Genome-Wide Analysis of NBS-LRR-Encoding Genes in Arabidopsis

@article{citeulike:789726, abstract = {The Arabidopsis genome contains [\~{}]200 genes that encode proteins with similarity to the nucleotide binding site and other domains characteristic of plant resistance proteins. Through a reiterative process of sequence analysis and reannotation, we identified 149 NBS-LRR-encoding genes in the Arabidopsis (ecotype Columbia) genomic sequence. Fifty-six of these genes were corrected from earlier annotations. At least 12 are predicted to be pseudogenes. As described previously, two distinct groups of sequences were identified: those that encoded an N-terminal domain with Toll/Interleukin-1 Receptor homology (TIR-NBS-LRR, or TNL), and those that encoded an N-terminal coiled-coil motif (CC-NBS-LRR, or CNL). The encoded proteins are distinct from the 58 predicted adapter proteins in the previously described TIR-X, TIR-NBS, and CC-NBS groups. Classification based on protein domains, intron positions, sequence conservation, and genome distribution defined four subgroups of CNL proteins, eight subgroups of TNL proteins, and a pair of divergent NL proteins that lack a defined N-terminal motif. CNL proteins generally were encoded in single exons, although two subclasses were identified that contained introns in unique positions. TNL proteins were encoded in modular exons, with conserved intron positions separating distinct protein domains. Conserved motifs were identified in the LRRs of both CNL and TNL proteins. In contrast to CNL proteins, TNL proteins contained large and variable C-terminal domains. The extant distribution and diversity of the NBS-LRR sequences has been generated by extensive duplication and ectopic rearrangements that involved segmental duplications as well as microscale events. The observed diversity of these NBS-LRR proteins indicates the variety of recognition molecules available in an individual genotype to detect diverse biotic challenges. 10.1105/tpc.009308}, author = {Meyers, Blake C. and Kozik, Alexander and Griego, Alyssa and Kuang, Hanhui and Michelmore, Richard W. }, citeulike-article-id = {789726}, doi = {http://dx.doi.org/10.1105/tpc.009308}, journal = {Plant Cell}, keywords = {arabidopsis, gene, plant, r\_gene, resistance, rga}, month = {April}, number = {4}, pages = {809--834}, posted-at = {2006-11-27 14:23:26}, priority = {2}, title = {Genome-Wide Analysis of NBS-LRR-Encoding Genes in Arabidopsis}, url = {http://dx.doi.org/10.1105/tpc.009308}, volume = {15}, year = {2003} }

TY - JOUR ID - citeulike:789726 L3 - citeulike-article-id:789726 TI - Genome-Wide Analysis of NBS-LRR-Encoding Genes in Arabidopsis JF - Plant Cell VL - 15 IS - 4 SP - 809 EP - 834 N2 - The Arabidopsis genome contains [~]200 genes that encode proteins with similarity to the nucleotide binding site and other domains characteristic of plant resistance proteins. Through a reiterative process of sequence analysis and reannotation, we identified 149 NBS-LRR-encoding genes in the Arabidopsis (ecotype Columbia) genomic sequence. Fifty-six of these genes were corrected from earlier annotations. At least 12 are predicted to be pseudogenes. As described previously, two distinct groups of sequences were identified: those that encoded an N-terminal domain with Toll/Interleukin-1 Receptor homology (TIR-NBS-LRR, or TNL), and those that encoded an N-terminal coiled-coil motif (CC-NBS-LRR, or CNL). The encoded proteins are distinct from the 58 predicted adapter proteins in the previously described TIR-X, TIR-NBS, and CC-NBS groups. Classification based on protein domains, intron positions, sequence conservation, and genome distribution defined four subgroups of CNL proteins, eight subgroups of TNL proteins, and a pair of divergent NL proteins that lack a defined N-terminal motif. CNL proteins generally were encoded in single exons, although two subclasses were identified that contained introns in unique positions. TNL proteins were encoded in modular exons, with conserved intron positions separating distinct protein domains. Conserved motifs were identified in the LRRs of both CNL and TNL proteins. In contrast to CNL proteins, TNL proteins contained large and variable C-terminal domains. The extant distribution and diversity of the NBS-LRR sequences has been generated by extensive duplication and ectopic rearrangements that involved segmental duplications as well as microscale events. The observed diversity of these NBS-LRR proteins indicates the variety of recognition molecules available in an individual genotype to detect diverse biotic challenges. 10.1105/tpc.009308 KW - arabidopsis KW - gene KW - plant KW - r_gene KW - resistance KW - rga AU - Meyers, Blake AU - Kozik, Alexander AU - Griego, Alyssa AU - Kuang, Hanhui AU - Michelmore, Richard PY - 2003/04/01/ UR - http://dx.doi.org/10.1105/tpc.009308 ER -