Despite a century of research, the evolutionary origin of angiosperms remains uncertain. Morphological studies have identified the gnetophytes as the sister group of angiosperms mainly because of the similar organization of their reproductive structures. Molecular studies have been ambiguous as to whether these two groups are closely related. Study of the development of seed plant reproductive structures can help to untangle this issue. Here, I report the cloning of five MARS-box floral homeotic gene homologues from the gnetophyte Ephedra andina. Three of these genes belong to AG, AGL6 and TM3 subfamilies. These monophyletic groups comprise angiosperm as well as conifer homologues. Phylogenetic analysis of the plant MADS-box gene family reveals that within subfamilies, Ephedra genes always form subclades with other gymnosperm genes to the exclusion of all angiosperm genes. These results suggest that gnetophytes are more closely related to conifers than to angiosperms.

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