Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatula

Abstract

The nucleotide-binding site (NBS)-Leucine-rich repeat (LRR) gene family accounts for the largest number of known disease resistance genes, and is one of the largest gene families in plant genomes. We have identified 333 nonredundant NBS-LRRs in the current Medicago truncatula draft genome (Mt1.0), likely representing 400 to 500 NBS-LRRs in the full genome, or roughly 3 times the number present in Arabidopsis (Arabidopsis thaliana). Although many characteristics of the gene family are similar to those described on other plant genomes, several evolutionary features are particularly pronounced in M. truncatula, including a high degree of clustering, evidence of significant numbers of ectopic translocations from clusters to other parts of the genome, a small number of more evolutionarily stable NBS-LRRs, and numerous truncations and fusions leading to novel domain compositions. The gene family clearly has had a large impact on the structure of the genome, both through ectopic translocations (potentially, a means of seeding new NBS-LRR clusters), and through two extraordinarily large superclusters. Chromosome 6 encodes approximately 34% of all TIR-NBS-LRRs, while chromosome 3 encodes approximately 40% of all coiled-coil-NBS-LRRs. Almost all atypical domain combinations are in the TIR-NBS-LRR subfamily, with many occurring within one genomic cluster. This analysis shows the gene family not only is important functionally and agronomically, but also plays a structural role in the genome.

Figure 1.

Distribution of NBS-LRR encoded genes on the eight chromosomes of M. truncatula. Red (TNL) and green (CNL) sequences on M. truncatula 1.0 draft chromosome assemblies. NBS consensus sequences, derived from TNL and CNL alignments, were used as blastp queries, and displayed using CViT-blast (www.medicago.org). Pseudochromosomes are represented by the succession of BACs (vertical, gray thick lines) separated by gaps (black, horizontal lines). Not all gaps are visible at this resolution. Unmapped BACs are shown on the right as MtChr0. For more detail, including BAC accessions, see Supplemental Data S6.

Figure 2.

Phylogenetic tree of NBS domains of NBS-LRR predicted proteins from M. truncatula. A and B, Tree of CNL predicted proteins. C, Tree of TNL predicted proteins. These are maximum parsimony trees with maximum likelihood branch lengths (“Materials and Methods”). Chromosomal origin of each gene is indicated with color and in the third character (Mt1, etc.) of each sequence name. For example, the large orange clades near the top of A consists of sequences primarily from chromosome 3. Right-hand digits in each gene name indicate predicted gene order in this version of the draft genome pseudomolecule assembly. For stable public gene names, see Supplemental Table S1. Pink dots indicate approximate coalescence points for NBS sequences from Arabidopsis and/or poplar (Supplemental Data S3 and S11–S14). Bootstrap values for important basal clades are indicated in blue. Black arrows indicate pairs of clades that can be mapped to an internal genomic duplication within M. truncatula. For example, in A, arrows in the middle of the figure show sequences from M. truncatula chromosomes 1 and 3 that both come from syntenic duplications blocks from those chromosomes. Columns on the right side show domain configurations (Supplemental Table S1; Table I), numbers of predicted LRR units, and predicted regulatory elements (Supplemental Table S1). Note: Gene names shown in this figure are intended to simplify analysis, but are specific to this study only. For persistent gene names, please consult Supplemental Table S1.

Figure 2.

Phylogenetic tree of NBS domains of NBS-LRR predicted proteins from M. truncatula. A and B, Tree of CNL predicted proteins. C, Tree of TNL predicted proteins. These are maximum parsimony trees with maximum likelihood branch lengths (“Materials and Methods”). Chromosomal origin of each gene is indicated with color and in the third character (Mt1, etc.) of each sequence name. For example, the large orange clades near the top of A consists of sequences primarily from chromosome 3. Right-hand digits in each gene name indicate predicted gene order in this version of the draft genome pseudomolecule assembly. For stable public gene names, see Supplemental Table S1. Pink dots indicate approximate coalescence points for NBS sequences from Arabidopsis and/or poplar (Supplemental Data S3 and S11–S14). Bootstrap values for important basal clades are indicated in blue. Black arrows indicate pairs of clades that can be mapped to an internal genomic duplication within M. truncatula. For example, in A, arrows in the middle of the figure show sequences from M. truncatula chromosomes 1 and 3 that both come from syntenic duplications blocks from those chromosomes. Columns on the right side show domain configurations (Supplemental Table S1; Table I), numbers of predicted LRR units, and predicted regulatory elements (Supplemental Table S1). Note: Gene names shown in this figure are intended to simplify analysis, but are specific to this study only. For persistent gene names, please consult Supplemental Table S1.

Figure 2.

Phylogenetic tree of NBS domains of NBS-LRR predicted proteins from M. truncatula. A and B, Tree of CNL predicted proteins. C, Tree of TNL predicted proteins. These are maximum parsimony trees with maximum likelihood branch lengths (“Materials and Methods”). Chromosomal origin of each gene is indicated with color and in the third character (Mt1, etc.) of each sequence name. For example, the large orange clades near the top of A consists of sequences primarily from chromosome 3. Right-hand digits in each gene name indicate predicted gene order in this version of the draft genome pseudomolecule assembly. For stable public gene names, see Supplemental Table S1. Pink dots indicate approximate coalescence points for NBS sequences from Arabidopsis and/or poplar (Supplemental Data S3 and S11–S14). Bootstrap values for important basal clades are indicated in blue. Black arrows indicate pairs of clades that can be mapped to an internal genomic duplication within M. truncatula. For example, in A, arrows in the middle of the figure show sequences from M. truncatula chromosomes 1 and 3 that both come from syntenic duplications blocks from those chromosomes. Columns on the right side show domain configurations (Supplemental Table S1; Table I), numbers of predicted LRR units, and predicted regulatory elements (Supplemental Table S1). Note: Gene names shown in this figure are intended to simplify analysis, but are specific to this study only. For persistent gene names, please consult Supplemental Table S1.