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

ABSTRACT: 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 Cuc

SUBMITTER: Song H 

PROVIDER: S-EPMC10548412 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature