Genome-Wide Analysis of NBS-LRR–Encoding Genes in Arabidopsis[W]
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- 1 April 2003
- journal article
- review article
- Published by Oxford University Press (OUP) in Plant Cell
- Vol. 15 (4) , 809-834
- https://doi.org/10.1105/tpc.009308
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.Keywords
This publication has 119 references indexed in Scilit:
- Mosaic Organization of Orthologous Sequences in Grass GenomesGenome Research, 2002
- Plant pathogens and integrated defence responses to infectionNature, 2001
- T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. ThorntonJournal of Molecular Biology, 2000
- Resistance Gene Candidates Identified by PCR with Degenerate Oligonucleotide Primers Map to Clusters of Resistance Genes in LettuceMolecular Plant-Microbe Interactions®, 1998
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choiceNucleic Acids Research, 1994
- Predicting Coiled Coils from Protein SequencesScience, 1991
- The GTPase superfamily: conserved structure and molecular mechanismNature, 1991
- A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequencesJournal of Molecular Evolution, 1980
- Current Status of the Gene-For-Gene ConceptAnnual Review of Phytopathology, 1971