A Genome-Wide Comparison of NB-LRR Type of Resistance Gene Analogs (RGA) in the Plant Kingdom

Abstract

Plants express resistance (R) genes to recognize invaders and prevent the spread of pathogens. To analyze nucleotide binding site, leucine-rich repeat (NB-LRR) genes, we constructed a fast pipeline to predict and classify the R gene analogs (RGAs) by applying in-house matrices. With predicted ~37,000 RGAs, we can directly compare RGA contents across entire plant lineages, from green algae to flowering plants. We focused on the highly divergent NBLRRs in land plants following the emergence of mosses. We identified entire loss of Toll/Interleukin-1 receptor, NB-LRR (TNL) in Poaceae family of monocots and interestingly from Mimulus guttatus (a dicot), which leads to the possibility of species-specific TNL loss in other sequenced flowering plants. Using RGA maps, we have elucidated a positive correlation between the cluster sizes of NB-LRRs and their numbers. The cluster members were observed to consist of the same class of NB-LRRs or their variants, which were probably generated from a single locus for an R gene. Our website (http://sol.kribb.re.kr/PRGA/), called plant resistance gene analog (PRGA), provides useful information, such as RGA annotations, tools for predicting RGAs, and analyzing domain profiles. Therefore, PRGA provides new insights into R-gene evolution and is useful in applying RGA as markers in breeding and or systematic studies.

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

“…We predicted and classified resistance gene analogue (RGA) genes by applying a modified version of an HMM-based pipeline 43 46 against RefBeet (see Supplementary Methods). Expanded and potentially lost gene families in Beta vulgaris.…”

Phased, Secondary, Small Interfering RNAs in Posttranscriptional Regulatory Networks

“…Within these domains (TIR, CC, NB, and LRR) there are numerous highly conserved motifs, and the nucleotides encoding some of these motifs are important targets of miRNAs, as described below. Genes encoding the CNLtype (CNLs) are found in both dicots and monocots, whereas TNL-encoding genes (TNLs) are found exclusively in dicots (Kim et al, 2012). Both CNLs and TNLs are found in mosses, early land plants, as well as two other types of NB-LRRs that apparently were not retained in angiosperms (Xue et al, 2012).…”

“…Both CNLs and TNLs are found in mosses, early land plants, as well as two other types of NB-LRRs that apparently were not retained in angiosperms (Xue et al, 2012). It is believed that TNLs were lost in the monocots (Pan et al, 2000) and perhaps some dicot lineages such as Mimulus guttatus (Kim et al, 2012). Most plant genomes encode hundreds of R proteins, ranging from the reported low of ;55 NB-containing proteins in papaya (Carica papaya) (Ming et al, 2008) and ;62 in cucumber (Cucumis sativus; Yang et al, 2013), to ;150 in Arabidopsis (Meyers et al, 2003) and more than 500 in rice and 700 in Medicago truncatula, a model species for legumes (Zhou et al, 2004;Young et al, 2011).…”

Adaptive response of Pinus monticola driven by positive selection upon resistance gene analogs (RGAs) of the TIR-NBS-LRR subfamily

“…PCR approaches implementing mainly degenerate primers were extensively applied in order to isolate members of the NBS family (nucleotide-binding site) / LRRs (LeucineRich Repeats) -containing genes, the most highly expanded group of genes linked directly to resistance (R) genes mediated functions in plants (Debener & Byrne 2014). This protein family is further classified into two major subfamilies based on structural characteristics of their putative amino-terminal signaling domain (Kim et al 2012). One subfamily, TIR-NBS-LRR, contains an amino-terminal signaling domain that depicts homology with Toll and interleukin-1 receptor (TIR), whilst the other subfamily, CC-NBS-LRR, instead of the TIR domain, carries a putative coiled-coil structure (CC) one (Kim et al 2012).…”

“…This protein family is further classified into two major subfamilies based on structural characteristics of their putative amino-terminal signaling domain (Kim et al 2012). One subfamily, TIR-NBS-LRR, contains an amino-terminal signaling domain that depicts homology with Toll and interleukin-1 receptor (TIR), whilst the other subfamily, CC-NBS-LRR, instead of the TIR domain, carries a putative coiled-coil structure (CC) one (Kim et al 2012). Both these subfamilies have been reported to mediate resistance to a wide range of phytopathenic fungi (Wan et al 2010).…”