The Basic Helix-Loop-Helix Transcription Factor Family in the Sacred Lotus, Nelumbo Nucifera

Nelumbo nucifera (Sacred Lotus) is a basal eudicot with exceptional physiological and metabolic properties including seed longevity, adaptations for an aquatic habit, and floral thermiogenesis. It also occupies a unique position in the phylogeny of land plants and can be a useful species for studies of conserved plant gene families. The basic-helix-loop-helix (bHLH) proteins represent one of the largest transcription factor families in plants and has undergone extensive duplication and expansion during plant evolution. One hundred and seventeen transcript models encoding canonical bHLHs were identified in the sacred lotus genome, as well as several "atypical" bHLH-encoding genes. The canonical bHLH proteins fall into 23 previously characterized subfamilies also present in other sequenced plant genomes, and are expressed as mRNA. Analysis of bHLHs from sacred lotus and other sequenced angiosperms indicates most of these families of bHLHs, along with secondary motifs associated with the bHLH domain, were likely present in the progenitor of flowering plants. The absence of a bHLH subfamily involved in root development in sacred lotus is consistent with the possibility that the development of specialized root structures may be mediated in part by changes in the bHLH families that regulate root development in dicots.