A matrix plot of synteny assessed between allotetraploid Trifolium repens and diploid Medicago truncatula genomes. A total of 376 T. repens sequences among 822 queried showed sequence homology to M. truncatula. SSR-containing T. repens GeneThresher® (purple dots), EST (green dots), and genomic (black dots) sequences and candidate genes (red ∆) were ordered according to proportion of distance along merged T. repens homoeologue linkage maps (1–8) then aligned by BLAST analysis with homologous (E-value threshold of 1e-20) sequences in the Medicago truncatula genome (v 3.0) which were ordered by proportion of distance along M. truncatula pseudomolecules (1–8). Candidate genes are in the order of the first 15 listed in Table 1. For ease of comparison with previous T. repens linkage map literature, the Barrett et al.  A-H nomenclature and relative alignment (inv=inverted) is provided in brackets.