ArticleThe Plant cell2024
Identification and functional characterization of conserved cis-regulatory elements responsible for early fruit development in cucurbit crops.
Article in The Plant cell, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 13 citations in OpenAlex.
- Pangenome-resolved structural variation drives adaptation and trait evolution in cucumber.Nature genetics · 2026Article
- Single-Cell CRISPR: An Efficient Strategy for Decoding Plant Cis-Regulatory Complexity.Plant biotechnology journal · 2026Review
- Telomere-to-telomere genome assembly and comprehensive mutation library facilitate bitter gourd breeding and functional genomics research.Plant communications · 2026Article
- A new super-pangenome pipeline reveals domestication signatures of conserved noncoding sequences in the orange subfamily.Molecular biology and evolution · 2026Article
- Text mining reveals the increasing importance of genomic approaches in crop research and breeding.Molecular breeding : new strategies in plant improvement · 2025Review
- Review
- Editing multiple genes in Physalis pubescens provides valuable lessons and implications for creating new germplasm and varieties of Physalis crops.Plant & cell physiology · 2025Article
- Enhancers in Plant Development, Adaptation and Evolution.Plant & cell physiology · 2025Review
- Genome-Wide Identification ofInternational journal of molecular sciences · 2025Article
- Constraint of accessible chromatins maps regulatory loci involved in maize speciation and domestication.Nature communications · 2025Article
- Review
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Authors and funding
12 authors at 6 institutions in 1 country.
Funding
Abstract
A number of cis-regulatory elements (CREs) conserved during evolution have been found to be responsible for phenotypic novelty and variation. Cucurbit crops such as cucumber (Cucumis sativus), watermelon (Citrullus lanatus), melon (Cucumis melo), and squash (Cucurbita maxima) develop fruits from an inferior ovary and share some similar biological processes during fruit development. Whether conserved regulatory sequences play critical roles in fruit development of cucurbit crops remains to be explored. In six well-studied cucurbit species, we identified 392,438 conserved noncoding sequences (CNSs), including 82,756 that are specific to cucurbits, by comparative genomics. Genome-wide profiling of accessible chromatin regions (ACRs) and gene expression patterns mapped 20,865 to 43,204 ACRs and their potential target genes for two fruit tissues at two key developmental stages in six cucurbits. Integrated analysis of CNSs and ACRs revealed 4,431 syntenic orthologous CNSs, including 1,687 cucurbit-specific CNSs that overlap with ACRs that are present in all six cucurbit crops and that may regulate the expression of 757 adjacent orthologous genes. CRISPR mutations targeting two CNSs present in the 1,687 cucurbit-specific sequences resulted in substantially altered fruit shape and gene expression patterns of adjacent NAC1 (NAM, ATAF1/2, and CUC2) and EXT-like (EXTENSIN-like) genes, validating the regulatory roles of these CNSs in fruit development. These results not only provide a number of target CREs for cucurbit crop improvement, but also provide insight into the roles of CREs in plant biology and during evolution.
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