Datasets | Rice Genome Hub

Name	Description	Type
CGSNL annotation and manual curation data	The Rice Annotation Project (RAP) was conceptualized in 2004 upon the completion of the Oryza sativa ssp. japonica cv. Nipponbare genome sequencing by the International Rice Genome Sequencing Project with the aim of providing the scientific community with an accurate and timely annotation of the rice genome sequence. One of the major objectives of this project is to facilitate a comprehensive analysis of the genome structure and function of rice on the basis of the annotation.
Whole Genome Assembly and Annotation of R498	A high quality reference genome would enable discovery of genome structure and genetic variation. Here we report an integrative method to generate a 390.3-megabase assembly covering over 99% of the indica rice genome Shuhui498 with 7 of the 12 chromosomes complete and the rest 5 each containing only one gap in its centromeric region. We predicted 38,714 high confidence protein coding genes in R498 through an evidence-based gene prediction pipeline by combining known proteins, experimentally... read more	Annotation of a genome.
Whole Genome Assembly and Annotation of IR8	This data package contains processed data from the International Oryza Map Alignment Project (IOMAP) covering annotation and comparative genomics in 13 species of the Oryzeae tribe in relation to the following reference genome assemblies; Oryza sativa vg. indica [IR 8], Oryza sativa vg. aus [N 22], Oryza sativa vg. japonica [IRGSP-1.0], Oryza sativa vg. indiac [93-11], Oryza nivara, Oryza rufipogon, Oryza barthii, Oryza glaberrima, Oryza glumaepatula, Oryza meridionalis, Oryza punctata, Oryza... read more	Annotation of a genome.
Whole Genome Assembly and Annotation of Oryza sativa (v7.1)	This is MSU Release 7.0 of the annotation of the genome of the Nipponbare/ japonica subspecies of Oryza sativa . This release is based on a new pseudomolecule assembly (Os-Nipponbare-Reference-IRGSP-1.0) made in collaboration with the Agrogenomics Research Center at the National Institute of Agrobiological Sciences, Tsukuba, Japan. This set of pseudomolecules unifies the previous MSU with the IRGSP/RAP effort.	Annotation of a genome.

Whole Genome Assembly and Annotation of Oryza sativa Kitaake		Annotation of a genome.
Whole Genome Assembly and Annotation of N22	This data package contains processed data from the International Oryza Map Alignment Project (IOMAP) covering annotation and comparative genomics in 13 species of the Oryzeae tribe in relation to the following reference genome assemblies; Oryza sativa vg. indica [IR 8], Oryza sativa vg. aus [N 22], Oryza sativa vg. japonica [IRGSP-1.0], Oryza sativa vg. indiac [93-11], Oryza nivara, Oryza rufipogon, Oryza barthii, Oryza glaberrima, Oryza glumaepatula, Oryza meridionalis, Oryza punctata, Oryza... read more	Annotation of a genome.
The Whole African Rice Genome resequencing project	The Whole African Rice Genome resequencing project is a collaboration between Genoscope, CIRAD and IRD (UMR DIADE). In this project, a focus have been done on 300 cultivated African Rice (O. glaberrima) and 100 wild relative (O. barthii). A SNP analysis have been performed and results have been used for evolution study, new gene discovery, QTL cloning, forward/reverse genetics and allele identification. This work was supported by a grant from the France Genomique French National infrastructure and... read more

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Rice GH is a collaborative project among rice teams from IRD & CIRAD. Funding has been provided by CRP Rice, IRD and CIRAD

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