title: De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions.
abstract: BACKGROUND
  The phytoflagellated protozoan, Euglena gracilis, has been proposed as an attractive feedstock for the accumulation of valuable compounds such as β-1,3-glucan, also known as paramylon, and wax esters. The production of wax esters proceeds under anaerobic conditions, designated as wax ester fermentation. In spite of the importance and usefulness of Euglena, the genome and transcriptome data are currently unavailable, though another research group has recently published E.gracilis transcriptome study during our submission. We herein performed an RNA-Seq analysis to provide a comprehensive sequence resource and some insights into the regulation of genes including wax ester metabolism by comparative transcriptome analysis of E.gracilis under aerobic and anaerobic conditions.
  
  
  RESULTS
  The E.gracilis transcriptome analysis was performed using the Illumina platform and yielded 90.3 million reads after the filtering steps. A total of 49,826 components were assembled and identified as a reference sequence of E.gracilis, of which 26,479 sequences were considered to be potentially expressed (having FPKM value of greater than 1). Approximately half of all components were estimated to be regulated in a trans-splicing manner, with the addition of protruding spliced leader sequences. Nearly 40 % of 26,479 sequences were annotated by similarity to Swiss-Prot database using the BLASTX program. A total of 2080 transcripts were identified as differentially expressed genes (DEGs) in response to anaerobic treatment for 24 h. A comprehensive pathway enrichment analysis using the KEGG pathway revealed that the majority of DEGs were involved in photosynthesis, nucleotide metabolism, oxidative phosphorylation, fatty acid metabolism. We successfully identified a candidate gene set of paramylon and wax esters, including novel β-1,3-glucan and wax ester synthases. A comparative expression analysis of aerobic- and anaerobic-treated E.gracilis cells indicated that gene expression changes in these components were not extensive or dynamic during the anaerobic treatment.
  
  
  CONCLUSIONS
  The RNA-Seq analysis provided comprehensive transcriptome information on E.gracilis for the first time, and this information will advance our understanding of this unique organism. The comprehensive analysis indicated that paramylon and wax ester metabolic pathways are regulated at post-transcriptional rather than the transcriptional level in response to anaerobic conditions.
authors.affiliation: Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan. freedomandfavor@gmail.com.|Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, 252-0882, Japan. freedomandfavor@gmail.com.
authors.forename: Yuta
authors.initials: Y
authors.lastname: Yoshida
authors.affiliation: Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, 1060 Nishikawatsu, Matsue, Shimane, 690-8504, Japan. takaratommy@gmail.com.|Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo, 102-0076, Japan. takaratommy@gmail.com.
authors.forename: Takuya
authors.initials: T
authors.lastname: Tomiyama
authors.affiliation: Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, 1060 Nishikawatsu, Matsue, Shimane, 690-8504, Japan. maruta@life.shimane-u.ac.jp.|Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo, 102-0076, Japan. maruta@life.shimane-u.ac.jp.
authors.forename: Takanori
authors.initials: T
authors.lastname: Maruta
authors.affiliation: Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan. mt@sfc.keio.ac.jp.|Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, 252-0882, Japan. mt@sfc.keio.ac.jp.
authors.forename: Masaru
authors.initials: M
authors.lastname: Tomita
authors.affiliation: Department of Life Science and Biotechnology, Faculty of Life and Environmental Science, Shimane University, 1060 Nishikawatsu, Matsue, Shimane, 690-8504, Japan. ishikawa@life.shimane-u.ac.jp.|Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo, 102-0076, Japan. ishikawa@life.shimane-u.ac.jp.
authors.forename: Takahiro
authors.initials: T
authors.lastname: Ishikawa
authors.affiliation: Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan. gaou@sfc.keio.ac.jp.|Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, 252-0882, Japan. gaou@sfc.keio.ac.jp.
authors.forename: Kazuharu
authors.initials: K
authors.lastname: Arakawa
mesh_terms: D005056:Euglena gracilis / Q000235:genetics* / Q000378:metabolism; D005936:Glucans / Q000378:metabolism; D050356:Lipid Metabolism / Q000235:genetics*; D058977:Molecular Sequence Annotation; D012326:RNA Splicing; D016053:RNA, Protozoan / Q000235:genetics; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D014885:Waxes / Q000378:metabolism
chemical_list: D005936:Glucans; D016053:RNA, Protozoan; D014885:Waxes; C003045:paramylon