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Article|19 Feb 2022|OPEN
Comparative genomics analysis of bHLH genes in cucurbits identifies a novel gene regulating cucurbitacin biosynthesis
Yuanchao Xu1 , Huimin Zhang2 , Yang Zhong1,3 , Naiyu Jiang2 , Xiaoyun Zhong1 , Qiqi Zhang1 , Sen Chai2 and Hongbo Li3 , Zhonghua Zhang,2 ,
1Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
2Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
3Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
*Corresponding author. E-mail:

Horticulture Research 9,
Article number: uhac038 (2022)
Views: 387

Received: 23 Nov 2021
Revised: 16 Jun 2022
Accepted: 30 Jan 2022
Published online: 19 Feb 2022


The basic helix–loop–helix (bHLH) family of transcription factors (TFs) participate in a variety of biological regulatory processes in plants, and have undergone significant expansion during land plant evolution by gene duplications. In cucurbit crops, several bHLH genes have been found to be responsible for agronomic traits such as bitterness. However, the characterization of bHLH genes across the genomes of cucurbit species has not been reported, and how they have evolved and diverged remains largely unanswered. Here we identified 1,160 bHLH genes in seven cucurbit crops and performed a comprehensive comparative genomics analysis. We determined orthologous and paralogous bHLH genes across cucurbit crops by syntenic analysis between or within species. Orthology and phylogenetic analysis of the tandem-duplicated bHLH genes in the Bt cluster, which regulate the biosynthesis of cucurbitacins, suggest that this cluster is derived from three ancestral genes after the cucurbit-common tetraploidization event. Interestingly, we identified a new conserved cluster paralogous to the Bt cluster that includes two tandem bHLH genes, and the evolutionary history and expression profiles of these two genes in the new cluster suggest the involvement of one gene (Brp) in the regulation of cucurbitacin biosynthesis in roots. Further biochemical and transgenic assays in melon hairy roots supported the function of Brp. This study provides useful information for further investigating the functions of bHLH TFs and novel insights into the regulation of cucurbitacin biosynthesis in cucurbit crops and other plants.