Identification of clade-wide putative -regulatory elements from conserved non-coding sequences in Cucurbitaceae genomes.

-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 -regulatory elements. They control the development of various lineages. However, predicting clade-wide -regulatory elements across several closely related species remains challenging. Based on the relationship between CNSs and -regulatory elements, we present a computational approach that predicts the clade-wide putative -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 -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 -regulatory elements, and their target genes are accessible at http://cmb.bnu.edu.cn/cisRCNEs_cucurbit/. These elements are valuable resources for functionally annotating CNSs and their regulatory roles in Cucurbitaceae genomes.