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Euglena gracilis Genome and Transcriptome: Organelles, Nuclear Genome Assembly Strategies and Initial Features

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Euglena: Biochemistry, Cell and Molecular Biology

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 979))

Abstract

Euglena gracilis is a major component of the aquatic ecosystem and together with closely related species, is ubiquitous worldwide. Euglenoids are an important group of protists, possessing a secondarily acquired plastid and are relatives to the Kinetoplastidae, which themselves have global impact as disease agents. To understand the biology of E. gracilis, as well as to provide further insight into the evolution and origins of the Kinetoplastidae, we embarked on sequencing the nuclear genome; the plastid and mitochondrial genomes are already in the public domain. Earlier studies suggested an extensive nuclear DNA content, with likely a high degree of repetitive sequence, together with significant extrachromosomal elements. To produce a list of coding sequences we have combined transcriptome data from both published and new sources, as well as embarked on de novo sequencing using a combination of 454, Illumina paired end libraries and long PacBio reads. Preliminary analysis suggests a surprisingly large genome approaching 2 Gbp, with a highly fragmented architecture and extensive repeat composition. Over 80% of the RNAseq reads from E. gracilis maps to the assembled genome sequence, which is comparable with the well assembled genomes of T. brucei and T. cruzi. In order to achieve this level of assembly we employed multiple informatics pipelines, which are discussed here. Finally, as a preliminary view of the genome architecture, we discuss the tubulin and calmodulin genes, which highlight potential novel splicing mechanisms.

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Acknowledgements

We are greatly indebted to the following for their contributions of data, advice and suggestions: Peter Myler (Seattle), Purificacion Gacia-Lopes and David Moreira (Orsay), Rob Field (Norwich) and Vladimir Hampl (Praha).

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Authors and Affiliations

  1. Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK

    ThankGod Echezona Ebenezer & Mark Carrington Ph.D.

  2. School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK

    ThankGod Echezona Ebenezer & Mark C. Field D.Phil.

  3. Cell Biology Division, Department of Biology, University of Erlangen-Nuremberg, Staudtstraβe 5, Erlangen, 91058, Germany

    Michael Lebert Ph.D.

  4. Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK

    Steven Kelly Ph.D.

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  1. ThankGod Echezona Ebenezer
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  3. Michael Lebert Ph.D.
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  4. Steven Kelly Ph.D.
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  5. Mark C. Field D.Phil.
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Corresponding authors

Correspondence to Steven Kelly Ph.D. or Mark C. Field D.Phil. .

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Editors and Affiliations

  1. Department of Biological Sciences, University of Memphis, Memphis, Tennessee, USA

    Steven D. Schwartzbach

  2. Faculty of Agriculture, Kindai University, Nara, Japan

    Shigeru Shigeoka

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Ebenezer, T.E., Carrington, M., Lebert, M., Kelly, S., Field, M.C. (2017). Euglena gracilis Genome and Transcriptome: Organelles, Nuclear Genome Assembly Strategies and Initial Features. In: Schwartzbach, S., Shigeoka, S. (eds) Euglena: Biochemistry, Cell and Molecular Biology. Advances in Experimental Medicine and Biology, vol 979. Springer, Cham. https://doi.org/10.1007/978-3-319-54910-1_7

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