ArticleNature genetics2013
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions.
Article in Nature genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 190 papers, 1 of them a synthesis that pooled it.
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Who cites it
190 citing papers in PubMed, 1 synthesis or guideline pooled it.
- ChIP-Hub provides an integrative platform for exploring plant regulome.Nature communications · 2022Pooled it
- Mesopolyploidy as a taxonomic clade marker for Brassica and relatives (tribe Brassiceae).Annals of botany · 2026Article
- What has population genomics told us about the dynamics of selection and plant adaptation?Molecular biology and evolution · 2026Review
- CNEwrap: a scalable toolkit with a novel algorithm for large-scale genome-wide accelerated conserved non-coding elements detection.Nucleic acids research · 2026Article
- A new super-pangenome pipeline reveals domestication signatures of conserved noncoding sequences in the orange subfamily.Molecular biology and evolution · 2026Article
- The landscape of regulatory element evolution in a C4 perennial grass.BMC genomics · 2026Article
- Gene function predicts divergence across molecular levels.bioRxiv : the preprint server for biology · 2026Article
- Inferring fungal cis-regulatory networks from genome sequences via unsupervised and interpretable representation learning.Genetics · 2026Article
- Widespread turnover of a conserved cis-regulatory code across 589 grass species.Molecular biology and evolution · 2026Article
- Evolution of Repetitive Genomic Content and Gene Families Over Geo-Climatic Gradients in Brassicaceae.Ecology and evolution · 2025Article
- Vegetative to generative1 (Vgt1) is an enhancer affecting flowering time and jasmonate signaling in maize by promoting the expression of Zea mays Related to APETALA 2.7.Plant physiology · 2025Article
- Two deeply conserved non-coding sequences control PLETHORA1/2 expression and coordinate embryo and root development.Plant communications · 2025Article
- Text mining reveals the increasing importance of genomic approaches in crop research and breeding.Molecular breeding : new strategies in plant improvement · 2025Review
- Uncovering the multi-layer cis-regulatory landscape of rice via integrative nascent RNA analysis.Genome biology · 2025Article
- deepTFBS: Improving within- and Cross-Species Prediction of Transcription Factor Binding Using Deep Multi-Task and Transfer Learning.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Recruitment, rewiring and deep conservation in flowering plant gene regulation.Nature plants · 2025Article
- A map of integrated cis-regulatory elements enhances gene-regulatory analysis in maize.Plant communications · 2025Article
- Dissecting the Emerging Regulatory and Mechanistic Paradigms of Transcribed Conserved Non-Coding Elements in Breast Cancer.Biomolecules · 2025Article
- Pangeneric genome analyses reveal the evolution and diversity of the orchid genus Dendrobium.Nature plants · 2025Article
- Extensive genome evolution distinguishes maize within a stable tribe of grasses.bioRxiv : the preprint server for biology · 2025Article
130 more citing papers are in PubMed but not listed here.
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Authors and funding
29 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite the central importance of noncoding DNA to gene regulation and evolution, understanding of the extent of selection on plant noncoding DNA remains limited compared to that of other organisms. Here we report sequencing of genomes from three Brassicaceae species (Leavenworthia alabamica, Sisymbrium irio and Aethionema arabicum) and their joint analysis with six previously sequenced crucifer genomes. Conservation across orthologous bases suggests that at least 17% of the Arabidopsis thaliana genome is under selection, with nearly one-quarter of the sequence under selection lying outside of coding regions. Much of this sequence can be localized to approximately 90,000 conserved noncoding sequences (CNSs) that show evidence of transcriptional and post-transcriptional regulation. Population genomics analyses of two crucifer species, A. thaliana and Capsella grandiflora, confirm that most of the identified CNSs are evolving under medium to strong purifying selection. Overall, these CNSs highlight both similarities and several key differences between the regulatory DNA of plants and other species.
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