Comparative analysis of the NLR gene family in the genomes of garden asparagus (Asparagus officinalis) and its wild relatives

Garden asparagus (<i>Asparagus officinalis</i>), a prominent horticultural crop recognized as the "king of vegetables" in the international market, is usually threatened by severe disease challenges that hinder its sustainable cultivation. Nucleotide-binding leucine-rich repeat receptors (NLRs) are key components of plant immune systems, yet their specific role and evolutionary patterns in <i>A. officinalis</i> and its related species remain poorly characterized. In this study, we conducted a comprehensive analysis of NLR gene distribution patterns, structural features, phylogenetic characterization, and evolutionary dynamics across <i>A. officinalis</i> and two phylogenetically related species, <i>Asparagus kiusianus</i> and <i>Asparagus setaceus</i>, and conducted expression studies after <i>Phomopsis asparagi</i> infection in <i>A. officinalis</i>. Our findings demonstrate that NLR genes in all three species display chromosomal clustering patterns. Phylogenetic reconstruction and N-terminal domain classification categorized these NLRs into three distinct subfamilies, with their promoters containing numerous cis-elements responsive to defense signals and phytohormones. Comparative genomic analysis revealed a marked contraction of the NLR genes from the wild species to the domesticated <i>A. officinalis</i>, with gene counts of 63, 47, and 27 NLR genes identified in <i>A. setaceus</i>, <i>A. kiusianus</i>, and <i>A. officinalis</i>, respectively. Orthologous gene analysis identified 16 conserved NLR gene pairs between <i>A. setaceus</i> and <i>A. officinalis</i>, which are likely the NLR genes preserved during the domestication process of <i>A. officinalis</i>. Pathogen inoculation assays revealed distinct phenotypic responses: <i>A. officinalis</i> was susceptible, while <i>A. setaceus</i> remained asymptomatic. Notably, the majority of preserved NLR genes in <i>A. officinalis</i> demonstrated either unchanged or downregulated expression following fungal challenge, indicating a potential functional impairment in disease resistance mechanisms. In conclusion, our findings suggest that the increased disease susceptibility of domesticated <i>A. officinalis</i> is driven by both the contraction of NLR gene repertoire and the functional reduced or inconsistent induction of retained NLR genes-potentially a consequence of artificial selection favoring yield and quality. This study provides important insights into the evolutionary dynamics of NLR genes within the <i>Asparagus</i> genus and may contribute to future efforts aimed at disease-resistant breeding in <i>A. officinalis</i>.