RefPlantNLR is a comprehensive collection of experimentally validated plant disease resistance proteins from the NLR family

Kourelis, Jiorgos, Sakai, Toshiyuki, Adachi, Hiroaki and Kamoun, Sophien (2021) RefPlantNLR is a comprehensive collection of experimentally validated plant disease resistance proteins from the NLR family. PLoS Biology, 19 (10). ISSN 1545-7885

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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 nucleotide-binding leucine-rich repeat (NLR) immune receptors. RefPlantNLR consists of 481 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 5 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 from protein or transcript files 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 understudied taxa. We hope that the RefPlantNLR resource will contribute to moving the field beyond a uniform view of NLR structure and function.

Item Type: Article
Additional Information: Funding Information: This work has been supported by Gatsby Charitable Foundation (https://www.gatsby.org.uk/) (TS, SK), Biotechnology and Biological Sciences Research Council (BBSRC BB/P012574 (Plant Health ISP)) (SK), European Research Council (grant number 743165, https://cordis.europa.eu/ project/id/743165) (SK), Japan Society for the Promotion of Plant Science Postdoctoral fellowship (HA), and BASF Plant Science (JK, SK). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Uncontrolled Keywords: neuroscience(all),biochemistry, genetics and molecular biology(all),immunology and microbiology(all),agricultural and biological sciences(all) ,/dk/atira/pure/subjectarea/asjc/2800
Faculty \ School:
Faculty of Science > School of Biological Sciences
Related URLs:
Depositing User: LivePure Connector
Date Deposited: 29 Oct 2021 00:41
Last Modified: 02 Dec 2021 02:48
URI: https://ueaeprints.uea.ac.uk/id/eprint/81916
DOI: 10.1371/journal.pbio.3001124

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