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...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2021-10-01
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| Series: | PLoS Biology |
| Online Access: | https://doi.org/10.1371/journal.pbio.3001124 |
| _version_ | 1819101807561932800 |
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| author | Jiorgos Kourelis Toshiyuki Sakai Hiroaki Adachi Sophien Kamoun |
| author_facet | Jiorgos Kourelis Toshiyuki Sakai Hiroaki Adachi Sophien Kamoun |
| author_sort | Jiorgos Kourelis |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-22T01:24:32Z |
| format | Article |
| id | doaj.art-33905e38031a4ff7bf30da3fc029eced |
| institution | Directory Open Access Journal |
| issn | 1544-9173 1545-7885 |
| language | English |
| last_indexed | 2024-12-22T01:24:32Z |
| publishDate | 2021-10-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Biology |
| spelling | doaj.art-33905e38031a4ff7bf30da3fc029eced2022-12-21T18:43:38ZengPublic Library of Science (PLoS)PLoS Biology1544-91731545-78852021-10-011910e300112410.1371/journal.pbio.3001124RefPlantNLR is a comprehensive collection of experimentally validated plant disease resistance proteins from the NLR family.Jiorgos KourelisToshiyuki SakaiHiroaki AdachiSophien KamounReference 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.https://doi.org/10.1371/journal.pbio.3001124 |
| spellingShingle | Jiorgos Kourelis Toshiyuki Sakai Hiroaki Adachi Sophien Kamoun RefPlantNLR is a comprehensive collection of experimentally validated plant disease resistance proteins from the NLR family. PLoS Biology |
| title | 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_short | 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 |
| url | https://doi.org/10.1371/journal.pbio.3001124 |
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