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BMC Biol. 2019 Feb 7;17(1):11. doi: 10.1186/s12915-019-0626-8.

Transcriptome, proteome and draft genome of Euglena gracilis.

Author information

1
School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
2
Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.
3
Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK.
4
Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic.
5
Department of Parasitology, Faculty of Science,, Charles University, BIOCEV, 252 50, Vestec, Czech Republic.
6
Cell Biology Division, Department of Biology, University of Erlangen-Nuremberg, 91058, Erlangen, Germany.
7
Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, Pablo de Olavide University, Seville, Spain.
8
Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK.
9
Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Alberta, T6G, Canada.
10
Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, 10065, USA.
11
Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
12
Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK.
13
Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Alberta, T6G, Canada. dacks@ualberta.ca.
14
Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK. dacks@ualberta.ca.
15
Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK. steven.kelly@plants.ox.ac.uk.
16
School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK. mfield@mac.com.
17
Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic. mfield@mac.com.

Abstract

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.

KEYWORDS:

Cellular evolution; Euglena gracilis; Excavata; Gene architecture; Horizontal gene transfer; Plastid; Secondary endosymbiosis; Splicing; Transcriptome

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