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Homology-guided re-annotation improves the gene models of the alloploid Nicotiana benthamiana

View ORCID ProfileJiorgos Kourelis, Farnusch Kaschani, View ORCID ProfileFriederike M. Grosse-Holz, Felix Homma, View ORCID ProfileMarkus Kaiser, View ORCID ProfileRenier A. L. van der Hoorn
doi: https://doi.org/10.1101/373506
Jiorgos Kourelis
1Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford, UK
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  • ORCID record for Jiorgos Kourelis
Farnusch Kaschani
2Chemische Biologie, Zentrum fur Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Essen, Germany
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Friederike M. Grosse-Holz
1Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford, UK
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  • ORCID record for Friederike M. Grosse-Holz
Felix Homma
1Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford, UK
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Markus Kaiser
2Chemische Biologie, Zentrum fur Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Essen, Germany
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Renier A. L. van der Hoorn
1Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford, UK
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  • For correspondence: renier.vanderhoorn@plants.ox.ac.uk
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Abstract

Nicotiana benthamiana is an important model organism of the Solanaceae (Nightshade) family. Several draft assemblies of the N. benthamiana genome have been generated, but many of the gene-models in these draft assemblies appear incorrect. Here we present an improved re-annotation of the Niben1.0.1 draft genome assembly guided by gene models from other Nicotiana species. This approach overcomes problems caused by mis-annotated exon-intron boundaries and mis-assigned short read transcripts to homeologs in polyploid genomes. With an estimated 98.1% completeness; only 53,411 protein-encoding genes; and improved protein lengths and functional annotations, this new predicted proteome is better than the preceding proteome annotations. This dataset is more sensitive and accurate in proteomics applications, clarifying the detection by activity-based proteomics of proteins that were previously mis-annotated to be inactive. Phylogenetic analysis of the subtilase family of hydrolases reveal a pseudogenisation of likely homeologs, associated with a contraction of the functional genome in this alloploid plant species. We use this gene annotation to assign extracellular proteins in comparison to a total leaf proteome, to display the enrichment of hydrolases in the apoplast.

Footnotes

  • Dataset availability. The NbD and NbE datasets can be downloaded from Oxford Research Archive: https://ora.ox.ac.uk/objects/uuid:f34c90af-9a2a-4279-a6d2-09cbdcb323a2. This new annotation is an improved version when compared to the NbC dataset that was previously posted on bioRxiv in 2018 (https://www.biorxiv.org/content/10.1101/373506v2). The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Vizcaíno et al., 2016) partner repository (https://www.ebi.ac.uk/pride/archive/) with the data set identifier PXD010435.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted March 27, 2019.
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Homology-guided re-annotation improves the gene models of the alloploid Nicotiana benthamiana
Jiorgos Kourelis, Farnusch Kaschani, Friederike M. Grosse-Holz, Felix Homma, Markus Kaiser, Renier A. L. van der Hoorn
bioRxiv 373506; doi: https://doi.org/10.1101/373506
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Homology-guided re-annotation improves the gene models of the alloploid Nicotiana benthamiana
Jiorgos Kourelis, Farnusch Kaschani, Friederike M. Grosse-Holz, Felix Homma, Markus Kaiser, Renier A. L. van der Hoorn
bioRxiv 373506; doi: https://doi.org/10.1101/373506

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