ArticleNature2011
Multiple reference genomes and transcriptomes for Arabidopsis thaliana.
Article in Nature, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 358 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
358 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Effect of Methodological Considerations on the Construction of Gene-Based Plant Pan-genomes.Genome biology and evolution · 2023Pooled it
- A conserved small RNA-generating gene cluster undergoes sequence diversification and contributes to plant immunity.Nature communications · 2026Article
- XtractPAV: an automated pipeline for identifying presence-absence variations across multiple genomes.BMC genomics · 2026Article
- Germline de novo mutation rate of the highly heterozygous amphioxus genome.Molecular biology and evolution · 2026Article
- Evolutionary history of Australian samphires (Salicornieae, Amaranthaceae).Annals of botany · 2026Article
- The distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana resolve the Central Dogma's information flow.Genome biology · 2025Article
- Comparison of linkage and association mapping in MAGIC lines identifies AtMTP3 as a new gene controlling natural variation in leaf zinc concentration in Arabidopsis.Journal of experimental botany · 2025Article
- Core biological principles and tools stemming from basic Arabidopsis research.The Plant cell · 2025Review
- The resistance awakens: Diversity at the DNA, RNA, and protein levels informs engineering of plant immune receptors from Arabidopsis to crops.The Plant cell · 2025Review
- Ectopic Gene Conversion Causing Quantitative Trait Variation.Molecular biology and evolution · 2025Article
- NAVIP: Unraveling the influence of neighboring small sequence variants on functional impact prediction.PLoS computational biology · 2025Article
- PangenePro: an automated pipeline for rapid identification and classification of gene family members.Bioinformatics advances · 2025Article
- Complexity welcome: Pangenome graphs for comprehensive population genomics.Quantitative plant biology · 2025Review
- Conserved features and diversity attributes of chimeric RNAs across accessions in four plants.Plant biotechnology journal · 2024Article
- TWAS facilitates gene-scale trait genetic dissection through gene expression, structural variations, and alternative splicing in soybean.Plant communications · 2024Article
- Population-level exploration of alternative splicing and its unique role in controlling agronomic traits of rice.The Plant cell · 2024Article
- Evolution of the Correlated Genomic Variation Landscape Across a Divergence Continuum in the Genus Castanopsis.Molecular biology and evolution · 2024Article
- Integration of shoot-derived polypeptide signals by root TGA transcription factors is essential for survival under fluctuating nitrogen environments.Nature communications · 2024Article
- Nitrate transporter protein NPF5.12 and major latex-like protein MLP6 are important defense factors against Verticillium longisporum.Journal of experimental botany · 2024Article
- A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range.Nature genetics · 2024Article
298 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
Authors and funding
23 authors.
Funding
Abstract
Genetic differences between Arabidopsis thaliana accessions underlie the plant's extensive phenotypic variation, and until now these have been interpreted largely in the context of the annotated reference accession Col-0. Here we report the sequencing, assembly and annotation of the genomes of 18 natural A. thaliana accessions, and their transcriptomes. When assessed on the basis of the reference annotation, one-third of protein-coding genes are predicted to be disrupted in at least one accession. However, re-annotation of each genome revealed that alternative gene models often restore coding potential. Gene expression in seedlings differed for nearly half of expressed genes and was frequently associated with cis variants within 5 kilobases, as were intron retention alternative splicing events. Sequence and expression variation is most pronounced in genes that respond to the biotic environment. Our data further promote evolutionary and functional studies in A. thaliana, especially the MAGIC genetic reference population descended from these accessions.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.