Genome

Oryza sativa (Asian cultivated rice) Oryza sativa Organism overview Lineage: Eukaryota[15557]; Viridiplantae[1758]; Streptophyta[1641]; Embryophyta[1630]; Tracheophyta[1603]; Spermatophyta[1585]; Magnoliopsida[1558]; Liliopsida[245]; Poales[144]; Poaceae[120]; BOP clade[66]; Oryzoideae[18]; Oryzeae[18]; Oryzinae[16]; Oryza[15]; Oryza sativa[1]

Rice is one of the most important food crops in the world and feeds more people than any other crop. Rice belongs to the genus Oryza which includes approximately 24 species. They are widely distributed growing in different habitats and different soil types. They show differences in plant growth, yield, pest and disease resistance, stress tolerance More...and water requirenment. Rice grain is classified as short, medium or long grain sizes and and exhibits colors like brown, black, purple, and red.The genus Oryza has ten recognized genome types. They are AA, BB, CC, BBCC, CCDD, EE, HHKK, HHJJ, FF, and GG. There is a five fold difference in genome size among the species with diploid species having 2n = 24 and tetraploid species having 2n = 48 chromosomes. The cultivated species are O. glaberrima, in West and Central Africa, and O. sativa with three cultivars, japonica, indica, and javanica.O. sativa L. is the most consumed rice species and is the staple food for more than half of the world's population. It grows through out the world and can be found in all kinds of climates. It is diploid with AA genome type. O. sativa L. ssp japonica is the rice variety grown in subtropics and temperate climates. It prefers heavy, relatively impervious soil and is tolerant to flooding. The grains are generally rounder and shorter. It has a genome size of 389 Mb. It has been sequenced to 10x coverage by the members of the International Rice Genome Sequencing Project (IRGSP). O. sativa L. ssp indica is a rice variety grown throughout the world. It has an estimated genome size of 466 Mb. It generally bears long, slender grains. A WGS project has developed an improved version of this at 6.28x coverage. Less...

Summary Sequence data:  genome assemblies: 105; sequence reads: 3204  (See  Genome Assembly and Annotation report) Statistics:  median total length (Mb): 389.421  median protein count: 38007  median GC%: 43.5553 NCBI Annotation Release:  102 Publications (limited to 20 most recent records) Genome-wide association analysis uncovers rice blast resistance alleles of Ptr and Pia. Greenwood JR, et al. Commun Biol 2024 May 20 A complete assembly of the rice Nipponbare reference genome. Shang L, et al. Mol Plant 2023 Aug 7 Development and Genome-Wide Analysis of a Blast-Resistant japonica Rice Variety. Escolà G, et al. Plants (Basel) 2023 Oct 11 Development of a Temperate Climate-Adapted indica Multi-stress Tolerant Rice Variety by Pyramiding Quantitative Trait Loci. Shin NH, et al. Rice (N Y) 2022 Apr 9 GLW7.1, a Strong Functional Allele of Ghd7, Enhances Grain Size in Rice. Liu R, et al. Int J Mol Sci 2022 Aug 5 Chromosome-Level Genome Assembly of a Fragrant Japonica Rice Cultivar 'Changxianggeng 1813' Provides Insights into Genomic Variations between Fragrant and Non-Fragrant Japonica Rice. Lu R, et al. Int J Mol Sci 2022 Aug 26 Rationally Designed APOBEC3B Cytosine Base Editors with Improved Specificity. Jin S, et al. Mol Cell 2020 Sep 3 Multicentric origin and diversification of atp6-orf79-like structures reveal mitochondrial gene flows in Oryza rufipogon and Oryza sativa. He W, et al. Evol Appl 2020 Oct Large-scale identification and functional analysis of NLR genes in blast resistance in the Tetep rice genome sequence. Wang L, et al. Proc Natl Acad Sci U S A 2019 Sep 10 Genome sequence of the model rice variety KitaakeX. Jain R, et al. BMC Genomics 2019 Nov 27 N(6)-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses. Zhang Q, et al. Mol Plant 2018 Dec 3 Tracking the genome-wide outcomes of a transposable element burst over decades of amplification. Lu L, et al. Proc Natl Acad Sci U S A 2017 Dec 5 Assembly of an early-matured japonica (Geng) rice genome, Suijing18, based on PacBio and Illumina sequencing. Nie SJ, et al. Sci Data 2017 Dec 19 Indica rice genome assembly, annotation and mining of blast disease resistance genes. Mahesh HB, et al. BMC Genomics 2016 Mar 16 Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. Sakai H, et al. Plant Cell Physiol 2013 Feb Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences. Gao ZY, et al. Proc Natl Acad Sci U S A 2013 Aug 27 Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Kawahara Y, et al. Rice (N Y) 2013 Feb 6 Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms. Yamamoto T, et al. BMC Genomics 2010 Apr 27 The Rice Annotation Project Database (RAP-DB): 2008 update. Rice Annotation Project, et al. Nucleic Acids Res 2008 Jan Transposable element distribution, abundance and role in genome size variation in the genus Oryza. Zuccolo A, et al. BMC Evol Biol 2007 Aug 29 More...  Representative (genome information for reference and representative genomes) Reference genome:   Oryza sativa Japonica Group Submitter: National Institute of Agrobiological Sciences Loc Type Name RefSeq INSDC Size (Mb) GC% Protein rRNA tRNA Other RNA Gene Pseudogene Chr 1 NC_029256.1 AP014957.1 43.27 43.8 5,850 - 84 1,237 4,630 158 Chr 2 NC_029257.1 AP014958.1 35.94 43.3 4,826 2 69 1,311 3,769 117 Chr 3 NC_029258.1 AP014959.1 36.41 43.7 5,196 - 73 1,008 4,067 126 Chr 4 NC_029259.1 AP014960.1 35.5 44.3 3,712 - 63 918 3,098 141 Chr 5 NC_029260.1 AP014961.1 29.96 44.0 3,411 - 55 808 2,740 124 Chr 6 NC_029261.1 AP014962.1 31.25 43.6 3,458 - 33 872 2,852 127 Chr 7 NC_029262.1 AP014963.1 29.7 43.5 3,316 - 35 783 2,731 135 Chr 8 NC_029263.1 AP014964.1 28.44 43.4 2,874 - 44 778 2,400 117 Chr 9 NC_029264.1 AP014965.1 23.01 43.5 2,305 14 32 704 1,975 89 Chr 10 NC_029265.1 AP014966.1 23.21 43.6 2,160 - 47 709 1,994 117 Chr 11 NC_029266.1 AP014967.1 29.02 42.9 2,751 173 28 857 2,584 217 Chr 12 NC_029267.1 AP014968.1 27.53 43.0 2,533 - 52 801 2,108 122 MT NC_011033.1 - 0.49 43.9 53 3 22 - 81 6 Pltd NC_001320.1 - 0.13 39.0 108 8 38 - 159 5 Un - . - 0.55 45.9 25 - - 12 35 4 Chromosomes Click on chromosome name to open Genome Data Viewer External Resources ACWW ASPGC BIOTEC CSHL Chinese Academy of Sciences Clemson University Genetic Stocks - Oryza Genoscope Gramene IRGSP IRRI Inter-disciplinary Centre for Plant Genomics JIC KRGPP NCGR OSGDB OryGenesDB Oryzabase PGIR RAP-DB RGP Tos17 insertion mutants Univ. Of Wisconsin FTP