Genome-wide analysis of basic helix-loop-helix transcription factors in papaya (Carica papayaL.)

Abstract

<jats:p>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 (<jats:italic>Carica papaya</jats:italic> L.) has been reported previously. Here, a total of 73 <jats:italic>CpbHLHs</jats:italic> were identified in papaya, and these genes were classified into 18 subfamilies based on phylogenetic analysis. Almost all of the<jats:italic> CpbHLHs</jats:italic> 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 <jats:italic>CpbHLHs</jats:italic> 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 <jats:italic>cis</jats:italic>-element analysis revealed that most of the <jats:italic>CpbHLHs</jats:italic> contained <jats:italic>cis</jats:italic>-elements that can respond to various biotic/abiotic stress-related events. Gene ontology (GO) analysis revealed that <jats:italic>CpbHLHs</jats:italic> mainly functions in protein dimerization activity and DNA-binding, and most <jats:italic>CpbHLHs</jats:italic> were predicted to localize in the nucleus. Abiotic stress treatment and quantitative real-time PCR (qRT-PCR) revealed some important candidate <jats:italic>CpbHLHs</jats:italic> that might be responsible for abiotic stress responses in papaya. These findings would lay a foundation for further investigate of the molecular functions of <jats:italic>CpbHLHs</jats:italic>.</jats:p>

A Review of Omics Technologies and Bioinformatics to Accelerate Improvement of Papaya Traits

“…Such examples include the comparative genome-wide analysis of the papaya genome in order to identify, annotate, and classify the genes into several gene and transcriptionfactor families that are associated with abiotic stress [31], disease resistance [24,32], ripening [33,34], and flower development [35]. The identification and annotation of the selected gene families in the papaya genome have also provided information on their gene structure, and phylogenetic tree relationships in relation to orthologs or paralogs from other species.…”

“…The identification and annotation of the selected gene families in the papaya genome have also provided information on their gene structure, and phylogenetic tree relationships in relation to orthologs or paralogs from other species. Consequently, the potential genes and transcription factors were validated to further investigate their expression patterns under different conditions [31][32][33][34][35].…”

“…Using the genome sequence of the papaya, the basic helix-loop-helix (bHLH) transcription factors that were associated with abiotic stress were identified [31]. A total of 73 candidate genes from the bHLH family were detected using comparative genome-wide analysis.…”

The bHLH transcription factor AhbHLH112 improves the drought tolerance of peanut

“…The first member of this family was discovered in maize and interacts with members of the MYB family to control anthocyanin biosynthesis and pigmentation [ 14 ]. In all, 167, 165, 159, 127, 85, 107 and 97 bHLH family members have been found in Arabidopsis [ 15 ], Oryza [ 16 ], Solanum [ 17 ], Salvia miltiorrhiza [ 18 ], Ginkgo biloba [ 19 ], Capsicum [ 20 ] and Carica papaya [ 21 ], respectively. Genome-wide analyses have identified 261 bHLH genes in the peanut [ 22 ].…”

Systems biology applied to the study of papaya fruit ripening: the influence of ethylene

“…The MYB family, associated with anthocyanin synthesis and cell development, had three genes with decreased expression even with the increase in the color intensity of the fruit pulp, possibly because papaya has a greater influence on carotenoids than anthocyanins . Seven genes encoding for basic helix-loop-helix (bHLH), one of the largest families of transcription factors involved in many basal biological processes such as plant growth, development, and defense, presented isoforms with different levels of expression in treated groups (YANG et al, 2020). Heat shock proteins (HPSs) are numerous and involved in a wide range of processes, usually stress-mediated due to their chaperonelike function (WATERS; VIERLING, 2020).…”