FindPlantNLRs

FindPlantNLRs annotates predicted NLR (nucleotide-binding and leucine-rich repeat) genes from non-masked genome FASTA inputs to identify NLR loci, domains, and allelic diversity for studies of plant immunity and adaptation.

Key Features:

• Input data: Accepts non-masked genome FASTA files as input for NLR locus discovery.
• Identification and locus detection: Uses NLR-annotator, tblastn, and Hidden Markov Model (HMM) searches to detect candidate NLR loci.
• Annotation: Annotates identified loci with Braker2 using experimentally validated resistance genes as references.
• Domain screening: Performs InterProScan on annotated amino acid FASTA files to detect NB-ARC and LRR domains.
• Mapping and export: Maps sequences back to scaffolds or chromosomes and extracts results in FASTA and GFF3 formats.
• Integrated domain detection: Identifies novel integrated domains within NLR genes.
• Allelic and cluster analysis: Reveals variations in NLR gene counts across haplotypes and differences in gene clusters.

Scientific Applications:

• NLR annotation in complex genomes: Enables annotation of NLR genes in species with large or complex genomes, including long-lived trees.
• Allelic diversity characterization: Supports comparison of NLR allelic diversity across haplotypes in chromosome-level assemblies.
• Integrated domain discovery: Facilitates identification of integrated domains that may inform effector recognition and immune function.
• Functional and evolutionary studies: Provides annotated NLR repertoires suitable for downstream functional and evolutionary analyses of plant immunity and adaptation.
• Case application: Applied to a chromosome-level pseudo-phased genome of Melaleuca quinquenervia to describe full allelic diversity of NLRs.

Methodology:

Run NLR-annotator, tblastn, and HMM searches on non-masked genome FASTA to identify NLR loci; annotate identified loci with Braker2 using experimentally validated resistance genes as references; translate annotations to amino acid FASTA and run InterProScan to detect NB-ARC and LRR domains; map domain-containing sequences back to scaffolds/chromosomes and extract outputs in FASTA and GFF3 while reporting integrated domains and haplotype-level variations.