ArticleProceedings of the National Academy of Sciences of the United States of America2011
Reference-guided assembly of four diverse Arabidopsis thaliana genomes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 138 papers.
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
138 citing papers in PubMed.
- The origin and evolution of HKT proteins with TrkH domain from aquatic plants to flowering plants.Horticulture research · 2025Article
- CLAE: A High-Fidelity Nanopore Sequencing Strategy for Read-Level Viral Variant Detection and Environmental RNA Virus Discovery.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Identification of a natural RcLOG1 allele linked to prickle development in Rose (Rosa spp.).Planta · 2025Article
- Comparative genomics profiling of Citrus species reveals the diversity and disease responsiveness of the GLP pangenes family.BMC plant biology · 2025Article
- NAVIP: Unraveling the influence of neighboring small sequence variants on functional impact prediction.PLoS computational biology · 2025Article
- Complexity welcome: Pangenome graphs for comprehensive population genomics.Quantitative plant biology · 2025Review
- Two adjacent NLR genes conferring quantitative resistance to clubroot disease in Arabidopsis are regulated by a stably inherited epiallelic variation.Plant communications · 2024Article
- MCPtaggR: R package for accurate genotype calling in reduced representation sequencing data by eliminating error-prone markers based on genome comparison.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- Hound: a novel tool for automated mapping of genotype to phenotype in bacterial genomes assembled de novo.Briefings in bioinformatics · 2024Article
- Origin and evolution of the triploid cultivated banana genome.Nature genetics · 2024Article
- Choclo virus (CHOV) recovered from deep metatranscriptomics of archived frozen tissues in natural history biorepositories.PLoS neglected tropical diseases · 2024Article
- De novo assembled mitogenome analysis of Trichuris trichiura from Korean individuals using nanopore-based long-read sequencing technology.PLoS neglected tropical diseases · 2023Article
- Epigenetic Regulation in Heterosis and Environmental Stress: The Challenge of Producing Hybrid Epigenomes to Face Climate Change.Epigenomes · 2023Review
- The FANCC-FANCE-FANCF complex is evolutionarily conserved and regulates meiotic recombination.Nucleic acids research · 2023Article
- Extensive sequence duplication in Arabidopsis revealed by pseudo-heterozygosity.Genome biology · 2023Article
- GALA: a computational framework for de novo chromosome-by-chromosome assembly with long reads.Nature communications · 2023Article
- Genome-wide identification, evolution and expression pattern analysis of theFrontiers in plant science · 2023Article
- Reference-based read clustering improves theComputational and structural biotechnology journal · 2023Article
- Optimization of the "Ecology and evolution · 2023Article
- Easy353: A Tool to Get Angiosperms353 Genes for Phylogenomic Research.Molecular biology and evolution · 2022Article
78 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present whole-genome assemblies of four divergent Arabidopsis thaliana strains that complement the 125-Mb reference genome sequence released a decade ago. Using a newly developed reference-guided approach, we assembled large contigs from 9 to 42 Gb of Illumina short-read data from the Landsberg erecta (Ler-1), C24, Bur-0, and Kro-0 strains, which have been sequenced as part of the 1,001 Genomes Project for this species. Using alignments against the reference sequence, we first reduced the complexity of the de novo assembly and later integrated reads without similarity to the reference sequence. As an example, half of the noncentromeric C24 genome was covered by scaffolds that are longer than 260 kb, with a maximum of 2.2 Mb. Moreover, over 96% of the reference genome was covered by the reference-guided assembly, compared with only 87% with a complete de novo assembly. Comparisons with 2 Mb of dideoxy sequence reveal that the per-base error rate of the reference-guided assemblies was below 1 in 10,000. Our assemblies provide a detailed, genomewide picture of large-scale differences between A. thaliana individuals, most of which are difficult to access with alignment-consensus methods only. We demonstrate their practical relevance in studying the expression differences of polymorphic genes and show how the analysis of sRNA sequencing data can lead to erroneous conclusions if aligned against the reference genome alone. Genome assemblies, raw reads, and further information are accessible through http://1001genomes.org/projects/assemblies.html.
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.