# RiceReceptor: The Cell-Surface and Intracellular Immune Receptors of the Oryza Genus

## TL;DR

This study identifies and analyzes immune receptors in rice genomes, offering insights for improving disease resistance and breeding strategies.

## Contribution

The discovery of 454 TIR-NB-LRR genes in rice challenges previous assumptions about their rarity in monocots.

## Key findings

- LRR receptor-like kinases (LRR-RLKs) are the most common immune receptors in rice.
- Five O. glaberrima TNL genes cluster with dicot TNLs, showing unique domain fusions.
- High-quality rice genomes were analyzed, revealing insights into immune receptor evolution.

## Abstract

Introduction: Rice, a cornerstone of global food security, faces escalating demands for enhanced yield and disease resistance. We collected 300 high-quality genomes, representing both cultivated (Oryza sativa indica, O. sativa japonica, and O. sativa aus) and wild species (O. rufipogon, O. glaberrima, and O. barthii). Methods: Leveraging HMMER, NLR-Annotator, and OrthoFinder, we systematically identified 148,077 leucine-rich repeat (LRR) and 143,459 nucleotide-binding leucine-rich repeat (NLR) genes, with LRR receptor-like kinases (LRR-RLKs) dominating immune receptor proportions, followed by coiled-coil domain containing (CNL)-type NLRs and LRR receptor-like proteins (LRR-RLPs). Results: Benchmarking Universal Single-Copy Orthologs (BUSCO) assessments confirmed robust genome quality (average score: 94.78). Strikingly, 454 TIR-NB-LRR (TNL) genes—typically rare in monocots—were detected, challenging prior assumptions. Phylogenetic analysis with Arabidopsis TNLs highlighted five O. glaberrima genes clustering with dicot TNLs; these genes featured truncated PLN03210 motifs fused to nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 (NB-ARC) and LRR domains. Conclusions: By bridging structural genomics, evolutionary dynamics, and domestication-driven adaptation, this work provides a foundation for targeted breeding strategies and advances functional studies of plant immunity in rice.