
  We first classified RNA-Seq reads from an interface region between the non-model parasitic plant Cuscuta japonica and the non-model host plant Impatiens balsamina. Without established reference sequences, we classified reads as originating from either of the plants by stepwise similarity search against de novo assembled transcript sets of C. japonica and I. balsamina, unigene sets of the same genus, and cDNA sequences of the same family. We then assembled de novo transcriptomes from the classified read sets. We assessed the quality of the classification by mapping reads to contigs of both plants, achieving a misclassification rate low enough (0.22-0.39%) to be used reliably for differential gene expression analysis. Finally, we applied our read classification method to RNA-Seq data from the interface between the non-model parasitic plant C. japonica and the model host plant Glycine max. Analysis of gene expression profiles at 5 parasitizing stages revealed differentially expressed genes from both C. japonica and G. max, and uncovered the coordination of cellular processes between the two plants.
  
  
  CONCLUSIONS
  We demonstrated that reliable identification of differentially expressed transcripts in undissected interface region of the parasite-host association is feasible and informative with respect to differential-expression patterns.
authors.affiliation: Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-Cho, Naka-Ku, Sakai, Osaka, 599-8531 Japan.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Ikeue
authors.affiliation: Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Potsdam-Golm, Am Mühlenberg 1, Potsdam, 14476 Germany ; Present Address: Bioinformatics Group, The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH UK.
authors.forename: Christian
authors.initials: C
authors.lastname: Schudoma
authors.affiliation: Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Potsdam-Golm, Am Mühlenberg 1, Potsdam, 14476 Germany.
authors.forename: Wenna
authors.initials: W
authors.lastname: Zhang
authors.affiliation: Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-Cho, Naka-Ku, Sakai, Osaka, 599-8531 Japan.
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Ogata
authors.affiliation: Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, 630-0192 Japan.
authors.forename: Tomoaki
authors.initials: T
authors.lastname: Sakamoto
authors.affiliation: Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology (NAIST), 8916-5 Takayama, Ikoma, 630-0192 Japan.
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Kurata
authors.affiliation: Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science (CSRC), 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045 Japan ; Present Address: Department of Molecular Systems Biology (Ecogenomics and Systems Biology), Vienna University, Althanstraße 14, Vienna, A-1090 Austria.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Furuhashi
authors.affiliation: Max Planck Institute of Molecular Plant Physiology, Wissenschaftspark Potsdam-Golm, Am Mühlenberg 1, Potsdam, 14476 Germany.
authors.forename: Friedrich
authors.initials: F
authors.lastname: Kragler
authors.affiliation: Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-Cho, Naka-Ku, Sakai, Osaka, 599-8531 Japan.
authors.forename: Koh
authors.initials: K
authors.lastname: Aoki
keywords: Classification; Cuscuta japonica; Cuscuta reflexa; Parasite-host interaction; Parasitic plant; Transcriptome