ArticleGenome biology2014
Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 144 papers, 1 of them a synthesis that pooled it.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
144 citing papers in PubMed, 1 synthesis or guideline pooled it, 247 citations in OpenAlex.
- Pooled it
- Pangenomic analyses in the cultivated grapevine confirm high genomic collinearity and extensive dispensable gene content likely involved in adaptation.G3 (Bethesda, Md.) · 2026Article
- Empowering Plant Biotechnology Research: Super-Pangenomes as a Novel Arsenal for Crop Breeding and Improvement.Molecular biotechnology · 2026Review
- Challenges in Bringing Pangenome Research Into Breeding: A Case Study in Rice.Plant biotechnology journal · 2026Review
- Chromosome-Level Genome Assembly Identifies RIRE2 and CACTA Transposable Elements at the Sub1 Locus in Submergence-Tolerant Rice Varieties.Rice (New York, N.Y.) · 2026Article
- Genomic resources for Australian alfalfa (Medicago sativa L.) genomics: reformatted reference genome, annotated variants, gene presence-absence and diversity analysis from genome re-sequencing.BMC plant biology · 2025Article
- Developing pangenomes for large and complex plant genomes and their representation formats.Journal of advanced research · 2025Review
- Comprehensive Analysis ofGenes · 2025Article
- Comparative genomics profiling of Citrus species reveals the diversity and disease responsiveness of the GLP pangenes family.BMC plant biology · 2025Article
- Revealing Genomic Traits and Evolutionary Insights of Oryza officinalis from Southern China Through Genome Assembly and Transcriptome Analysis.Rice (New York, N.Y.) · 2025Article
- Introgression among subgroups is an important driving force for genetic improvement and evolution of the Asian cultivated riceFrontiers in plant science · 2025Review
- From map to blueprint: the plant pan-genome unraveling genetic mysteries and powering precision breeding.Frontiers in plant science · 2025Review
- A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study.BMC genomics · 2024Review
- 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
- Multiplexed CRISPR-Cas9 mutagenesis of riceScience advances · 2024Article
- Technological Development and Advances for Constructing and Analyzing Plant Pangenomes.Genome biology and evolution · 2024Review
- Exploring Genetic Diversity within aus Rice Germplasm: Insights into the Variations in Agro-morphological Traits.Rice (New York, N.Y.) · 2024Article
- Exploring Pan-Genomes: An Overview of Resources and Tools for Unraveling Structure, Function, and Evolution of Crop Genes and Genomes.Biomolecules · 2023Review
- The Progression in Developing Genomic Resources for Crop Improvement.Life (Basel, Switzerland) · 2023Review
- Two complementary genes in a presence-absence variation contribute to indica-japonica reproductive isolation in rice.Nature communications · 2023Article
84 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
15 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundThe use of high throughput genome-sequencing technologies has uncovered a large extent of structural variation in eukaryotic genomes that makes important contributions to genomic diversity and phenotypic variation. When the genomes of different strains of a given organism are compared, whole genome resequencing data are typically aligned to an established reference sequence. However, when the reference differs in significant structural ways from the individuals under study, the analysis is often incomplete or inaccurate.
resultsHere, we use rice as a model to demonstrate how improvements in sequencing and assembly technology allow rapid and inexpensive de novo assembly of next generation sequence data into high-quality assemblies that can be directly compared using whole genome alignment to provide an unbiased assessment. Using this approach, we are able to accurately assess the "pan-genome" of three divergent rice varieties and document several megabases of each genome absent in the other two.
conclusionsMany of the genome-specific loci are annotated to contain genes, reflecting the potential for new biological properties that would be missed by standard reference-mapping approaches. We further provide a detailed analysis of several loci associated with agriculturally important traits, including the S5 hybrid sterility locus, the Sub1 submergence tolerance locus, the LRK gene cluster associated with improved yield, and the Pup1 cluster associated with phosphorus deficiency, illustrating the utility of our approach for biological discovery. All of the data and software are openly available to support further breeding and functional studies of rice and other species.
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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 OpenQuestion graph.