ArticleBMC genomics2019
Genome sequence of the model rice variety KitaakeX.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed.
- Dissecting Agronomically favorable genotypes in temperate japonica rice via haplotype analysis of a Japan-MAGIC population.The Plant journal : for cell and molecular biology · 2026Article
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- KitBase Expanded: An Integrated Genomic and Phenotypic Resource for 3,268 Fast-Neutron-Irradiated Rice Mutants.Database : the journal of biological databases and curation · 2026Article
- Variability in drought gene expression datasets highlights the need for paired physiology and community standardization.Plant physiology · 2026Article
- Genome-wide identification of the BBX gene family in kiwifruit and analysis of its expression responses to multiple types of stress.BMC genomics · 2026Article
- Capturing protein-protein interactions in plants: recent advances, challenges, and opportunities.Frontiers in molecular biosciences · 2026Review
- The rice cellulose synthase-like D4 gene (PeerJ · 2026Article
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- SPEECHLESS duplication in grasses expands potential for environmental regulation of stomatal development.bioRxiv : the preprint server for biology · 2025Article
- Accurate detections of the heterozygous SNPs with rice genomic data and prediction of de novo spontaneous mutation rate.Plant methods · 2025Article
- Physiological and molecular responses to high-temperature stress at anthesis in Brazilian flooded rice.AoB PLANTS · 2025Article
- Bioinformatics Analysis Reveals PPR Genes Modulation by Ahyp-miR0005 Under Abiotic Stress Across Diverse Plant Species.Plants (Basel, Switzerland) · 2025Article
- Distinct classes of 21- and 24-nt phasiRNAs suggests diverse mechanisms of biogenesis and function in rice anther development.The plant genome · 2025Article
- Integration of crop modeling and sensing into molecular breeding for nutritional quality and stress tolerance.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- Genome-wide identification, transcriptome dynamics, and expression regulation of the key lignin biosynthesis gene families PAL and CAD in black walnut shell.BMC plant biology · 2025Article
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- GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data.Database : the journal of biological databases and curation · 2025Article
- Effects of the sucrose concentrations and incubation periods on in vitro pollen germination and pollen tube growth in three rice cultivars.Plant biotechnology (Tokyo, Japan) · 2025Article
- The Genome of the Lima Bean Variety Baiyu Bean Highlights Its Evolutionary Characteristics.Ecology and evolution · 2025Article
4 more citing papers are in PubMed but not listed here.
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Authors and funding
23 authors.
Funding
Abstract
backgroundThe availability of thousands of complete rice genome sequences from diverse varieties and accessions has laid the foundation for in-depth exploration of the rice genome. One drawback to these collections is that most of these rice varieties have long life cycles, and/or low transformation efficiencies, which limits their usefulness as model organisms for functional genomics studies. In contrast, the rice variety Kitaake has a rapid life cycle (9 weeks seed to seed) and is easy to transform and propagate. For these reasons, Kitaake has emerged as a model for studies of diverse monocotyledonous species.
resultsHere, we report the de novo genome sequencing and analysis of Oryza sativa ssp. japonica variety KitaakeX, a Kitaake plant carrying the rice XA21 immune receptor. Our KitaakeX sequence assembly contains 377.6 Mb, consisting of 33 scaffolds (476 contigs) with a contig N50 of 1.4 Mb. Complementing the assembly are detailed gene annotations of 35,594 protein coding genes. We identified 331,335 genomic variations between KitaakeX and Nipponbare (ssp. japonica), and 2,785,991 variations between KitaakeX and Zhenshan97 (ssp. indica). We also compared Kitaake resequencing reads to the KitaakeX assembly and identified 219 small variations. The high-quality genome of the model rice plant KitaakeX will accelerate rice functional genomics.
conclusionsThe high quality, de novo assembly of the KitaakeX genome will serve as a useful reference genome for rice and will accelerate functional genomics studies of rice and other species.
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