ArticleMolecular biology and evolution2021
Evolution of Conserved Noncoding Sequences in Arabidopsis thaliana.
Article in Molecular biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 28 citations in OpenAlex.
- Genome evolution through polyploidy: Enhancing plant stress resilience in agriculture.Proceedings of the National Academy of Sciences of the United States of America · 2026Review
- ProtDML: label-aware representation learning for broad-spectrum protein function prediction.Briefings in bioinformatics · 2026Article
- The landscape of regulatory element evolution in a C4 perennial grass.BMC genomics · 2026Article
- Lineage-specific evolution of regulatory landscapes in a polyploid plant and its diploid progenitors.bioRxiv : the preprint server for biology · 2026Article
- Pangenome-Wide Identification, Evolutionary Analysis of Maize ZmPLD Gene Family, and Functional Validation of ZmPLD15 in Cold Stress Tolerance.Plants (Basel, Switzerland) · 2025Article
- Predicting Gene Expression Responses to Cold inGenes · 2025Article
- Review
- Uncovering the multi-layer cis-regulatory landscape of rice via integrative nascent RNA analysis.Genome biology · 2025Article
- Substitution-Mutation Rate Ratio (c/µ) As Molecular Adaptation Test Beyond Ka/Ks: A SARS-COV-2 Case Study.Journal of molecular evolution · 2025Article
- Characterization and functional analysis of conserved non-coding sequences among poaceae: insights into gene regulation and phenotypic variation in maize.BMC genomics · 2025Article
- Article
- Modern Plant Breeding Techniques in Crop Improvement and Genetic Diversity: From Molecular Markers and Gene Editing to Artificial Intelligence-A Critical Review.Plants (Basel, Switzerland) · 2024Review
- Maternal dominance contributes to subgenome differentiation in allopolyploid fishes.Nature communications · 2023Article
- Blueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts.Horticulture research · 2023Article
- Dynamics ofProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Review
- Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation.Genome biology · 2022Article
- Chromosome-Scale Genome for a Red-Fruited, Perpetual Flowering and Runnerless Woodland Strawberry (Frontiers in genetics · 2021Article
- Expansion of the circadian transcriptome ineLife · 2020Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent pangenome studies have revealed a large fraction of the gene content within a species exhibits presence-absence variation (PAV). However, coding regions alone provide an incomplete assessment of functional genomic sequence variation at the species level. Little to no attention has been paid to noncoding regulatory regions in pangenome studies, though these sequences directly modulate gene expression and phenotype. To uncover regulatory genetic variation, we generated chromosome-scale genome assemblies for thirty Arabidopsis thaliana accessions from multiple distinct habitats and characterized species level variation in Conserved Noncoding Sequences (CNS). Our analyses uncovered not only PAV and positional variation (PosV) but that diversity in CNS is nonrandom, with variants shared across different accessions. Using evolutionary analyses and chromatin accessibility data, we provide further evidence supporting roles for conserved and variable CNS in gene regulation. Additionally, our data suggests that transposable elements contribute to CNS variation. Characterizing species-level diversity in all functional genomic sequences may later uncover previously unknown mechanistic links between genotype and phenotype.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.