This study is led by associate professor Gan Ai and associate professor Jinding Liu (College of Plant Protection, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China). Nucleotide-binding leucine-rich repeat (NLR) proteins function as key intracellular receptors in the plant immune system, recognizing pathogens' effectors and activating defenses. Identifying NLRs is a critical step in breeding disease-resistant crops. However, NLRs are frequently misannotated or entirely overlooked in automated genome annotations due to their complex genomic structures and low expression levels.
To address this, the authors developed NLRSeek, an NLR identification pipeline based on genome reannotation. The workflow first uses NLR-Annotator to identify NLR loci at the genomic level, then performs targeted local genome reannotation, and finally merges these new results with existing proteome annotations for a final high-precision classification using NLRtracker.
NLRSeek demonstrated superior performance compared to conventional methods in Arabidopsis, wheat, rice and banana genomes. Even in the well-annotated model plant Arabidopsis thaliana, it identified one previously unannotated NLR gene, whose expression and translation were confirmed by transcriptome and ribosome-profiling data.
The pipeline showed particularly strong performance in non-model species. In three yam (Dioscorea) species, NLRSeek identified 33.8% to 127.5% more NLR genes than conventional methods. Importantly, 45.1% of the newly discovered NLRs in D. zingiberensis were found to be expressed, confirming they are functional genes that were previously overlooked. This more complete set of NLRs enabled new evolutionary analysis, revealing that tandem duplication has driven the expansion of NLRs in this species.
In summary, NLRSeek tool might recover a significant number of missing NLR genes, providing a more comprehensive view of the plant immune repertoire and offering valuable new genetic resources for engineering disease resistance in crops
See the article:
NLRSeek: A reannotation–based pipeline for mining missing NLR genes in sequenced genomes
https://www.sciencedirect.com/science/article/pii/S2662173825002085
