title: Characterization of the watercress (Nasturtium officinale R. Br.; Brassicaceae) transcriptome using RNASeq and identification of candidate genes for important phytonutrient traits linked to human health.
abstract: Consuming watercress is thought to provide health benefits as a consequence of its phytonutrient composition. However, for watercress there are currently limited genetic resources underpinning breeding efforts for either yield or phytonutritional traits. In this paper, we use RNASeq data from twelve watercress accessions to characterize the transcriptome, perform candidate gene mining and conduct differential expression analysis for two key phytonutritional traits: antioxidant (AO) capacity and glucosinolate (GLS) content.
  
  
  
  The watercress transcriptome was assembled to 80,800 transcripts (48,732 unigenes); 71 % of which were annotated based on orthology to Arabidopsis. Differential expression analysis comparing watercress accessions with 'high' and 'low' AO and GLS resulted in 145 and 94 differentially expressed loci for AO capacity and GLS respectively. Differentially expressed loci between high and low AO watercress were significantly enriched for genes involved in plant defence and response to stimuli, in line with the observation that AO are involved in plant stress-response. Differential expression between the high and low GLS watercress identified links to GLS regulation and also novel transcripts warranting further investigation. Additionally, we successfully identified watercress orthologs for Arabidopsis phenylpropanoid, GLS and shikimate biosynthesis pathway genes, and compiled a catalogue of polymorphic markers for future applications.
  
  
  
  Our work describes the first transcriptome of watercress and establishes the foundation for further molecular study by providing valuable resources, including sequence data, annotated transcripts, candidate genes and markers.
authors.affiliation: Centre for Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
authors.forename: Nikol
authors.initials: N
authors.lastname: Voutsina
authors.affiliation: Centre for Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
authors.forename: Adrienne C
authors.initials: AC
authors.lastname: Payne
authors.affiliation: Cell and Molecular Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK.
authors.forename: Robert D
authors.initials: RD
authors.lastname: Hancock
authors.affiliation: Vitacress Salads Ltd, Lower Link Farm, St Mary Bourne, Andover, SP11 6DB, UK.
authors.forename: Graham J J
authors.initials: GJ
authors.lastname: Clarkson
authors.affiliation: Vitacress Salads Ltd, Lower Link Farm, St Mary Bourne, Andover, SP11 6DB, UK.
authors.forename: Steve D
authors.initials: SD
authors.lastname: Rothwell
authors.affiliation: Centre for Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Chapman
authors.affiliation: Centre for Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK. G.Taylor@soton.ac.uk.
authors.forename: Gail
authors.initials: G
authors.lastname: Taylor
mesh_terms: D000975:Antioxidants / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D017343:Genes, Plant; D005961:Glucosinolates / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D058977:Molecular Sequence Annotation; D031223:Nasturtium / Q000737:chemistry / Q000235:genetics*; D010641:Phenotype; D010802:Phylogeny; D064209:Phytochemicals; D010945:Plants, Edible / Q000737:chemistry / Q000235:genetics; D011110:Polymorphism, Genetic; D019655:Quantitative Trait, Heritable; D015398:Signal Transduction; D059467:Transcriptome
chemical_list: D000975:Antioxidants; D005961:Glucosinolates; D064209:Phytochemicals
keywords: Antioxidant capacity; Brassicaceae; Differential expression; Gluconasturtiin; Glucosinolates; Nasturtium officinale; Phenylpropanoid pathway; RNASeq; Watercress; de novo assembly