Evolutionary Analysis of the <i>YABBY</i> Gene Family in Brassicaceae

The <i>YABBY</i> gene family is one of the plant transcription factors present in all seed plants. The family members were extensively studied in various plants and shown to play important roles in plant growth and development, such as the polarity establishment in lateral organs, the formation and development of leaves and flowers, and the response to internal plant hormone and external environmental stress signals. In this study, a total of 364 <i>YABBY</i> genes were identified from 37 Brassicaceae genomes, of which 15 were incomplete due to sequence gaps, and nine were imperfect (missing C2C2 zinc-finger or YABBY domain) due to sequence mutations. Phylogenetic analyses resolved these <i>YABBY</i> genes into six compact clades except for a <i>YAB3</i>-like gene identified in <i>Aethionema arabicum</i>. Seventeen Brassicaceae species each contained a complete set of six basic <i>YABBY genes</i> (i.e., 1 <i>FIL</i>, 1 <i>YAB</i>2, 1 <i>YAB3</i>, 1 <i>YAB5</i>, 1 <i>INO</i> and 1 <i>CRC</i>), while 20 others each contained a variable number of <i>YABBY</i> genes (5–25) caused mainly by whole-genome duplication/triplication followed by gene losses, and occasionally by tandem duplications. The fate of duplicate <i>YABBY</i> genes changed considerably according to plant species, as well as to <i>YABBY</i> gene type. These <i>YABBY</i> genes were shown to be syntenically conserved across most of the Brassicaceae species, but their functions might be considerably diverged between species, as well as between paralogous copies, as demonstrated by the promoter and expression analysis of <i>YABBY</i> genes in two <i>Brassica</i> species (<i>B. rapa</i> and <i>B. oleracea</i>). Our study provides valuable insights for understanding the evolutionary story of <i>YABBY</i> genes in Brassicaceae and for further functional characterization of each <i>YABBY</i> gene across the Brassicaceae species.