Phylogenomic insights into NLR diversity and evolution in Caryophyllales

The order Caryophyllales encompasses a wide diversity of plant species, including crops and stress-adapted xerophytes, yet the composition of their immune receptor repertoire remains largely unexplored. To investigate resistance gene diversity in this lineage, we performed a phylogenomic analysis of 5,277 nucleotide-binding leucine-rich repeat (NLR) immune proteins across 29 Caryophyllales species. Our findings reveal substantial variation in NLR abundance and composition compared to well-studied plant orders like Solanales and Asterales, with an average of 181 NLRs per species. Notably, CC-NLRs (coiled-coil domain) and CCG10-NLRs dominate this lineage, whereas TIR-NLRs and CCR-NLRs are less expanded, with fewer than two copies per species on average. The TIR-NLR repertoire of Caryophyllales only includes the conserved TNL1 clade, which is also present in other plant phyla such as superasterids, superrosids, and magnolids. Furthermore, we found that NRG1, a well-known CCR-NLR involved in immune signaling, is absent across all analysed Caryophyllales species, while ADR1 remains present, suggesting a lineage-specific loss of NRG1. This comprehensive analysis of the Caryophyllales NLR repertoire provides a valuable resource for comparative genomics and resistance breeding in crops and wild species.