Nucleotide-binding site (NBS) disease resistance genes play an important role in defending plants from a variety of pathogens and insect pests. Many R-genes have been identified in various plant species. However, little is known about the NBS-encoding genes in Brachypodium distachyon. In this study, using computational analysis of the B. distachyon genome, we identified 126 regular NBS-encoding genes and characterized them on the bases of structural diversity, conserved protein motifs, chromosomal locations, gene duplications, promoter region, and phylogenetic relationships. EST hits and full-length cDNA sequences (from Brachypodium database) of 126 R-like candidates supported their existence. Based on the occurrence of conserved protein motifs such as coiled-coil (CC), NBS, leucine-rich repeat (LRR), these regular NBS-LRR genes were classified into four subgroups: CC-NBS-LRR, NBS-LRR, CC-NBS, and X-NBS. Further expression analysis of the regular NBS-encoding genes in Brachypodium database revealed that these genes are expressed in a wide range of libraries, including those constructed from various developmental stages, tissue types, and drought challenged or nonchallenged tissue. 1. Introduction To ward off the attacks of bacteria, fungi, oomycetes, viruses, and nematodes, plants have evolved various defense mechanisms to protect themselves. One of the major mechanisms is characterized by a gene-for-gene interaction that required a specific plant resistance (R) gene and a cognate pathogen avirulence (Avr) gene [1]. This type of specific resistance is often associated with a localized hypersensitive response, a form of programmed cell death, in the plant cells proximal to the site of infection triggered by the recognition of a pathogen product [2, 3]. Previous works show that the plant genomes contain a large number of R-genes to counter a variety of pathogens. Most characterized R-genes contain the regions that encode NBS at the N-proximal part and a series of leucine-rich repeats (LRRs) at the C-proximal part [4]. The NBS domain is involved in signaling and includes several highly conserved and strictly ordered motifs such as P-loop, kinase-2, and GLPL motifs [5], which has been demonstrated by the binding and hydrolysis of ATP and GTP. However, the LRR motif is typically involved in protein-protein interactions and ligand binding with pathogen-derived molecules, suggesting that this domain may play a pivotal role in defining pathogen recognition specificity [6]. In plants, the NBS-LRR genes have been subdivided into two main groups based on the
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