Genome-wide analysis of basic helix-loop-helix transcription factors in papaya ( <i>Carica papaya</i> L.)

Abstract

The basic helix-loop-helix (bHLH) transcription factors (TFs) have been identified and functionally characterized in many plants. However, no comprehensive analysis of the bHLH family in papaya (<i>Carica papaya</i> L.) has been reported previously. Here, a total of 73 <i>CpbHLHs</i> were identified in papaya, and these genes were classified into 18 subfamilies based on phylogenetic analysis. Almost all of the <i>CpbHLHs</i> in the same subfamily shared similar gene structures and protein motifs according to analysis of exon/intron organizations and motif compositions. The number of exons in <i>CpbHLHs</i> varied from one to 10 with an average of five. The amino acid sequences of the bHLH domains were quite conservative, especially Leu-27 and Leu-63. Promoter <i>cis</i>-element analysis revealed that most of the <i>CpbHLHs</i> contained <i>cis</i>-elements that can respond to various biotic/abiotic stress-related events. Gene ontology (GO) analysis revealed that <i>CpbHLHs</i> mainly functions in protein dimerization activity and DNA-binding, and most <i>CpbHLHs</i> were predicted to localize in the nucleus. Abiotic stress treatment and quantitative real-time PCR (qRT-PCR) revealed some important candidate <i>CpbHLHs</i> that might be responsible for abiotic stress responses in papaya. These findings would lay a foundation for further investigate of the molecular functions of <i>CpbHLHs</i>.