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...| Sequence data: | genome assemblies: 81; sequence reads: 2952 | (See Genome Assembly and Annotation report) | | | Statistics: | median total length (Mb): 385.345 | | median protein count: 38007 | | median GC%: 43.5909 | | NCBI Annotation Release: | 102 |
- Rationally Designed APOBEC3B Cytosine Base Editors with Improved Specificity. Jin S, et al. Mol Cell 2020 Sep 3
- Genome sequence of the model rice variety KitaakeX. Jain R, et al. BMC Genomics 2019 Nov 27
- N6-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
- 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
- Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Rice Annotation Project., et al. Genome Res 2007 Feb
- The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information. Ohyanagi H, et al. Nucleic Acids Res 2006 Jan 1
- The rice mitochondrial genomes and their variations. Tian X, et al. Plant Physiol 2006 Feb
- The Genomes of Oryza sativa: a history of duplications. Yu J, et al. PLoS Biol 2005 Feb
- The map-based sequence of the rice genome. International Rice Genome Sequencing Project. Nature 2005 Aug 11
- The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. Rice Chromosomes 11 and 12 Sequencing Consortia. BMC Biol 2005 Sep 27
- Sequencing of a rice centromere uncovers active genes. Nagaki K, et al. Nat Genet 2004 Feb
- Composition and structure of the centromeric region of rice chromosome 8. Wu J, et al. Plant Cell 2004 Apr
- Structural features of the rice chromosome 4 centromere. Zhang Y, et al. Nucleic Acids Res 2004
- A comparison of rice chloroplast genomes. Tang J, et al. Plant Physiol 2004 May
More...
Reference genome:  
Oryza sativa Japonica Group|
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 | | | | Pltd | NC_001320.1 | - | 0.13 | 39.0 | 108 | 8 | 38 | - | 159 | 5 | | | | MT | NC_011033.1 | - | 0.49 | 43.9 | 53 | 3 | 22 | - | 81 | 6 | | | Un | - | . | - | 0.55 | 45.9 | 25 | - | - | 12 | 35 | 4 | |
Click on chromosome name to open Genome Data Viewer |