ArticleGenome biology2025
Oatk: a de novo assembly tool for complex plant organelle genomes.
Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 121 papers.
What it found
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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.
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Who cites it
121 citing papers in PubMed.
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- European ash pangenome reveals widespread structural variation and genetic basis of low ash dieback susceptibility.Nature communications · 2026Article
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- Phased-genome assemblies of saltgrass reveal structural dynamics and genomic basis for extreme salt tolerance and dioecy.Plant communications · 2026Article
- A haplotype-resolved, chromosome-scale genome assembly and annotation for Carya glabra (pignut hickory; Juglandaceae).G3 (Bethesda, Md.) · 2026Article
- A Compact Multipartite Mitogenome ofInternational journal of molecular sciences · 2026Article
- Chromosomal evolution and speciation inferred from chromosome-scale genome assemblies in three Cupressaceae species.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026Article
- Assembly and Comparative Analysis of Five Complete Mitochondrial Genomes of theInternational journal of molecular sciences · 2026Article
- Assembly and annotation of the 'Golden Delicious' Doubled-Haploid GDDH18 apple genome.G3 (Bethesda, Md.) · 2026Article
- The origin of the octoploid cloudberry (Rubus chamaemorus) genome is the result of multiple and complex polyploidization events.The Journal of heredity · 2026Article
- Chromosome-level reference genome of a foundational California native legume, Acmispon strigosus.The Journal of heredity · 2026Article
- Chromosomal fusions shaped the genome of the greater hornwrack bryozoan (Flustra foliacea) (Linnaeus, 1758).The Journal of heredity · 2026Article
- Chromosome-Scale Genome Assemblies of Duckweeds Provide Insights Into Genomic Plasticity, Aquatic Adaptation, and Morphological Reduction.Genome biology and evolution · 2026Article
- Loss of Major Histocompatibility Complex I and II Function in the Genome of Glacier Lanternfish Provides Insight Into Evolution of Vertebrate Immune Systems.Genome biology and evolution · 2026Article
- A fourth subgenome of the Camelina genus reveals gene dominance is influenced by chromosomal proximity.Nature communications · 2026Article
- Phylogenomic discordance among plastid genes in endangered Maltese Limonium.Scientific reports · 2026Article
- Two Australian genome assemblies expand the genomic blueprint of giant kelp.BMC genomics · 2026Article
- An improved Solanum verrucosum genome provides insight into potato centromeres and epigenetic regulation.G3 (Bethesda, Md.) · 2026Article
61 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
6 authors.
Funding
Abstract
Plant organelle genomes, particularly large mitochondrial genomes with complex repeats, present significant challenges for assembly. The advent of long-read sequencing enables the assembly of complete genomes, but problems of resolving alternative structures remain. Here we introduce a novel tool that employs a syncmer-based assembler for rapid assembly graph construction, integrates a profile-HMM database for robust organelle identification, and leverages a new search method to find the best supported path through the assembly graph. We describe high-quality organelle assemblies for 195 plant species, demonstrating improvements over other methods, and providing multiple insights into structural complexity, heteroplasmy, and DNA exchange between organelles.
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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 Socratic graph.