Highly syntenic regions in the genomes of soybean, Medicago truncatula, and Arabidopsis thaliana

Abstract

Background: Recent genome sequencing enables mega-base scale comparisons between related genomes. Comparisons between animals, plants, fungi, and bacteria demonstrate extensive synteny tempered by rearrangements. Within the legume plant family, glimpses of synteny have also been observed. Characterizing syntenic relationships in legumes is important in transferring knowledge from model legumes to crops that are important sources of protein, fixed nitrogen, and health-promoting compounds.

Results: We have uncovered two large soybean regions exhibiting synteny with M. truncatula and with a network of segmentally duplicated regions in Arabidopsis. In all, syntenic regions comprise over 500 predicted genes spanning 3 Mb. Up to 75% of soybean genes are colinear with M. truncatula, including one region in which 33 of 35 soybean predicted genes with database support are colinear to M. truncatula. In some regions, 60% of soybean genes share colinearity with a network of A. thaliana duplications. One region is especially interesting because this 500 kbp segment of soybean is syntenic to two paralogous regions in M. truncatula on different chromosomes. Phylogenetic analysis of individual genes within these regions demonstrates that one is orthologous to the soybean region, with which it also shows substantially denser synteny and significantly lower levels of synonymous nucleotide substitutions. The other M. truncatula region is inferred to be paralogous, presumably resulting from a duplication event preceding speciation.

Conclusion: The presence of well-defined M. truncatula segments showing orthologous and paralogous relationships with soybean allows us to explore the evolution of contiguous genomic regions in the context of ancient genome duplication and speciation events.

Figure 1

Synteny block 1. A syntenic block of soybean, M. truncatula and A. thaliana genes surrounding soybean's rhg1 gene (Gm gene 21). Solid black lines connect homologs. Dotted black lines indicate that the absence of a homolog in the syntenic position. Blue lines connect orthologs. Pink lines connect paralogs. M. truncatula genes are shown in red, soybean in brown, and A. thaliana in blue. Lighter colored genes represent those that had no significant similarity to Genbank's nonredundant protein database. Gray genes are repetitive elements. A thick gray vertical line connecting sequence assemblies indicate regions in which sequence is not yet available but in which linkage and approximate distance were determined. Genbank accessions are shown in gray.

Figure 2

Synteny block 2. A syntenic block of soybean, M. truncatula and A. thaliana sequence assemblies surrounding soybean's Rhg4 gene (Gm gene 29). Solid black lines connect homologs. Blue lines connect orthologs. Pink lines connect paralogs. Dotted black lines indicate that the absence of a homolog in the syntenic position. M. truncatula genes are shown in red, soybean in brown, and A. thaliana in blue. Lighter colored genes represent those that had no significant similarity to Genbank's nonredundant protein database. Gray genes are repetitive elements. A thick gray line connecting sequence assemblies indicate regions in which sequence is not yet available but in which physical linkage and approximate physical distance were determined. Numbers along the sequence assemblies indicate gene numbers. Genbank accessions are shown in gray. Green boxes identify a 25 kbp duplication.

Figure 3

Histograms of synonymous distance between soybean and M. truncatula homologs or M. truncatula homoeologs in a) synteny block 1 and b) synteny block 2. For synteny block 2, only the 8 genes with homologs in soybean and both M. truncatula duplicates are shown.