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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.    Conclusion  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.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-2540-6) contains supplementary material, which is available to authorized users.

De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions