Resistify: A Novel NLR Classifier That Reveals Helitron-Associated NLR Expansion in Solanaceae
Nucleotide-binding domain leucine-rich repeat (NLR) proteins are a key component of the plant innate immune system. In plant genomes, NLRs exhibit considerable presence/absence variation and sequence diversity. Recent advances in sequencing technologies have made the generation of high-quality novel...
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2025-01-01
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| Series: | Bioinformatics and Biology Insights |
| Online Access: | https://doi.org/10.1177/11779322241308944 |
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| author | Moray Smith John T Jones Ingo Hein |
| author_facet | Moray Smith John T Jones Ingo Hein |
| author_sort | Moray Smith |
| collection | DOAJ |
| description | Nucleotide-binding domain leucine-rich repeat (NLR) proteins are a key component of the plant innate immune system. In plant genomes, NLRs exhibit considerable presence/absence variation and sequence diversity. Recent advances in sequencing technologies have made the generation of high-quality novel plant genome assemblies considerably more straightforward. Accurately identifying NLRs from these genomes is a prerequisite for improving our understanding of NLRs and identifying novel sources of disease resistance. While several tools have been developed to predict NLRs, they are hampered by low accuracy, speed, and availability. Here, the NLR annotation tool Resistify is presented. Resistify is an easy-to-use, rapid, and accurate tool to identify and classify NLRs from protein sequences. Applying Resistify to the RefPlantNLR database demonstrates that it can correctly identify NLRs from a diverse range of species. Applying Resistify in combination with tools to identify transposable elements to a panel of Solanaceae genomes reveals a previously undescribed association between NLRs and Helitron transposable elements. |
| format | Article |
| id | doaj-art-145fcf0baf424164b9ba47d1b2ab372b |
| institution | Kabale University |
| issn | 1177-9322 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Bioinformatics and Biology Insights |
| spelling | doaj-art-145fcf0baf424164b9ba47d1b2ab372b2025-01-22T12:03:40ZengSAGE PublishingBioinformatics and Biology Insights1177-93222025-01-011910.1177/11779322241308944Resistify: A Novel NLR Classifier That Reveals Helitron-Associated NLR Expansion in SolanaceaeMoray Smith0John T Jones1Ingo Hein2School of Biology, University of St Andrews, St Andrews, UKSchool of Biology, University of St Andrews, St Andrews, UKSchool of Life Sciences, University of Dundee, Dundee, UKNucleotide-binding domain leucine-rich repeat (NLR) proteins are a key component of the plant innate immune system. In plant genomes, NLRs exhibit considerable presence/absence variation and sequence diversity. Recent advances in sequencing technologies have made the generation of high-quality novel plant genome assemblies considerably more straightforward. Accurately identifying NLRs from these genomes is a prerequisite for improving our understanding of NLRs and identifying novel sources of disease resistance. While several tools have been developed to predict NLRs, they are hampered by low accuracy, speed, and availability. Here, the NLR annotation tool Resistify is presented. Resistify is an easy-to-use, rapid, and accurate tool to identify and classify NLRs from protein sequences. Applying Resistify to the RefPlantNLR database demonstrates that it can correctly identify NLRs from a diverse range of species. Applying Resistify in combination with tools to identify transposable elements to a panel of Solanaceae genomes reveals a previously undescribed association between NLRs and Helitron transposable elements.https://doi.org/10.1177/11779322241308944 |
| spellingShingle | Moray Smith John T Jones Ingo Hein Resistify: A Novel NLR Classifier That Reveals Helitron-Associated NLR Expansion in Solanaceae Bioinformatics and Biology Insights |
| title | Resistify: A Novel NLR Classifier That Reveals Helitron-Associated NLR Expansion in Solanaceae |
| title_full | Resistify: A Novel NLR Classifier That Reveals Helitron-Associated NLR Expansion in Solanaceae |
| title_fullStr | Resistify: A Novel NLR Classifier That Reveals Helitron-Associated NLR Expansion in Solanaceae |
| title_full_unstemmed | Resistify: A Novel NLR Classifier That Reveals Helitron-Associated NLR Expansion in Solanaceae |
| title_short | Resistify: A Novel NLR Classifier That Reveals Helitron-Associated NLR Expansion in Solanaceae |
| title_sort | resistify a novel nlr classifier that reveals helitron associated nlr expansion in solanaceae |
| url | https://doi.org/10.1177/11779322241308944 |
| work_keys_str_mv | AT moraysmith resistifyanovelnlrclassifierthatrevealshelitronassociatednlrexpansioninsolanaceae AT johntjones resistifyanovelnlrclassifierthatrevealshelitronassociatednlrexpansioninsolanaceae AT ingohein resistifyanovelnlrclassifierthatrevealshelitronassociatednlrexpansioninsolanaceae |