ArticleNucleic acids research2017
RPAN: rice pan-genome browser for ∼3000 rice genomes.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers, 2 of them syntheses that pooled it.
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Who cites it
86 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- GWAS meta-analysis using a graph-based pan-genome enhanced gene mining efficiency for agronomic traits in rice.Nature communications · 2025Pooled it
- Multi-omics revolution to promote plant breeding efficiency.Frontiers in plant science · 2022Pooled it
- Elucidating and exploring specialised plant metabolism through a pangenomic and pantranscriptomic lens.The Plant journal : for cell and molecular biology · 2026Review
- Empowering Plant Biotechnology Research: Super-Pangenomes as a Novel Arsenal for Crop Breeding and Improvement.Molecular biotechnology · 2026Review
- Identification of CAMTA transcription factors and functional analysis of OsCAMTA4 in rice blast and salt stress.Planta · 2026Article
- Network analysis reveals that bHLH transcription factors positively regulate rice resistance to Magnaporthe oryzae.BMC plant biology · 2026Article
- A natural variation in rice susceptibility factor Rsf1 confers resistance to root-knot nematode.Nature communications · 2026Article
- Challenges in Bringing Pangenome Research Into Breeding: A Case Study in Rice.Plant biotechnology journal · 2026Review
- From structural pangenomes to functional panomics in plants.Molecular biology and evolution · 2026Review
- Low-call-rate SNPs and presence-absence variation identified in the rice pan-genome can improve genomic prediction of rice gene bank accessions.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Natural variation in SBRR1 shows high potential for sheath blight resistance breeding in rice.Nature genetics · 2025Article
- Article
- Status on Genetic Resistance to Rice Blast Disease in the Post-Genomic Era.Plants (Basel, Switzerland) · 2025Review
- Pangenome graphs and their applications in biodiversity genomics.Nature genetics · 2025Review
- A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study.BMC genomics · 2024Review
- Lactuca super-pangenome reduces bias towards reference genes in lettuce research.BMC plant biology · 2024Article
- Evaluation of deep learning for predicting rice traits using structural and single-nucleotide genomic variants.Plant methods · 2024Article
- GeCKO: user-friendly workflows for genotyping complex genomes using target enrichment capture. A use case on the large tetraploid durum wheat genome.Plant methods · 2024Article
- A genome-wide association study of panicle blast resistance toMolecular breeding : new strategies in plant improvement · 2024Article
- A survey of BWT variants for string collections.Bioinformatics (Oxford, England) · 2024Article
26 more citing papers are in PubMed but not listed here.
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12 authors.
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No grant is acknowledged in the PubMed record.
Abstract
A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the presence/absence variations (PAVs) of genes among these genomes. With the progress of sequencing technologies, pan-genome study is becoming affordable for eukaryotes with large-sized genomes. The Asian cultivated rice, Oryza sativa L., is one of the major food sources for the world and a model organism in plant biology. Recently, the 3000 Rice Genome Project (3K RGP) sequenced more than 3000 rice genomes with a mean sequencing depth of 14.3×, which provided a tremendous resource for rice research. In this paper, we present a genome browser, Rice Pan-genome Browser (RPAN), as a tool to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding. It is available at http://cgm.sjtu.edu.cn/3kricedb/ or http://www.rmbreeding.cn/pan3k.
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