Conservation and divergence in the <i>AGAMOUS</i> subfamily of MADS‐box genes: evidence of independent sub‐ and neofunctionalization events

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<jats:title>SUMMARY</jats:title><jats:p>The MADS‐box gene <jats:italic>AGAMOUS</jats:italic> (<jats:italic>AG</jats:italic>) plays a key role in determining floral meristem and organ identities. We identified three <jats:italic>AG</jats:italic> homologs, <jats:italic>EScaAG1</jats:italic>, <jats:italic>EScaAG2</jats:italic>, and <jats:italic>EScaAGL11</jats:italic> from the basal eudicot <jats:italic>Eschscholzia californica</jats:italic> (California poppy). Phylogenetic analyses indicate that <jats:italic>EScaAG1</jats:italic> and <jats:italic>EScaAG2</jats:italic> are recent paralogs within the <jats:italic>AG</jats:italic> clade, independent of the duplication in ancestral core eudicots that gave rise to the <jats:italic>euAG</jats:italic> and <jats:italic>PLENA</jats:italic> (<jats:italic>PLE</jats:italic>) orthologs. <jats:italic>EScaAGL11</jats:italic> is basal to core eudicot <jats:italic>AGL11</jats:italic> orthologs in a clade representing an older duplication event after the divergence of the angiosperm and gymnosperm lineages. Detailed in situ hybridization experiments show that expression of <jats:italic>EScaAG1</jats:italic> and <jats:italic>EScaAG2</jats:italic> is similar to <jats:italic>AG</jats:italic>; however, both genes appear to be expressed earlier in floral development than described in the core eudicots. A thorough examination of available expression and functional data in a phylogenetic context for members of the <jats:italic>AG</jats:italic> and <jats:italic>AGL11</jats:italic> clades reveals that gene expression has been quite variable throughout the evolutionary history of the <jats:italic>AG</jats:italic> subfamily and that ovule‐specific expression might have evolved more than twice. Although sub‐ and neofunctionalization are inferred to have occurred following gene duplication, functional divergence among orthologs is evident, as is convergence, among paralogs sampled from different species. We propose that retention of multiple <jats:italic>AG</jats:italic> homologs in several paralogous lineages can be explained by the conservation of ancestral protein activity combined with evolutionarily labile regulation of expression in the <jats:italic>AG</jats:italic> and <jats:italic>AGL11</jats:italic> clades such that the collective functions of the <jats:italic>AG</jats:italic> subfamily in stamen and carpel development are maintained following gene duplication.</jats:p>

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