The Medicago genome provides insight into the evolution of rhizobial symbioses

Abstract

Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing ∼94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa's genomic toolbox.

Figure 1. Circos diagram illustrating syntentic relationships between Medicago, Glycine, Lotus and Vitis

Homologous gene pairs were identified for all pairwise comparisons between Mt, Gm, Lj and Vv genomes. Syntenic regions associated with the ancestral WGD events were identified by visually inspection of correponding dot-plots. The large Mt5–Mt8 synteny block (yellow) was found to have two syntenic regions in Lj (red), four syntenic regions in Gm (blue) and three in Vv (green).

Figure 2. Circos diagram illustrating the Medicago WGD and selected gene families

The 963 WGD-derived paralogous gene pairs were examined for overlap with the nodule-enhanced gene list (Datafile S2). Resulting gene pairs were joined and plotted as either blue circles (only one of the duplicates is nodule-enhanced) or red (both nodule enhanced). Gene densities of NBS-LRRs, NCRs and other defensin-like proteins are plotted against chromosome position. Density was calculated using a sliding window (100 kb window with 50 kb steps).

Figure 3. Microsynteny comparison between Medicago homoeologues and corresponding regions of Glycine and Vitis

Microsyntenic genome segments are centered around Medtr3g104510/Medtr1g015890 (Table S10), a duplicated region derived from the ~58 Mya WGD event noted in orange. The <13 Mya Gm-specific WGD is colored yellow. Orthologous/paralogous gene pairs are indicated through use of a common color. White arrows represent genes with no syntenic homologue(s) in this genome region. Gray arrow indicates a Mt gene model with syntenic homologue in soybean, but no soybean gene model in the current annotation (www.phytozome.net/soybean).