DaapNLRSeek, prediction, and evolution of resistance genes in polyploid sugarcane genomes

Sugarcane (Saccharum spp. hybrids) is an important crop for sugar and biofuel production. However, pathogens cause significant yield losses. Most plant resistance (R) proteins are nucleotide-binding leucine-rich repeat (NLR) proteins, which detect pathogen effectors and activate immune responses. Recent advances in polyploid sugarcane genomes will accelerate sugarcane resistance breeding, however, NLR gene prediction in the complex polyploid genomes remains challenging. To address this, we developed a diploidy-assisted annotation of polyploid NLRs (DaapNLRSeek) pipeline to accurately predict and annotate NLR genes from the complex polyploid sugarcane genomes. Using DaapNLRSeek, we annotated NLR genes in Erianthus rufipilus and five sugarcane cultivars (R570, ZZ1, XTT22, Np-X, and AP85-441), analyzing their architecture, collinearity, and evolution. We also identified paired NLRs, TIR-only, and TPK genes from these sugarcane genomes. Intriguingly, two sugarcane-paired NLRs induce immune responses in Nicotiana benthamiana. DaapNLRSeek bridges polyploid genome assembly with functional genomics and will accelerate sugarcane resistance breeding.