Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis

Blake C. Meyers, Alexander Kozik, Alyssa Griego, Hanhui Kuang, Richard W Michelmore

Research output: Contribution to journalArticle

964 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)809-834
Number of pages26
JournalPlant Cell
Volume15
Issue number4
DOIs
StatePublished - Apr 1 2003

Fingerprint

Gene encoding
Arabidopsis
Genes
Genome
genome
Proteins
genes
proteins
Introns
introns
Exons
Genomic Segmental Duplications
Inteins
exons
Ecotype
Plant Proteins
Pseudogenes
Interleukin-1 Receptors
pseudogenes
plant characteristics

ASJC Scopus subject areas

  • Plant Science
  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Cell Biology

Cite this

Meyers, B. C., Kozik, A., Griego, A., Kuang, H., & Michelmore, R. W. (2003). Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell, 15(4), 809-834. https://doi.org/10.1105/tpc.009308

Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. / Meyers, Blake C.; Kozik, Alexander; Griego, Alyssa; Kuang, Hanhui; Michelmore, Richard W.

In: Plant Cell, Vol. 15, No. 4, 01.04.2003, p. 809-834.

Research output: Contribution to journalArticle

Meyers, BC, Kozik, A, Griego, A, Kuang, H & Michelmore, RW 2003, 'Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis', Plant Cell, vol. 15, no. 4, pp. 809-834. https://doi.org/10.1105/tpc.009308
Meyers BC, Kozik A, Griego A, Kuang H, Michelmore RW. Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell. 2003 Apr 1;15(4):809-834. https://doi.org/10.1105/tpc.009308
Meyers, Blake C. ; Kozik, Alexander ; Griego, Alyssa ; Kuang, Hanhui ; Michelmore, Richard W. / Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. In: Plant Cell. 2003 ; Vol. 15, No. 4. pp. 809-834.
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