title: Meta-transcriptomics indicates biotic cross-tolerance in willow trees cultivated on petroleum hydrocarbon contaminated soil.
abstract: BACKGROUND
  High concentrations of petroleum hydrocarbon (PHC) pollution can be hazardous to human health and leave soils incapable of supporting agricultural crops. A cheap solution, which can help restore biodiversity and bring land back to productivity, is cultivation of high biomass yielding willow trees. However, the genetic mechanisms which allow these fast-growing trees to tolerate PHCs are as yet unclear.
  
  
  METHODS
  Salix purpurea 'Fish Creek' trees were pot-grown in soil from a former petroleum refinery, either lacking or enriched with C10-C50 PHCs. De novo assembled transcriptomes were compared between tree organs and impartially annotated without a priori constraint to any organism.
  
  
  RESULTS
  Over 45% of differentially expressed genes originated from foreign organisms, the majority from the two-spotted spidermite, Tetranychus urticae. Over 99% of T. urticae transcripts were differentially expressed with greater abundance in non-contaminated trees. Plant transcripts involved in the polypropanoid pathway, including phenylalanine ammonia-lyase (PAL), had greater expression in contaminated trees whereas most resistance genes showed higher expression in non-contaminated trees.
  
  
  CONCLUSIONS
  The impartial approach to annotation of the de novo transcriptomes, allowing for the possibility for multiple species identification, was essential for interpretation of the crop's response treatment. The meta-transcriptomic pattern of expression suggests a cross-tolerance mechanism whereby abiotic stress resistance systems provide improved biotic resistance. These findings highlight a valuable but complex biotic and abiotic stress response to real-world, multidimensional contamination which could, in part, help explain why crops such as willow can produce uniquely high biomass yields on challenging marginal land.
authors.affiliation: Institut de recherche en biologie végétale, University of Montreal, 4101 Sherbrooke E, Montreal, QC, H1X 2B2, Canada. emmanuel@transcriptomics.org.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Gonzalez
authors.affiliation: Institut de recherche en biologie végétale, University of Montreal, 4101 Sherbrooke E, Montreal, QC, H1X 2B2, Canada. nicholas.brereton@umontreal.ca.
authors.forename: Nicholas J B
authors.initials: NJ
authors.lastname: Brereton
authors.affiliation: Institut de recherche en biologie végétale, University of Montreal, 4101 Sherbrooke E, Montreal, QC, H1X 2B2, Canada. juliemarleau@hotmail.com.
authors.forename: Julie
authors.initials: J
authors.lastname: Marleau
authors.affiliation: Montreal Botanical Gardens, 4101 Sherbrooke E, Montreal, QC, H1X 2B2, Canada. werther.guidi.nissim@gmail.com.
authors.forename: Werther
authors.initials: W
authors.lastname: Guidi Nissim
authors.affiliation: Institut de recherche en biologie végétale, University of Montreal, 4101 Sherbrooke E, Montreal, QC, H1X 2B2, Canada. Michel.labrecque@umontreal.ca.|Montreal Botanical Gardens, 4101 Sherbrooke E, Montreal, QC, H1X 2B2, Canada. Michel.labrecque@umontreal.ca.
authors.forename: Michel
authors.initials: M
authors.lastname: Labrecque
authors.affiliation: Institut de recherche en biologie végétale, University of Montreal, 4101 Sherbrooke E, Montreal, QC, H1X 2B2, Canada. frederic.pitre@umontreal.ca.|Montreal Botanical Gardens, 4101 Sherbrooke E, Montreal, QC, H1X 2B2, Canada. frederic.pitre@umontreal.ca.
authors.forename: Frederic E
authors.initials: FE
authors.lastname: Pitre
authors.affiliation: Institut de recherche en biologie végétale, University of Montreal, 4101 Sherbrooke E, Montreal, QC, H1X 2B2, Canada. simon.joly@umontreal.ca.|Montreal Botanical Gardens, 4101 Sherbrooke E, Montreal, QC, H1X 2B2, Canada. simon.joly@umontreal.ca.
authors.forename: Simon
authors.initials: S
authors.lastname: Joly
mesh_terms: D000222:Adaptation, Physiological / Q000187:drug effects / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects; D060434:Herbivory / Q000187:drug effects / Q000235:genetics; D006838:Hydrocarbons / Q000633:toxicity*; D058977:Molecular Sequence Annotation; D010578:Petroleum / Q000633:toxicity*; D020005:Propanols / Q000378:metabolism; D032108:Salix / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development; D012989:Soil Pollutants / Q000633:toxicity*; D013312:Stress, Physiological / Q000187:drug effects / Q000235:genetics; D059467:Transcriptome / Q000187:drug effects / Q000235:genetics*; D014197:Trees / Q000187:drug effects / Q000235:genetics / Q000254:growth & development
chemical_list: D006838:Hydrocarbons; D010578:Petroleum; D020005:Propanols; D012989:Soil Pollutants; C439395:1-phenylpropanol