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Lotus ( Nelumbo nucifera  Gaertn.) is an economically important aquatic plant with multiple applications, but water salinity and cold stress seriously affect lotus yield and distribution. The basic helix-loop-helix (bHLH) transcription factors (TFs) play a vital role in plant growth and development, metabolic regulation processes and responses to environmental changes. However, systematic analyses of the bHLH TF family in lotus has not yet been reported. Here, we report the identification and description of bHLH genes in lotus ( NnbHLHs ) with a focus on functional prediction, particularly for those involved in stress resistance. In all, 115  NnbHLHs  were identified in the lotus genome and classified into 19 subfamilies. The chromosomal distribution, physicochemical properties, bHLH domain, conserved motif compositions and evolution of these 115  NnbHLHs  were further analyzed. To better understand the functions of the lotus bHLH family, gene ontology, cis-element, and phylogenetic analyses were conducted.  NnbHLHs  were predicted to be involved in plant development, metabolic regulation and responses to stress, in accordance with previous findings. Overall, 15  NnbHLHs  were further investigated with functional prediction via quantitative real-time PCR analyses. Meanwhile, expression profiles of  NnbHLHs  in four tissues indicated that many  NnbHLHs  showed tissue preference in their expression. This study is supposed to provide a good foundation for further research into the functions and evolution of  NnbHLHs , and identifies candidate genes for stress resistance in lotus.

Genome-wide analyses of the bHLH gene family reveals structural and functional characteristics in the aquatic plant Nelumbo nucifera