Macroevolution of NLR genes in family Fabaceae provides evidence of clade specific expansion and contraction of NLRome in Vicioid clade

Abstract

Whole genome duplication plays a significant role in plant genome evolution by providing raw materials that can be modified by natural or artificial selection. Nucleotide binding site leucine rich repeat receptor (NLRs) like other gene families are clusters of genes created by duplication and their size reflects the number of duplicated genes. NLR genes encode immune receptors that facilitate identification and binding of effector compounds produced by pathogen as a part of effector triggered immunity (ETI). The accurate identification and characterization of NLR genes substantially contributes to the repertoire of resistance and improves production. The ancestors of Fabaceae family have underwent whole genome duplication (WGD) approximately 58.5 million years ago. In this study, we focused on the subsequent effects of WGD on the evolution of NLR genes within the Vicioid clade, which consists of various legume crops such as chickpea, clover, alfalfa, and pea. The Vicioid clade is divided into three major tribes: Cicereae, Fabeae, and Trifolieae. The analysis of 22 species from the Vicioid clade revealed an overall contraction of the NLRome (the complete set of NLR genes) in members of the Cicereae and Fabeae tribes. This contraction aligns with previous observations that WGD events are often followed by diploidization, leading to a reduced number of duplicated genes. Contrary to this contraction trend, tribe Trifolieae have shown large scale expansion of NLRome irrespective to their genome size. Additionally, the primary diversification of relatively conserved NLR gene subclasses, including helper genes (CCR-NLR) and CCG10-NLR, was reported. Comprehensive evolutionary analysis suggests that NLRome expansion have occurred in during recent 1-6 Mya probably due to their higher substitutions per site per year in Trifolieae. We further hypothesized that this higher rate directed accelerated gene duplications after speciation from their common ancestor and later gene conversion and asymmetric recombination played an active role in subgroup diversification.