Towards a quantitative view of the NLR gene family 4evolution in the genome space

Plants and their pathogens coevolve over long time periods, and the history of coevolution is recorded in plant genes that confer pathogen resistance. Many of these code for Nucleotide-binding Leucine rich Repeat proteins (NLRs), which are crucial for distinguishing friends from foes and triggering potent defense responses. Advances in the ability to sequence genomes from many different species as well as many genomes from the same species reveal that 1) the number of NLR genes differ widely between species, and 2) NLR genes may exhibit extensive nucleotide variation as well as presence/absence polymorphism within species. The “birth-and-death process” is thus a generally useful framework for describing NLR gene evolution. In the light of the latest insights into the genomic features associated with NLR gene diversity, we aim here to evaluate the contribution of forces involved in NLR gene family evolution and presence/absence variation: mutation, recombination, gene duplication and deletion, and natural selection. To do so, we highlight novel combinations of population genomics methods and statistics that can provide an improved framework for describing NLR gene family evolution in the genome space, especially accounting for selective processes stemming from their function within resistance gene networks and the resulting quantitative defense response.