Diversity in Nucleotide Binding Site–Leucine-Rich Repeat Genes in Cereals

Abstract

The diversity of the largest group of plant disease resistance genes, the nucleotide binding site–leucine-rich repeat (NBS–LRR) genes, was examined in cereals following polymerase chain reaction (PCR) cloning and database mining. NBS–LRR genes in rice are a large and diverse class with more than 600 genes, at least three to four times the complement of Arabidopsis. Most occur in small families containing one or a few cross-hybridizing members. Unlike inArabidopsis and other dicots, the class of NBS–LRR genes coding for a Toll and mammalian interleukin-1 receptor (TIR) domain were not amplified during the evolution of the cereals. Genes coding for TIR domains are present in the rice genome, but have diverged from the NBS–LRR genes. Most cereal genes are similar in structure to the members of the non-TIR class of dicots, although many do not code for a coiled-coil domain in their amino termini. One unique class of cereal genes, with ∼50 members, codes for proteins similar to the N-termini and NBS domains of resistance genes but does not code for LRR domains. The resistance gene repertoire of grasses has changed from that of dicots in their independent evolution since the two groups diverged. It is not clear whether this reflects a difference in downstream defense signaling pathways.[Supplemental material is available online at www.genome.org. The sequence data from this study have been submitted to GenBank under accession nos.AF516886–AF516895.]

The Fractionated Orthology of Bs2 and Rx/Gpa2 Supports Shared Synteny of Disease Resistance in the Solanaceae

“…A motif that is fairly conserved in the N-terminal domain of most characterized non-TIR-NB-LRR proteins is the EDxxD motif, which is found adjacent to potential coiled-coils and forward of the NB-ARC (Bai et al 2002;Rairdan et al 2008). The region WVxxIRELAYDIEDIVDxY was aligned among all of the R genes in our study and grouped according to clades identified in Figure 1A (also see Figure 2B).…”

“…9FAM includes all nine families known to form coiled-coils and the MTK matrix is a smaller matrix including only myosins, tropomyosins, and kinesins. (B) An alignment of the N-terminal, non-TIR motif region described by Bai et al (2002) and Rairdan et al (2008) organized according to groups defined by the tree in Figure 1A. Amino acids are colored according to their properties.…”

“…Sequence relationships of the noncoding regions near and within R genes: We interpret the intron position within R genes (Bai et al 2002;Meyers et al 2003) as an indicator of orthology relationships. Introns and exons, both within the coding region and in the 59-and 39-UTR, are shown in Figure 1B.…”

Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns

“…1). It is widely recognized that the NBS domain effectively distinguishes NBS genes into TNL and nTNL classes (Bai et al, 2002;Meyers et al, 2003). Although a sister relationship between CNLs and RNLs has been established in rosids, it has not been examined at angiosperm level.…”

“…NBS genes are historically divided into two classes, namely, TIR-NBS-LRR (TNL) and the non-TIR-NBS-LRR (nTNL), which are differentiated by the presence of a Toll/IL-1 Receptor-like (TIR) domain in the protein amino terminus (Meyers et al, 1999;Bai et al, 2002;Zhou et al, 2004). Because most nTNL genes encode a coiled-coil (CC) domain at the N terminus, the nTNL genes often are called CC-NBS-LRR (CNL) genes (Meyers et al, 2003;Ameline-Torregrosa et al, 2008).…”