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 ( Carica papaya L.) has been reported previously. Here, a total of 73 CpbHLHs were identified in papaya, and these genes were classified into 18 subfamilies based on phylogenetic analysis. Almost all of the CpbHLHs in the same subfamily shared similar gene structures and protein motifs according to

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... is of exon/intron organizations and motif compositions. The number of exons in CpbHLHs varied from 1 to 10 with an average of 5. The amino acid sequences of the bHLH domains were quite conservative, especially Leu-27 and Leu-63. Promoter cis-element analysis revealed that most of the CpbHLHs contained cis-elements that can respond to various biotic/abiotic stress-related events. Gene ontology (GO) analysis revealed that CpbHLHs mainly functions in protein dimerization activity and DNA-binding, and most CpbHLHs were predicted to localize in the nucleus. Abiotic stress treatment and quantitative real-time PCR (qRT-PCR) revealed some important candidate CpbHLHs that might be responsible for abiotic stress responses in papaya. These findings would lay a foundation for further investigate of the molecular functions of CpbHLHs. PeerJ reviewing PDF | (2020:02:45453:1:0:CHECK 15 Apr 2020) Manuscript to be reviewed 1 2 Genome-wide analysis of basic helix-loop-helix 3 transcription factors in papaya (Carica papaya L.) 4 5 Abstract 43 The basic helix-loop-helix (bHLH) transcription factors (TFs) have been identified and 44 functionally characterized in many plants. However, no comprehensive analysis of the bHLH 45 family in papaya (Carica papaya L.) has been reported previously. Here, a total of 73 CpbHLHs 46 were identified in papaya, and these genes were classified into 18 subfamilies based on 47 phylogenetic analysis. Almost all of the CpbHLHs in the same subfamily shared similar gene 48 structures and protein motifs according to analysis of exon/intron organizations and motif 49 compositions. The number of exons in CpbHLHs varied from 1 to 10 with an average of 5. The 50 amino acid sequences of the bHLH domains were quite conservative, especially Leu-27 and Leu-51 63. Promoter cis-element analysis revealed that most of the CpbHLHs contained cis-elements 52 that can respond to various biotic/abiotic stress-related events. Gene ontology (GO) analysis 53 revealed that CpbHLHs mainly functions in protein dimerization activity and DNA-binding, and 54 most CpbHLHs were predicted to localize in the nucleus. Abiotic stress treatment and 55 quantitative real-time PCR (qRT-PCR) revealed some important candidate CpbHLHs that might 56 be responsible for abiotic stress responses in papaya. These findings would 57 lay a foundation for further investigate of the molecular functions of CpbHLHs.