PlantNLRatlas: a comprehensive dataset of full- and partial-length NLR resistance genes across 100 chromosome-level plant genomes
Plants have evolved two layers of protection against biotic stress: PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI). The primary mechanism of ETI involves nucleotide-binding leucine-rich repeat immune receptors (NLRs). Although NLR genes have been studied in several plant species...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-04-01
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| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1178069/full |
| _version_ | 1797847162943438848 |
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| author | Xiang Li Xiang Li Linna Ma Linna Ma Yingmin Wang Yingmin Wang Chen Ye Chen Ye Cunwu Guo Cunwu Guo Yingbin Li Yingbin Li Xinyue Mei Xinyue Mei Fei Du Fei Du Huichuan Huang Huichuan Huang |
| author_facet | Xiang Li Xiang Li Linna Ma Linna Ma Yingmin Wang Yingmin Wang Chen Ye Chen Ye Cunwu Guo Cunwu Guo Yingbin Li Yingbin Li Xinyue Mei Xinyue Mei Fei Du Fei Du Huichuan Huang Huichuan Huang |
| author_sort | Xiang Li |
| collection | DOAJ |
| description | Plants have evolved two layers of protection against biotic stress: PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI). The primary mechanism of ETI involves nucleotide-binding leucine-rich repeat immune receptors (NLRs). Although NLR genes have been studied in several plant species, a comprehensive database of NLRs across a diverse array of species is still lacking. Here, we present a thorough analysis of NLR genes across 100 high-quality plant genomes (PlantNLRatlas). The PlantNLRatlas includes a total of 68,452 NLRs, of which 3,689 are full-length and 64,763 are partial-length NLRs. The majority of NLR groups were phyletically clustered. In addition, the domain sequences were found to be highly conserved within each NLR group. Our PlantNLRatlas dataset is complementary to RefPlantNLR, a collection of NLR genes which have been experimentally confirmed. The PlantNLRatlas should prove helpful for comparative investigations of NLRs across a range of plant groups, including understudied taxa. Finally, the PlantNLRatlas resource is intended to help the field move past a monolithic understanding of NLR structure and function. |
| first_indexed | 2024-04-09T18:06:49Z |
| format | Article |
| id | doaj.art-704a1860c434410cbf7867881ddffaca |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-09T18:06:49Z |
| publishDate | 2023-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-704a1860c434410cbf7867881ddffaca2023-04-14T05:38:29ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2023-04-011410.3389/fpls.2023.11780691178069PlantNLRatlas: a comprehensive dataset of full- and partial-length NLR resistance genes across 100 chromosome-level plant genomesXiang Li0Xiang Li1Linna Ma2Linna Ma3Yingmin Wang4Yingmin Wang5Chen Ye6Chen Ye7Cunwu Guo8Cunwu Guo9Yingbin Li10Yingbin Li11Xinyue Mei12Xinyue Mei13Fei Du14Fei Du15Huichuan Huang16Huichuan Huang17State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, ChinaKey Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, ChinaState Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, ChinaKey Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, ChinaState Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, ChinaKey Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, ChinaState Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, ChinaKey Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, ChinaState Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, ChinaKey Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, ChinaState Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, ChinaKey Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, ChinaState Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, ChinaKey Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, ChinaState Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, ChinaKey Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, ChinaState Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, ChinaKey Laboratory for Agro-Biodiversity and Pest Control of Ministry of Education, Yunnan Agricultural University, Kunming, ChinaPlants have evolved two layers of protection against biotic stress: PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI). The primary mechanism of ETI involves nucleotide-binding leucine-rich repeat immune receptors (NLRs). Although NLR genes have been studied in several plant species, a comprehensive database of NLRs across a diverse array of species is still lacking. Here, we present a thorough analysis of NLR genes across 100 high-quality plant genomes (PlantNLRatlas). The PlantNLRatlas includes a total of 68,452 NLRs, of which 3,689 are full-length and 64,763 are partial-length NLRs. The majority of NLR groups were phyletically clustered. In addition, the domain sequences were found to be highly conserved within each NLR group. Our PlantNLRatlas dataset is complementary to RefPlantNLR, a collection of NLR genes which have been experimentally confirmed. The PlantNLRatlas should prove helpful for comparative investigations of NLRs across a range of plant groups, including understudied taxa. Finally, the PlantNLRatlas resource is intended to help the field move past a monolithic understanding of NLR structure and function.https://www.frontiersin.org/articles/10.3389/fpls.2023.1178069/fullgenome-wide analysisNB-LRRNLRsR genePlantNLRatlasbioinformatics |
| spellingShingle | Xiang Li Xiang Li Linna Ma Linna Ma Yingmin Wang Yingmin Wang Chen Ye Chen Ye Cunwu Guo Cunwu Guo Yingbin Li Yingbin Li Xinyue Mei Xinyue Mei Fei Du Fei Du Huichuan Huang Huichuan Huang PlantNLRatlas: a comprehensive dataset of full- and partial-length NLR resistance genes across 100 chromosome-level plant genomes Frontiers in Plant Science genome-wide analysis NB-LRR NLRs R gene PlantNLRatlas bioinformatics |
| title | PlantNLRatlas: a comprehensive dataset of full- and partial-length NLR resistance genes across 100 chromosome-level plant genomes |
| title_full | PlantNLRatlas: a comprehensive dataset of full- and partial-length NLR resistance genes across 100 chromosome-level plant genomes |
| title_fullStr | PlantNLRatlas: a comprehensive dataset of full- and partial-length NLR resistance genes across 100 chromosome-level plant genomes |
| title_full_unstemmed | PlantNLRatlas: a comprehensive dataset of full- and partial-length NLR resistance genes across 100 chromosome-level plant genomes |
| title_short | PlantNLRatlas: a comprehensive dataset of full- and partial-length NLR resistance genes across 100 chromosome-level plant genomes |
| title_sort | plantnlratlas a comprehensive dataset of full and partial length nlr resistance genes across 100 chromosome level plant genomes |
| topic | genome-wide analysis NB-LRR NLRs R gene PlantNLRatlas bioinformatics |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1178069/full |
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