Diversity in nucleotide binding site-leucine-rich repeat genes in cereals.

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 in Arabidopsis 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.

Bai J ，Pennill LA ，Ning J ，Lee SW ，Ramalingam J ，Webb CA ，Zhao B ，Sun Q ，Nelson JC ，Leach JE ，Hulbert SH ... -  《-》

Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana.

Plant disease resistance genes have been shown to be subject to positive selection, particularly in the leucine rich repeat (LRR) region that may determine resistance specificity. We performed a genome-wide analysis of positive selection in members of the nucleotide binding site (NBS)-LRR gene family of Arabidopsis thaliana. Analyses were possible for 103 of 163 NBS-LRR nucleotide sequences in the genome, and the analyses uncovered substantial evidence of positive selection. Sites under positive selection were detected and identified for 10 sequence groups representing 53 NBS-LRR sequences. Functionally characterized Arabidopsis resistance genes were in these 10 groups, but several groups with extensive evidence of positive selection contained no previously characterized resistance genes. Amino acid residues under positive selection were identified, and these residues were mapped onto protein secondary structure. Positively selected positions were disproportionately located in the LRR domain (P < 0.001), particularly a nine-amino acid beta-strand submotif that is likely to be solvent exposed. However, a substantial proportion (30%) of positively selected sites were located outside LRRs, suggesting that regions other than the LRR may function in determining resistance specificity. Because of the unusual sequence variability in the LRRs of this class of proteins, secondary-structure analysis identifies LRRs that are not identified by similarity analyses alone. LRRs also contain substantial indel variation, suggesting elasticity in LRR length could also influence resistance specificity.

Mondragón-Palomino M ，Meyers BC ，Michelmore RW ，Gaut BS ... -  《GENOME RESEARCH》

Comparative analysis of NBS domain sequences of NBS-LRR disease resistance genes from sunflower, lettuce, and chicory.

Plant resistance to many types of pathogens and pests can be achieved by the presence of disease resistance (R) genes. The nucleotide binding site-leucine rich repeat (NBS-LRR) class of R-genes is the most commonly isolated class of R-genes and makes up a super-family, which is often arranged in the genome as large multi-gene clusters. The NBS domain of these genes can be targeted by polymerase chain reaction (PCR) amplification using degenerate primers. Previous studies have used PCR derived NBS sequences to investigate both ancient R-gene evolution and recent evolution within specific plant families. However, comparative studies with the Asteraceae family have largely been ignored. In this study, we address recent evolution of NBS sequences within the Asteraceae and extend the comparison to the Arabidopsis thaliana genome. Using multiple sets of primers, NBS fragments were amplified from genomic DNA of three species from the family Asteraceae: Helianthus annuus (sunflower), Lactuca sativa (lettuce), and Cichorium intybus (chicory). Analysis suggests that Asteraceae species share distinct families of R-genes, composed of genes related to both coiled-coil (CC) and toll-interleukin-receptor homology (TIR) domain containing NBS-LRR R-genes. Between the most closely related species, (lettuce and chicory) a striking similarity of CC subfamily composition was identified, while sunflower showed less similarity in structure. These sequences were also compared to the A. thaliana genome. Asteraceae NBS gene subfamilies appear to be distinct from Arabidopsis gene clades. These data suggest that NBS families in the Asteraceae family are ancient, but also that gene duplication and gene loss events occur and change the composition of these gene subfamilies over time.

Plocik A ，Layden J ，Kesseli R 《MOLECULAR PHYLOGENETICS AND EVOLUTION》

Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes.

A complete set of candidate disease resistance ( R) genes encoding nucleotide-binding sites (NBSs) was identified in the genome sequence of japonica rice ( Oryza sativaL. var. Nipponbare). These putative R genes were characterized with respect to structural diversity, phylogenetic relationships and chromosomal distribution, and compared with those in Arabidopsis thaliana. We found 535 NBS-coding sequences, including 480 non-TIR (Toll/IL-1 receptor) NBS-LRR (Leucine Rich Repeat) genes. TIR NBS-LRR genes, which are common in A. thaliana, have not been identified in the rice genome. The number of non-TIR NBS-LRR genes in rice is 8.7 times higher than that in A. thaliana, and they account for about 1% of all of predicted ORFs in the rice genome. Some 76% of the NBS genes were located in 44 gene clusters or in 57 tandem arrays, and 16 apparent gene duplications were detected in these regions. Phylogenetic analyses based both NBS and N-terminal regions classified the genes into about 200 groups, but no deep clades were detected, in contrast to the two distinct clusters found in A. thaliana. The structural and genetic diversity that exists among NBS-LRR proteins in rice is remarkable, and suggests that diversifying selection has played an important role in the evolution of R genes in this agronomically important species. (Supplemental material is available online at http://gattaca.nju.edu.cn.)

Zhou T ，Wang Y ，Chen JQ ，Araki H ，Jing Z ，Jiang K ，Shen J ，Tian D ... -  《-》

Divergent evolution of plant NBS-LRR resistance gene homologues in dicot and cereal genomes.

Pan Q ，Wendel J ，Fluhr R 《JOURNAL OF MOLECULAR EVOLUTION》