Majority of the highly variable NLRs in maize share genomic location and contain additional target-binding domains

Abstract

Nucleotide-binding Leucine Rich Repeat proteins (NLRs) are a major class of immune receptors in plants. NLRs include both conserved and rapidly evolving members, however their evolutionary trajectory in crops remains understudied. Availability of crop pan-genomes enables analysis of the recent events in the evolution of this highly complex gene family within domesticated species. Here, we investigated the NLR complement of 26 nested association mapping (NAM) founder lines of maize. We found that maize has just four main subfamilies containing rapidly evolving highly variable NLR (hvNLR) receptors. Curiously, three of these phylogenetically distinct hvNLR lineages are located in adjacent clusters on chromosome 10. By combining sequence diversity analysis and AlphaFold2 computational structure prediction we predicted ligand binding sites in the hvNLRs. We also observed novel insertion domains in the LRR regions of two hvNLR subfamilies that likely contribute to target recogniton. To make this analysis accessible, we created NLRCladeFinder, a Google Colaboratory notebook, that accepts any newly identified NLR sequence, places it in the evolutionary context of maize pan-NLRome, and provides an updated clade alignment, phylogenetic tree, and sequence diversity information for the gene of interest.

Pseudomonas syringaepv.tomatoDC3000 induces defense responses in diverse maize inbred lines

“…Such knowledge will be valuable in determining the molecular and cellular mechanisms underlying nucleotide-binding leucine-rich repeat immune receptors (NLR)-dependent recognition of P. syringae pv. tomato DC3000 effectors (Prigozhin et al, 2022; Thatcher et al, 2023).…”