Genome-wide identification and characterization of melon bHLH transcription factors in regulation of fruit development

Background: The basic helix-loop-helix (bHLH) transcription factor family is one of the largest transcription factor families in plants, and plays crucial roles in plant development. Melon is one of an important horticulture plants, and is an attractive model plant for studying fruit ripening. However, the bHLH gene family of melon has not been identified yet, and functions in fruit growth and ripening are seldom researched. Results: In this study, 118 bHLH genes were identified in the genome of melon. Phylogenetic analysis illustrated that these CmbHLHs could be classified into 16 subfamilies. Intron distribution pattern analysis of bHLH domain found 13 intron distribution patterns in CmbHLHs. CmbHLH genes were unevenly distributed on chromosomes 1 to 12 of the melon genome, and five CmbHLH s were tandem repeat on chromosomes 4 and 8. Expression characters of CmbHLH genes were studied using the transcriptome data. Tissue analysis of indicated CmbHLH32 high expressed in female flowers and early fruit growth stage. Transgenic plant lines of overexpression of CmbHLH32 were constructed, and overexpression of CmbHLH32 result in early fruit ripening compared to the wild type fruit. Conclusions: The bHLH transcription factor family was identified and analyzed for the first time in the melon, overexpression of CmbHLH32 will affect the ripening time of melon fruit, these findings laid a theoretical foundation for further study on the role of bHLH family members in the growth and development of melon .

Identification of Homeobox Genes Associated with Lignification and Their Expression Patterns in Bamboo Shoots

Homeobox (HB) genes play critical roles in regulating various aspects of plant growth and development. However, little is known about HB genes in bamboo. In this study, a total of 115 HB genes (PeHB001–PeHB115) were identified from moso bamboo (Phyllostachys edulis) and grouped into 13 distinct classes (BEL, DDT, HD-ZIP I–IV, KNOX, NDX, PHD, PINTOX, PLINC, SAWADEE, and WOX) based on the conserved domains and phylogenetic analysis. The number of members in the different classes ranged from 2 to 24, and they usually varied in terms of exon–intron distribution pattern and length. There were 20 conserved motifs found in 115 PeHBs, with motif 1 being the most common. Gene ontology (GO) analysis showed that PeHBs had diverse molecular functions, with 19 PeHBs being annotated as having xylem development, xylem, and phloem pattern formation functions. Co-expression network analysis showed that 10 of the 19 PeHBs had co-expression correlations, and three members of the KNOX class were hub proteins that interacted with other transcription factors (TFs) such as MYB, bHLH, and OVATE, which were associated with lignin synthesis. Yeast two-hybridization results further proved that PeHB037 (BEL class) interacted with PeHB057 (KNOX class). Transcriptome expression profiling indicated that all PeHBs except PeHB017 were expressed in at least one of the seven tissues of moso bamboo, and 90 PeHBs were expressed in all the tissues. The qRT-PCR results of the 19 PeHBs showed that most of them were upregulated in shoots as the height increased. Moreover, a KNOX binding site was found in the promoters of the key genes involved in lignin synthesis such as Pe4CL, PeC3H, PeCCR, and PeCOMT, which had positive expression correlations with five KNOX genes. Similar results were found in winter bamboo shoots with prolonged storage time, which was consistent with the degree of lignification. These results provide basic data on PeHBs in moso bamboo, which will be helpful for future functional research on PeHBs with positive regulatory roles in the process of lignification.