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Background  Soybean lipoxygenases ( Lxs ) play important roles in plant resistance and in conferring the distinct bean flavor.  Lxs  comprise a multi-gene family that includes  GmLx1 ,  GmLx2  and  GmLx3 , and many of these genes have been characterized. We were interested in investigating the relationship between the soybean lipoxygenase isozymes from an evolutionary perspective, since soybean has undergone two rounds of polyploidy. Here we report the tetrad genome structure of soybean  Lx  regions produced by ancient and recent polyploidy. Also, comparative genomics with  Medicago truncatula  was performed to estimate  Lxs  in the common ancestor of soybean and  Medicago .    Results  Two  Lx  regions in  Medicago truncatula  showing synteny with soybean were analyzed. Differential evolutionary rates between soybean and  Medicago  were observed and the median Ks values of Mt-Mt, Gm-Mt, and Gm-Gm paralogs were determined to be 0.75, 0.62, and 0.46, respectively. Thus the comparison of Gm-Mt paralogs (Ks = 0.62) and Gm-Mt orthologs (Ks = 0.45) supports the ancient duplication of  Lx  regions in the common ancestor prior to the  Medicago - Glycine  split. After speciation, no  Lx  regions generated by another polyploidy were identified in  Medicago . Instead tandem duplication of  Lx  genes was observed. On the other hand, a lineage-specific duplication occurred in soybean resulting in two pairs of  Lx  regions. Each pair of soybean regions was co-orthologous to one  Lx  region in  Medicago . A total of 34  Lx  genes (15  MtLxs  and 19  GmLxs)  were divided into two groups by phylogenetic analysis. Our study shows that the  Lx  gene family evolved from two distinct  Lx  genes in the most recent common ancestor.    Conclusion  This study analyzed two pairs of  Lx  regions generated by two rounds of polyploidy in soybean. Each pair of soybean homeologous regions is co-orthologous to one region of  Medicago , demonstrating the quartet structure of the soybean genome. Differential evolutionary rates between soybean and  Medicago  were observed; thus optimized rates of Ks per year should be applied for accurate estimation of coalescence times to each case of comparison: soybean-soybean, soybean- Medicago , or  Medicago - Medicago . In conclusion, the soybean  Lx  gene family expanded by ancient polyploidy prior to taxon divergence, followed by a soybean- specific duplication and tandem duplications, respectively.

The lipoxygenase gene family: a genomic fossil of shared polyploidy between Glycine max and Medicago truncatula