ArticleThe Plant journal : for cell and molecular biology2022
Prediction of NB-LRR resistance genes based on full-length sequence homology.
Article in The Plant journal : for cell and molecular biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 36 citations in OpenAlex.
- Network analysis reveals that bHLH transcription factors positively regulate rice resistance to Magnaporthe oryzae.BMC plant biology · 2026Article
- Advances in Genome Editing for Plant Disease Resistance Breeding.Plants (Basel, Switzerland) · 2026Review
- Role of RyScientific reports · 2025Article
- Hazelnut allergome overview and Cor a gRNAs identification.BMC plant biology · 2025Article
- PRGminer: harnessing deep learning for the prediction of resistance genes involved in plant defense mechanisms.Frontiers in plant science · 2025Article
- A landscape of resistance gene analogs in sour cherry (Prunus cerasus L.).BMC research notes · 2024Article
- Genome-wide identification and characterization of NBLRR genes in finger millet (Eleusine coracana L.) and their expression in response to Magnaporthe grisea infection.BMC plant biology · 2024Article
- DeepFrontiers in plant science · 2024Article
- Telomere-to-telomere and gap-free genome assembly of a susceptible grapevine species (Thompson Seedless) to facilitate grape functional genomics.Horticulture research · 2024Article
- NLR- andPlants (Basel, Switzerland) · 2023Review
- The First Genome-Wide Mildew Locus O Genes Characterization in theInternational journal of molecular sciences · 2023Article
- Molecular Mechanisms Underlying Potential Pathogen Resistance inPlants (Basel, Switzerland) · 2023Review
- Genome engineering of disease susceptibility genes for enhancing resistance in plants.Functional & integrative genomics · 2023Review
- PlantNLRatlas: a comprehensive dataset of full- and partial-length NLR resistance genes across 100 chromosome-level plant genomes.Frontiers in plant science · 2023Article
- NB-LRR Lineage-Specific Equipment Is Sorted Out by Sequence Pattern Adaptation and Domain Segment Shuffling.International journal of molecular sciences · 2022Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The activation of plant immunity is mediated by resistance (R)-gene receptors, also known as nucleotide-binding leucine-rich repeat (NB-LRR) genes, which in turn trigger the authentic defense response. R-gene identification is a crucial goal for both classic and modern plant breeding strategies for disease resistance. The conventional method identifies NB-LRR genes using a protein motif/domain-based search (PDS) within an automatically predicted gene set of the respective genome assembly. PDS proved to be imprecise since repeat masking prior to automatic genome annotation unwittingly prevented comprehensive NB-LRR gene detection. Furthermore, R-genes have diversified in a species-specific manner, so that NB-LRR gene identification cannot be universally standardized. Here, we present the full-length Homology-based R-gene Prediction (HRP) method for the comprehensive identification and annotation of a genome's R-gene repertoire. Our method has substantially addressed the complex genomic organization of tomato (Solanum lycopersicum) NB-LRR gene loci, proving to be more performant than the well-established RenSeq approach. HRP efficiency was also tested on three differently assembled and annotated Beta sp. genomes. Indeed, HRP identified up to 45% more full-length NB-LRR genes compared to previous approaches. HRP also turned out to be a more refined strategy for R-gene allele mining, testified by the identification of hitherto undiscovered Fom-2 homologs in five Cucurbita sp. genomes. In summary, our high-performance method for full-length NB-LRR gene discovery will propel the identification of novel R-genes towards development of improved cultivars.
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