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Article|28 Feb 2023|OPEN
Identification of clade-wide putative cis-regulatory elements from conserved non-coding sequences in Cucurbitaceae genomes 
Hongtao Song1 , Qi Wang1 , Zhonghua Zhang2 , Kui Lin1 and Erli Pang,1 ,
1MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
2College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
*Corresponding author. E-mail:

Horticulture Research 10,
Article number: uhad038 (2023)
Views: 216

Received: 22 Aug 2022
Accepted: 20 Feb 2023
Published online: 28 Feb 2023


Cis-regulatory elements regulate gene expression and play an essential role in the development and physiology of organisms. Many conserved non-coding sequences (CNSs) function as cis-regulatory elements. They control the development of various lineages. However, predicting clade-wide cis-regulatory elements across several closely related species remains challenging. Based on the relationship between CNSs and cis-regulatory elements, we present a computational approach that predicts the clade-wide putative cis-regulatory elements in 12 Cucurbitaceae genomes. Using 12-way whole-genome alignment, we first obtained 632 112 CNSs in Cucurbitaceae. Next, we identified 16 552 Cucurbitaceae-wide cis-regulatory elements based on collinearity among all 12 Cucurbitaceae plants. Furthermore, we predicted 3 271 potential regulatory pairs in the cucumber genome, of which 98 were verified using integrative RNA sequencing and ChIP sequencing datasets from samples collected during various fruit development stages. The CNSs, Cucurbitaceae-wide cis-regulatory elements, and their target genes are accessible at These elements are valuable resources for functionally annotating CNSs and their regulatory roles in Cucurbitaceae genomes.