Genome-wide analysis of nucleotide-binding site disease resistance genes in Medicago truncatula

The class of nucleotide-binding site (NBS)-Leucine-rich repeat (LRR) disease resistance genes play an important role in defending plants from a variety of pathogens and insect pests. Consequently, many NBS-LRR genes have been identified in various plant species. In this study, we identified 617 NBS-encoding genes in the Medicago truncatula genome (Mt3.5v5) and divided them into two groups, regular (490) and non-regular (127) NBS-LRR genes. The regular NBS-LRR genes were characterized on the bases of structural diversity, chromosomal location, gene duplication, conserved protein motifs, and EST expression profiling. According to N-terminal motifs and LRR motifs, the 490 regular NBS-LRR genes were then classified into 10 types: CC-NBS (4), CC-NBS-LRR (212), TIR-NBS (20), TIR-NBS-LRR (160), TIR-NBS-TIR (1), TIR-NBS-TIR-LRR (2), NBS-TIR (7), NBS-TIR-LRR (1), NBS (10), and NBS-LRR (73). Analysis of the physical location and duplications of the regular NBS-LRR genes revealed that the M. truncatula genome is similar to rice. Interestingly, we found that TIR-type genes are more frequently expressed than non-TIR-type genes in M. truncatula, whereas the number of non-TIR-type regular NBS-LRR genes was greater than TIR-type genes, suggesting the gene expression was not associated with the total number of NBS-LRR genes. Moreover, we found that the phylogenetic tree supported our division of the regular NBS-LRR genes into two distinct clades (TIR-type and non-TIR-type), but some of the non-TIR-type lineages contain TIR-type genes. These analyses provide a robust database of NBS-LRR genes in M. truncatula that will facilitate the isolation of new resistance genes and breeding strategies to engineer disease resistance in leguminous crop.