ArticlePloS one2019
A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 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
33 citing papers in PubMed.
- Dissecting root-specific non-conventional effector-triggered immunity and its role in defense and shifting the microbiome.Nature communications · 2026Article
- DupyliCate: mining, classifying, and characterizing gene duplications.Scientific reports · 2026Article
- Transcription fidelity and control of alternative splicing contribute to heat stress survival in Arabidopsis.The Plant cell · 2025Article
- Mapping-based genome size estimation.BMC genomics · 2025Article
- Disruption of recombination machinery alters the mutational landscape in plant organellar genomes.G3 (Bethesda, Md.) · 2025Article
- NAVIP: Unraveling the influence of neighboring small sequence variants on functional impact prediction.PLoS computational biology · 2025Article
- Disruption of recombination machinery alters the mutational landscape in plant organellar genomes.bioRxiv : the preprint server for biology · 2024Article
- Article
- A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range.Nature genetics · 2024Article
- Automatic annotation of the bHLH gene family in plants.BMC genomics · 2023Article
- Data literacy in genome research.Journal of integrative bioinformatics · 2023Review
- Clarifying CRISPR: Why Repeats Identified in the Human Genome Should Not Be Considered CRISPRs.The CRISPR journal · 2023Article
- GALA: a computational framework for de novo chromosome-by-chromosome assembly with long reads.Nature communications · 2023Article
- KIPEs3: Automatic annotation of biosynthesis pathways.PloS one · 2023Article
- The Arabidopsis WRR4A and WRR4B paralogous NLR proteins both confer recognition of multiple Albugo candida effectors.The New phytologist · 2023Article
- Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes.Nucleic acids research · 2022Article
- Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome.Genome biology and evolution · 2022Article
- Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection.BMC genomics · 2022Article
- Article
- Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions.Quantitative plant biology · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In addition to the BAC-based reference sequence of the accession Columbia-0 from the year 2000, several short read assemblies of THE plant model organism Arabidopsis thaliana were published during the last years. Also, a SMRT-based assembly of Landsberg erecta has been generated that identified translocation and inversion polymorphisms between two genotypes of the species. Here we provide a chromosome-arm level assembly of the A. thaliana accession Niederzenz-1 (AthNd-1_v2c) based on SMRT sequencing data. The best assembly comprises 69 nucleome sequences and displays a contig length of up to 16 Mbp. Compared to an earlier Illumina short read-based NGS assembly (AthNd-1_v1), a 75 fold increase in contiguity was observed for AthNd-1_v2c. To assign contig locations independent from the Col-0 gold standard reference sequence, we used genetic anchoring to generate a de novo assembly. In addition, we assembled the chondrome and plastome sequences. Detailed analyses of AthNd-1_v2c allowed reliable identification of large genomic rearrangements between A. thaliana accessions contributing to differences in the gene sets that distinguish the genotypes. One of the differences detected identified a gene that is lacking from the Col-0 gold standard sequence. This de novo assembly extends the known proportion of the A. thaliana pan-genome.
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.