AUTHOR=He Xiaomei , Zhang Wenwu , Sabir Irfan Ali , Jiao Chunyan , Li Guohui , Wang Yan , Zhu Fucheng , Dai Jun , Liu Longyun , Chen Cunwu , Zhang Yingyu , Song Cheng 

TITLE=The spatiotemporal profile of Dendrobium huoshanense and functional identification of bHLH genes under exogenous MeJA using comparative transcriptomics and genomics

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1169386

DOI=10.3389/fpls.2023.1169386

ISSN=1664-462X

ABSTRACT=<sec><title>Introduction</title><p>Alkaloids are one of the main medicinal components of <italic>Dendrobium</italic> species. <italic>Dendrobium</italic> alkaloids are mainly composed of terpene alkaloids. Jasmonic acid (JA) induce the biosynthesis of such alkaloids, mainly by enhancing the expression of JA-responsive genes to increase plant resistance and increase the content of alkaloids. Many JA-responsive genes are the target genes of bHLH transcription factors (TFs), especially the MYC2 transcription factor.</p></sec><sec><title>Methods</title><p>In this study, the differentially expressed genes involved in the JA signaling pathway were screened out from <italic>Dendrobium huoshanense</italic> using comparative transcriptomics approaches, revealing the critical roles of basic helix-loop-helix (bHLH) family, particularly the MYC2 subfamily.</p></sec><sec><title>Results and discussion</title><p>Microsynteny-based comparative genomics demonstrated that whole genome duplication (WGD) and segmental duplication events drove <italic>bHLH</italic> genes expansion and functional divergence. Tandem duplication accelerated the generation of <italic>bHLH</italic> paralogs. Multiple sequence alignments showed that all bHLH proteins included bHLH-zip and ACT-like conserved domains. The MYC2 subfamily had a typical bHLH-MYC_N domain. The phylogenetic tree revealed the classification and putative roles of bHLHs. The analysis of <italic>cis</italic>-acting elements revealed that promoter of the majority of <italic>bHLH</italic> genes contain multiple regulatory elements relevant to light response, hormone responses, and abiotic stresses, and the <italic>bHLH</italic> genes could be activated by binding these elements. The expression profiling and <italic>q</italic>RT-PCR results indicated that <italic>bHLH</italic> subgroups IIIe and IIId may have an antagonistic role in JA-mediated expression of stress-related genes. <italic>DhbHLH20</italic> and <italic>DhbHLH21</italic> were considered to be the positive regulators in the early response of JA signaling, while <italic>DhbHLH24</italic> and <italic>DhbHLH25</italic> might be the negative regulators. Our findings may provide a practical reference for the functional study of <italic>DhbHLH</italic> genes and the regulation of secondary metabolites.</p></sec>