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

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. Re...

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Autores principales:	Jiorgos Kourelis, Toshiyuki Sakai, Hiroaki Adachi, Sophien Kamoun
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/33905e38031a4ff7bf30da3fc029eced
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spelling	oai:doaj.org-article:33905e38031a4ff7bf30da3fc029eced2021-12-02T19:54:18ZRefPlantNLR is a comprehensive collection of experimentally validated plant disease resistance proteins from the NLR family.1544-91731545-788510.1371/journal.pbio.3001124https://doaj.org/article/33905e38031a4ff7bf30da3fc029eced2021-10-01T00:00:00Zhttps://doi.org/10.1371/journal.pbio.3001124https://doaj.org/toc/1544-9173https://doaj.org/toc/1545-7885Reference 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.Jiorgos KourelisToshiyuki SakaiHiroaki AdachiSophien KamounPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Biology, Vol 19, Iss 10, p e3001124 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Jiorgos Kourelis Toshiyuki Sakai Hiroaki Adachi Sophien Kamoun RefPlantNLR is a comprehensive collection of experimentally validated plant disease resistance proteins from the NLR family.
description	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.
format	article
author	Jiorgos Kourelis Toshiyuki Sakai Hiroaki Adachi Sophien Kamoun
author_facet	Jiorgos Kourelis Toshiyuki Sakai Hiroaki Adachi Sophien Kamoun
author_sort	Jiorgos Kourelis
title	RefPlantNLR is a comprehensive collection of experimentally validated plant disease resistance proteins from the NLR family.
title_short	RefPlantNLR is a comprehensive collection of experimentally validated plant disease resistance proteins from the NLR family.
title_full	RefPlantNLR is a comprehensive collection of experimentally validated plant disease resistance proteins from the NLR family.
title_fullStr	RefPlantNLR is a comprehensive collection of experimentally validated plant disease resistance proteins from the NLR family.
title_full_unstemmed	RefPlantNLR is a comprehensive collection of experimentally validated plant disease resistance proteins from the NLR family.
title_sort	refplantnlr is a comprehensive collection of experimentally validated plant disease resistance proteins from the nlr family.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/33905e38031a4ff7bf30da3fc029eced
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RefPlantNLR is a comprehensive collection of experimentally validated plant disease resistance proteins from the NLR family.

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