Phylogeny and diversification of B‐function MADS‐box genes in angiosperms: evolutionary and functional implications of a 260‐million‐year‐old duplication

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Abstract
B‐function MADS‐box genes play crucial roles in floral development in model angiosperms. We reconstructed the structural and functional implications of B‐function gene phylogeny in the earliest extant flowering plants based on analyses that include 25 newAP3andPIsequences representing critical lineages of the basalmost angiosperms:Amborella,Nuphar(Nymphaeaceae), andIllicium(Austrobaileyales). The ancestral size of exon 5 inPI‐homologues is 42 bp, typical of exon 5 in other plant MADS‐box genes. This 42‐bp length is found inPI‐homologues fromAmborellaand Nymphaeaceae, successive sisters to all other angiosperms. Following these basalmost branches, a deletion occurred in exon 5, yielding a length of 30 bp, a condition that unites all other angiosperms. Several shared amino acid strings, including a prominent “DEAER” motif, are present in the AP3‐ and PI‐homologues ofAmborella. These may be ancestral motifs that were present before the duplication that yielded the AP3 and PI lineages and subsequently were modified after the divergence ofAmborella. Other structural features were identified, including a motif that unites the previously described TM6 clade and a deletion inAP3‐homologues that unites all Magnoliales. Phylogenetic analyses ofAP3‐ andPI‐homologues yielded gene trees that generally track organismal phylogeny as inferred by multigene data sets. With both AP3 and PI amino acid sequences,Amborellaand Nymphaeaceae are sister to all other angiosperms. Using nonparametric rate smoothing (NPRS), we estimated that the duplication that produced theAP3andPIlineages occurred approximately 260 mya (231–290). This places the duplication after the split between extant gymnosperms and angiosperms, but well before the oldest angiosperm fossils. A striking similarity in the multimer‐signalling C domains of theAmborellaproteins suggests the potential for the formation of unique transcription‐factor complexes. The earliest angiosperms may have been biochemically flexible in their B function and “tinkered” with floral organ identity.
Funding Information
  • National Science Foundation (PGR‐0115684)