NLRSeek: A reannotation-based pipeline for mining missing NLR genes in sequenced genomes

Area of Science:

• Plant molecular biology
• Genomics
• Plant immunity

Background:

• Nucleotide-binding leucine-rich repeat (NLR) proteins are crucial for plant immune responses.
• Accurate identification of NLR genes is essential for developing disease-resistant crops.
• Existing annotation tools often misannotate or miss NLR proteins, especially in non-model species.

Purpose of the Study:

• To develop a robust genome reannotation-based pipeline, NLRSeek, for comprehensive NLR gene identification.
• To improve the accuracy and completeness of NLR gene discovery in plant genomes.
• To uncover novel NLR genes for enhancing crop disease resistance.

Main Methods:

• Developed NLRSeek, a pipeline integrating de novo NLR locus detection and targeted genome reannotation.
• Systematically reconciled new predictions with existing annotations for comprehensive NLR sets.
• Validated findings using transcriptome and ribosome-profiling data in *Arabidopsis thaliana* and yam species.

Main Results:

• NLRSeek identified more NLR genes than conventional tools, including a previously unannotated NLR in *Arabidopsis thaliana*.
• In yam species (*Dioscorea* spp.), NLRSeek discovered 33.8%–127.5% more NLR genes compared to existing methods.
• Over 45% of newly identified NLRs showed detectable expression, indicating their functional relevance.
• Identified tandem duplication as a mechanism for NLR expansion in *D. zingiberensis*.

Conclusions:

• NLRSeek provides a superior method for comprehensive NLR gene identification across diverse plant species.
• The pipeline uncovers previously missed genetic resources for engineering improved crop disease resistance.
• This work enhances our understanding of NLR gene evolution and function in plant immunity.