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. Members of the same hvNLR clade show variable expression and methylation across lines and tissues, consistent with their rapid evolution. 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 the maize pan-NLRome, and provides an updated clade alignment, phylogenetic tree, and sequence diversity information for the gene of interest.