Diversity, Distribution, and Ancient Taxonomic Relationships Within the TIR and Non-TIR NBS-LRR Resistance Gene Subfamilies |
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| Authors: | Steven B Cannon Hongyan Zhu Andrew M Baumgarten Russell Spangler Georgiana May Douglas R Cook Nevin D Young |
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| Institution: | (1) Department of Plant Biology, University of Minnesota, St. Paul, MN 55108, USA, US;(2) Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA, US;(3) Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN 55108, USA, US;(4) Graduate Program in Genetics, Texas A&M University, College Station, TX 77843, USA, US;(5) Department of Plant Pathology, University of California, Davis, Davis, CA 95616, USA, US |
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| Abstract: | Phylogenetic relationships among the NBS-LRR (nucleotide binding site–leucine-rich repeat) resistance gene homologues (RGHs)
from 30 genera and nine families were evaluated relative to phylogenies for these taxa. More than 800 NBS-LRR RGHs were analyzed,
primarily from Fabaceae, Brassicaceae, Poaceae, and Solanaceae species, but also from representatives of other angiosperm
and gymnosperm families. Parsimony, maximum likelihood, and distance methods were used to classify these RGHs relative to
previously observed gene subfamilies as well as within more closely related sequence clades. Grouping sequences using a distance
cutoff of 250 PAM units (point accepted mutations per 100 residues) identified at least five ancient sequence clades with
representatives from several plant families: the previously observed TIR gene subfamily and a minimum of four deep splits
within the non-TIR gene subfamily. The deep splits in the non-TIR subfamily are also reflected in comparisons of amino acid
substitution rates in various species and in ratios of nonsynonymous-to-synonymous nucleotide substitution rates (K
A/K
S values) in Arabidopsis thaliana. Lower K
A/K
S values in the TIR than the non-TIR sequences suggest greater functional constraints in the TIR subfamily. At least three
of the five identified ancient clades appear to predate the angiosperm–gymnosperm radiation. Monocot sequences are absent
from the TIR subfamily, as observed in previous studies. In both subfamilies, clades with sequences separated by approximately
150 PAM units are family but not genus specific, providing a rough measure of minimum dates for the first diversification
event within these clades. Within any one clade, particular taxa may be dramatically over- or underrepresented, suggesting
preferential expansions or losses of certain RGH types within particular taxa and suggesting that no one species will provide
models for all major sequence types in other taxa.
Received: 13 June 2001 / Accepted: 22 October 2001 |
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| Keywords: | : NBS-LRR disease resistance gene — Multigene families — Protein sequence evolution — Glycine max— Medicago truncatula— Birth and death model |
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