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Background  The  Arabidopsis FLOWERING LOCUS T  ( FT ) gene, a member of the phosphatidylethanolamine binding protein (PEBP) family, is a major controller of flowering in response to photoperiod, vernalization and light quality. In legumes,  FT  evolved into three, functionally diversified clades,  FTa ,  FTb  and  FTc . A milestone achievement in narrow-leafed lupin ( Lupinus angustifolius  L.) domestication was the loss of vernalization responsiveness at the  Ku  locus. Recently, one of two existing  L. angustifolius  homologs of  FTc ,  LanFTc1 , was revealed to be the gene underlying  Ku . It is the first recorded involvement of an  FTc  homologue in vernalization. The evolutionary basis of this phenomenon in lupin has not yet been deciphered.    Results  Bacterial artificial chromosome (BAC) clones carrying  LanFTc1  and  LanFTc2  genes were localized in different mitotic chromosomes and constituted sequence-specific landmarks for linkage groups NLL-10 and NLL-17. BAC-derived superscaffolds containing  LanFTc  genes revealed clear microsyntenic patterns to genome sequences of nine legume species. Superscaffold-1 carrying  LanFTc1  aligned to regions encoding one or more  FT -like genes whereas superscaffold-2 mapped to a region lacking such a homolog. Comparative mapping of the  L. angustifolius  genome assembly anchored to linkage map localized superscaffold-1 in the middle of a 15 cM conserved, collinear region. In contrast, superscaffold-2 was found at the edge of a 20 cM syntenic block containing highly disrupted collinearity at the  LanFTc2  locus. 118 PEBP-family full-length homologs were identified in 10 legume genomes. Bayesian phylogenetic inference provided novel evidence supporting the hypothesis that whole-genome and tandem duplications contributed to expansion of PEBP-family genes in legumes. Duplicated genes were subjected to strong purifying selection. Promoter analysis of  FT  genes revealed no statistically significant sequence similarity between duplicated copies; only RE-alpha and CCAAT-box motifs were found at conserved positions and orientations.    Conclusions  Numerous lineage-specific duplications occurred during the evolution of legume PEBP-family genes. Whole-genome duplications resulted in the origin of subclades  FTa ,  FTb  and  FTc  and in the multiplication of  FTa  and  FTb  copy number.  LanFTc1  is located in the region conserved among all main lineages of Papilionoideae.  LanFTc1  is a direct descendant of ancestral  FTc , whereas  LanFTc2  appeared by subsequent duplication.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-3150-z) contains supplementary material, which is available to authorized users.

bmc genomics

Expansion of the phosphatidylethanolamine binding protein family in legumes: a case study of Lupinus angustifolius L. FLOWERING LOCUS T homologs, LanFTc1 and LanFTc2