Transcriptome, proteome and draft genome of Euglena gracilis

Thank God Ebenezer, Martin Zoltner, Alana Burrel, Anna Nenarokova, Anna Novak Vanclova, Binod Prasad, Petr Soukal, Carlos Santana-Molina, Ellis O'Neill, Nerissa Nankissoor, Nithya Vadakedath, Viktor Daiker, Samson Obado, Sara Silva Pereira, Andrew Jackson, Damien Devos, Julius Lukes, Michael Lebert, Sue Vaughan, Vladimir Hampl & 5 others Mark Carrington, Michael Ginger, Joel Dacks, Steven Kelly, Mark Field

Research output: Contribution to journalArticle

8 Citations (Scopus)

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.

Original languageEnglish
Article number11
Number of pages23
JournalBMC Biology
Volume17
Issue number1
DOIs
Publication statusPublished - 7 Feb 2019

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Euglena gracilis
Proteome
proteome
Transcriptome
transcriptome
nuclear genome
genome
Genes
Genome
Euglenida
endomembrane system
Trypanosomatidae
Euglena
genes
gene
plastids
eukaryotic cells
signal transduction
bags
proteins

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Ebenezer, T. G., Zoltner, M., Burrel, A., Nenarokova, A., Novak Vanclova, A., Prasad, B., ... Field, M. (2019). Transcriptome, proteome and draft genome of Euglena gracilis. BMC Biology, 17(1), [11]. https://doi.org/10.1186/s12915-019-0626-8
Ebenezer, Thank God ; Zoltner, Martin ; Burrel, Alana ; Nenarokova, Anna ; Novak Vanclova, Anna ; Prasad, Binod ; Soukal, Petr ; Santana-Molina, Carlos ; O'Neill, Ellis ; Nankissoor, Nerissa ; Vadakedath, Nithya ; Daiker, Viktor ; Obado, Samson ; Silva Pereira, Sara ; Jackson, Andrew ; Devos, Damien ; Lukes, Julius ; Lebert, Michael ; Vaughan, Sue ; Hampl, Vladimir ; Carrington, Mark ; Ginger, Michael ; Dacks, Joel ; Kelly, Steven ; Field, Mark. / Transcriptome, proteome and draft genome of Euglena gracilis. In: BMC Biology. 2019 ; Vol. 17, No. 1.
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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.",
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Ebenezer, TG, Zoltner, M, Burrel, A, Nenarokova, A, Novak Vanclova, A, Prasad, B, Soukal, P, Santana-Molina, C, O'Neill, E, Nankissoor, N, Vadakedath, N, Daiker, V, Obado, S, Silva Pereira, S, Jackson, A, Devos, D, Lukes, J, Lebert, M, Vaughan, S, Hampl, V, Carrington, M, Ginger, M, Dacks, J, Kelly, S & Field, M 2019, 'Transcriptome, proteome and draft genome of Euglena gracilis', BMC Biology, vol. 17, no. 1, 11. https://doi.org/10.1186/s12915-019-0626-8

Transcriptome, proteome and draft genome of Euglena gracilis. / Ebenezer, Thank God; Zoltner, Martin; Burrel, Alana; Nenarokova, Anna; Novak Vanclova, Anna; Prasad, Binod; Soukal, Petr; Santana-Molina, Carlos; O'Neill, Ellis; Nankissoor, Nerissa; Vadakedath, Nithya; Daiker, Viktor; Obado, Samson; Silva Pereira, Sara; Jackson, Andrew; Devos, Damien; Lukes, Julius; Lebert, Michael; Vaughan, Sue; Hampl, Vladimir; Carrington, Mark; Ginger, Michael; Dacks, Joel; Kelly, Steven; Field, Mark.

In: BMC Biology, Vol. 17, No. 1, 11, 07.02.2019.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Transcriptome, proteome and draft genome of Euglena gracilis

AU - Ebenezer, Thank God

AU - Zoltner, Martin

AU - Burrel, Alana

AU - Nenarokova, Anna

AU - Novak Vanclova, Anna

AU - Prasad, Binod

AU - Soukal, Petr

AU - Santana-Molina, Carlos

AU - O'Neill, Ellis

AU - Nankissoor, Nerissa

AU - Vadakedath, Nithya

AU - Daiker, Viktor

AU - Obado, Samson

AU - Silva Pereira, Sara

AU - Jackson, Andrew

AU - Devos, Damien

AU - Lukes, Julius

AU - Lebert, Michael

AU - Vaughan, Sue

AU - Hampl, Vladimir

AU - Carrington, Mark

AU - Ginger, Michael

AU - Dacks, Joel

AU - Kelly, Steven

AU - Field, Mark

PY - 2019/2/7

Y1 - 2019/2/7

N2 - 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.

AB - 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.

KW - Cellular evolution

KW - Euglena gracilis

KW - Excavata

KW - Gene architecture

KW - Horizontal gene transfer

KW - Plastid

KW - Secondary endosymbiosis

KW - Splicing

KW - Transcriptome

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DO - 10.1186/s12915-019-0626-8

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VL - 17

JO - BMC Biology

JF - BMC Biology

SN - 1741-7007

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ER -

Ebenezer TG, Zoltner M, Burrel A, Nenarokova A, Novak Vanclova A, Prasad B et al. Transcriptome, proteome and draft genome of Euglena gracilis. BMC Biology. 2019 Feb 7;17(1). 11. https://doi.org/10.1186/s12915-019-0626-8