title: Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes.
abstract: BACKGROUND
  Chrysophytes are protist model species in ecology and ecophysiology and important grazers of bacteria-sized microorganisms and primary producers. However, they have not yet been investigated in detail at the molecular level, and no genomic and only little transcriptomic information is available. Chrysophytes exhibit different trophic modes: while phototrophic chrysophytes perform only photosynthesis, mixotrophs can gain carbon from bacterial food as well as from photosynthesis, and heterotrophs solely feed on bacteria-sized microorganisms. Recent phylogenies and megasystematics demonstrate an immense complexity of eukaryotic diversity with numerous transitions between phototrophic and heterotrophic organisms. The question we aim to answer is how the diverse nutritional strategies, accompanied or brought about by a reduction of the plasmid and size reduction in heterotrophic strains, affect physiology and molecular processes.
  
  
  RESULTS
  We sequenced the mRNA of 18 chrysophyte strains on the Illumina HiSeq platform and analysed the transcriptomes to determine relations between the trophic mode (mixotrophic vs. heterotrophic) and gene expression. We observed an enrichment of genes for photosynthesis, porphyrin and chlorophyll metabolism for phototrophic and mixotrophic strains that can perform photosynthesis. Genes involved in nutrient absorption, environmental information processing and various transporters (e.g., monosaccharide, peptide, lipid transporters) were present or highly expressed only in heterotrophic strains that have to sense, digest and absorb bacterial food. We furthermore present a transcriptome-based alignment-free phylogeny construction approach using transcripts assembled from short reads to determine the evolutionary relationships between the strains and the possible influence of nutritional strategies on the reconstructed phylogeny. We discuss the resulting phylogenies in comparison to those from established approaches based on ribosomal RNA and orthologous genes. Finally, we make functionally annotated reference transcriptomes of each strain available to the community, significantly enhancing publicly available data on Chrysophyceae.
  
  
  CONCLUSIONS
  Our study is the first comprehensive transcriptomic characterisation of a diverse set of Chrysophyceaen strains. In addition, we showcase the possibility of inferring phylogenies from assembled transcriptomes using an alignment-free approach. The raw and functionally annotated data we provide will prove beneficial for further examination of the diversity within this taxon. Our molecular characterisation of different trophic modes presents a first such example.
authors.affiliation: Genome Informatics, University of Duisburg-Essen, Essen, Germany.
authors.forename: Daniela
authors.initials: D
authors.lastname: Beisser
authors.affiliation: Biodiversity, University of Duisburg-Essen, Essen, Germany.|Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany.
authors.forename: Nadine
authors.initials: N
authors.lastname: Graupner
authors.affiliation: Biodiversity, University of Duisburg-Essen, Essen, Germany.|Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany.
authors.forename: Christina
authors.initials: C
authors.lastname: Bock
authors.affiliation: Biodiversity, University of Duisburg-Essen, Essen, Germany.|Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany.
authors.forename: Sabina
authors.initials: S
authors.lastname: Wodniok
authors.affiliation: Biodiversity, University of Duisburg-Essen, Essen, Germany.|Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany.
authors.forename: Lars
authors.initials: L
authors.lastname: Grossmann
authors.affiliation: Theoretical and Applied Biodiversity, Ruhr-University Bochum, Bochum, Germany.
authors.forename: Matthijs
authors.initials: M
authors.lastname: Vos
authors.affiliation: Aquatic Ecology, University of Duisburg-Essen, Essen, Germany.
authors.forename: Bernd
authors.initials: B
authors.lastname: Sures
authors.affiliation: Genome Informatics, University of Duisburg-Essen, Essen, Germany.
authors.forename: Sven
authors.initials: S
authors.lastname: Rahmann
authors.affiliation: Biodiversity, University of Duisburg-Essen, Essen, Germany.|Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany.
authors.forename: Jens
authors.initials: J
authors.lastname: Boenigk
keywords: Alignment-free phylogeny; Chrysophyceae; Differential expression analysis; Molecular phylogeny; Nutritional strategy; Pathway analysis; Protists; RNA-Seq; Transcriptomics