Phylogenetic Diversity of the MADS-Box Gene Family in Loblolly Pine (Pinus taeda)

The MADS-box gene family encodes eukaryotic transcription factors acting in control of environmental responses and development, including reproductive organ specification.  Here we present the expressed MADS-box genes of Pinus taeda, the first complete view of this family in a gymnosperm.  Full-length protein coding sequences, alternative splice forms, and putative allelic variants were assembled and classified from broad transcript profiles generated from next-generation sequencing of RNA from reproductive and vegetative organs, seeds and whole seedlings. Loblolly MADS-box orthologs were identified by domain-based alignments to angiosperm, moss and lycopod proteins, and maximum likelihood phylogenetic analyses were performed.

The Type I group is represented by two Mβ members, while Mα and Mγ MADS-box lineages appear absent in pine. In the MIKC*-like Type II group, prior studies had shown gymnosperm members only in the P-clade.  We confirm the P-clade in pine and provide the first report of orthologs to the angiosperm S-clade in gymnosperms.

MIKC^C Type II MADS-box genes are represented by eleven lineages. Pine orthologs are phylogenetically nested within the B-class, C/D-class, B_sister, AGl6/AGL13, AGL15, AGL12/XAL1, AGL22/SVP/StMADS11, TM3/SOC, AGL17, and a DAL10-like gymnosperm specific lineage. Our transcriptome data support the hypothesis that the MADS-box gymnosperm specific lineage is more closely related to the B_sister group. The three MADS box lineages SOC1/TM3-like, TM8, and AGL22/SVP/StMADS11 reveal expansions in pine relative to other plants. We further detail highly conserved C-terminal motifs among Type II lineages, and organ specificities of expression that suggest substantial roles for MADS-box genes in male reproductive functions.