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RefPlantNLR: a comprehensive collection of experimentally validated plant NLRs

View ORCID ProfileJiorgos Kourelis, View ORCID ProfileToshiyuki Sakai, View ORCID ProfileHiroaki Adachi, View ORCID ProfileSophien Kamoun
doi: https://doi.org/10.1101/2020.07.08.193961
Jiorgos Kourelis
1The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
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Toshiyuki Sakai
1The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
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Hiroaki Adachi
1The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
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Sophien Kamoun
1The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
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  • ORCID record for Sophien Kamoun
  • For correspondence: sophien.kamoun@tsl.ac.uk
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ABSTRACT

Reference datasets are critical in computational biology. They help define canonical biological features and are essential for benchmarking studies. Here, we describe a comprehensive reference dataset of experimentally validated plant NLR immune receptors. RefPlantNLR consists of 442 NLRs from 31 genera belonging to 11 orders of flowering plants. This reference dataset has several applications. We used RefPlantNLR to determine the canonical features of functionally validated plant NLRs and to benchmark the five most popular NLR annotation tools. This revealed that although NLR annotation tools tend to retrieve the majority of NLRs, they frequently produce domain architectures that are inconsistent with the RefPlantNLR annotation. Guided by this analysis, we developed a new pipeline, NLRtracker, which extracts and annotates NLRs based on the core features found in the RefPlantNLR dataset. The RefPlantNLR dataset should also prove useful for guiding comparative analyses of NLRs across the wide spectrum of plant diversity and identifying under-studied taxa. We hope that the RefPlantNLR resource will contribute to moving the field beyond a uniform view of NLR structure and function.

Competing Interest Statement

The authors receive funding from industry on NLR biology.

Footnotes

  • This updated version of RefPlantNLR now consists of 442 NLRs from 31 genera belonging to 11 orders of flowering plants. We also used RefPlantNLR to benchmark the five most popular NLR annotation tools. Guided by this analysis, we developed a new pipeline, NLRtracker, which extracts and annotates NLRs based on the core features found in the RefPlantNLR dataset.

  • http://doi.org/10.5281/zenodo.3936022

Copyright 
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 January 31, 2021.
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RefPlantNLR: a comprehensive collection of experimentally validated plant NLRs
Jiorgos Kourelis, Toshiyuki Sakai, Hiroaki Adachi, Sophien Kamoun
bioRxiv 2020.07.08.193961; doi: https://doi.org/10.1101/2020.07.08.193961
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RefPlantNLR: a comprehensive collection of experimentally validated plant NLRs
Jiorgos Kourelis, Toshiyuki Sakai, Hiroaki Adachi, Sophien Kamoun
bioRxiv 2020.07.08.193961; doi: https://doi.org/10.1101/2020.07.08.193961

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