Abstract
Plants have evolved an elaborate innate immune system against invading pathogens. Within this system, intracellular nucleotide-binding leucine-rich repeat (NLR) immune receptors are known play critical roles in effector-triggered immunity (ETI) plant defense. We performed genome-wide identification and classification of NLR-coding sequences from the genomes of pepper, tomato, and potato using fixed criteria. We then compared genomic duplication and evolution features. We identified intact 267, 443, and 755 NLR-encoding genes in tomato, potato, and pepper genomes, respectively. Phylogenetic analysis and classification of Solanaceae NLRs revealed that the majority of NLR super family members fell into 14 subgroups, including a TIR-NLR (TNL) subgroup and 13 non-TNL subgroups. Specific subgroups have expanded in each genome, with the expansion in pepper showing subgroup-specific physical clusters. Comparative analysis of duplications showed distinct duplication patterns within pepper and among Solanaceae plants suggesting subgroup- or species-specific gene duplication events after speciation, resulting in divergent evolution. Taken together, genome-wide analysis of NLR family members provide insights into their evolutionary history in Solanaceae. These findings also provide important foundational knowledge for understanding NLR evolution and will empower broader characterization of disease resistance genes to be used for crop breeding.
Highlights
Plants and animals have immune systems that protect against invading pathogens, with members of the signal-transduction ATPases with numerous domains (STAND) superfamily of proteins playing important roles in these systems (Maekawa et al, 2011; Duxbury et al, 2016)
This result was due to the expansion of all types of genes belonging to the CNL group (CC-nucleotide-binding leucine-rich repeat (NLR), NBcc-leucine-rich repeat (LRR), CC-NB, NBcc; Table 1)
These results indicate that Solanaceae NLRs have evolved through a species-specific manner
Summary
Plants and animals have immune systems that protect against invading pathogens, with members of the signal-transduction ATPases with numerous domains (STAND) superfamily of proteins playing important roles in these systems (Maekawa et al, 2011; Duxbury et al, 2016). The first barrier is composed of cell-surface pattern recognition receptors that recognize conserved pathogen-associated molecular patterns (PAMPs), such as flagellin and chitin. Plants have a second defensive layer composed of intracellular immune receptors that induce effector-triggered immunity (ETI; Cui et al, 2015). Plants and their pathogens are hypothesized to have evolved attenuating each other (Jones and Dangl, 2006; Fei et al, 2016). Plant genomes contain numerous genes encoding intracellular immune receptors, which either directly or indirectly recognize effectors Such recognition mediates various downstream defense mechanisms including localized programmed cell death, known as hypersensitive response (Cui et al, 2015)
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