BACKGROUND: Photosynthetic euglenids are major contributors to fresh water ecosystems. Euglena gracilis in particular has noted metabolic flexibility, reflected by an ability to thrive in a range of harsh environments. E. gracilis has been a popular model organism and of considerable biotechnological interest, but the absence of a gene catalogue has hampered both basic research and translational efforts. RESULTS: We report a detailed transcriptome and partial genome for E. gracilis Z1. The nuclear genome is estimated to be around 500 Mb in size, and the transcriptome encodes over 36,000 proteins and the genome possesses less than 1% coding sequence. Annotation of coding sequences indicates a highly sophisticated endomembrane system, RNA processing mechanisms and nuclear genome contributions from several photosynthetic lineages. Multiple gene families, including likely signal transduction components, have been massively expanded. Alterations in protein abundance are controlled post-transcriptionally between light and dark conditions, surprisingly similar to trypanosomatids. CONCLUSIONS: Our data provide evidence that a range of photosynthetic eukaryotes contributed to the Euglena nuclear genome, evidence in support of the 'shopping bag' hypothesis for plastid acquisition. We also suggest that euglenids possess unique regulatory mechanisms for achieving extreme adaptability, through mechanisms of paralog expansion and gene acquisition.

Biology Centre Institute of Parasitology Czech Academy of Sciences and Faculty of Sciences University of South Bohemia 37005 České Budějovice Czech Republic

Cell Biology Division Department of Biology University of Erlangen Nuremberg 91058 Erlangen Germany

Centro Andaluz de Biología del Desarrollo CSIC Pablo de Olavide University Seville Spain

Department of Biochemistry University of Cambridge Cambridge CB2 1QW UK

Department of Biological and Geographical Sciences School of Applied Sciences University of Huddersfield Queensgate Huddersfield HD1 3DH UK

Department of Biological and Medical Sciences Faculty of Health and Life Sciences Oxford Brookes University Oxford OX3 0BP UK

Department of Infection Biology Institute of Infection and Global Health University of Liverpool Liverpool UK

Department of Life Sciences The Natural History Museum Cromwell Road London SW7 5BD UK

Department of Parasitology Faculty of Science Charles University BIOCEV 252 50 Vestec Czech Republic

Department of Plant Sciences University of Oxford Oxford OX1 3RB UK

Division of Infectious Disease Department of Medicine University of Alberta Edmonton Alberta T6G Canada

Laboratory of Cellular and Structural Biology The Rockefeller University New York NY 10065 USA

School of Life Sciences University of Dundee Dundee DD1 5EH UK

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Visualisation of Euglena gracilis organelles and cytoskeleton using expansion microscopy

On the possibility of yet a third kinetochore system in the protist phylum Euglenozoa

Comprehensive analysis of the Kinetoplastea intron landscape reveals a novel intron-containing gene and the first exclusively trans-splicing eukaryote

A lineage-specific protein network at the trypanosome nuclear envelope

New plastids, old proteins: repeated endosymbiotic acquisitions in kareniacean dinoflagellates

Lessons from the deep: mechanisms behind diversification of eukaryotic protein complexes

Comparative analysis of mitochondrion-related organelles in anaerobic amoebozoans

A unique mRNA decapping complex in trypanosomes

Functional differentiation of Sec13 paralogues in the euglenozoan protists

Recent expansion of metabolic versatility in Diplonema papillatum, the model species of a highly speciose group of marine eukaryotes

Euglenozoan kleptoplasty illuminates the early evolution of photoendosymbiosis

Euglena International Network (EIN): Driving euglenoid biotechnology for the benefit of a challenged world

Sending the message: specialized RNA export mechanisms in trypanosomes

Evolution and diversification of the nuclear envelope

Highly flexible metabolism of the marine euglenozoan protist Diplonema papillatum

Heterotrophic euglenid Rhabdomonas costata resembles its phototrophic relatives in many aspects of molecular and cell biology

Euglenozoa: taxonomy, diversity and ecology, symbioses and viruses

The Lipid Composition of Euglena gracilis Middle Plastid Membrane Resembles That of Primary Plastid Envelopes

A Uniquely Complex Mitochondrial Proteome from Euglena gracilis

Catalase and Ascorbate Peroxidase in Euglenozoan Protists