Database Commons
Database Commons

a catalog of worldwide biological databases

Database Profile

General information

URL: http://rice.plantbiology.msu.edu
Full name: Rice Genome Annotation Project Database
Description: The Rice Genome Annotation Project Database and Resource is a National Science Foundation project and provides sequence and annotation data for the rice genome. This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. These data are available through search pages and our Genome Browser that provides an integrated display of annotation data.
Year founded: 2009
Last update: 2021
Version: Release 7
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: United States

Classification and Labelling

Data type:
DNA
Data object:
Database category:
Major species:
Keywords:

Contact information

University/Institution: University of Georgia
Address:
City:
Province/State:
Country/Region: United States
Contact name (PI/Team): Robin Buell
Contact email (PI/Helpdesk): buell.lab.web@gmail.com

Publications

24280374
Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. [PMID: 24280374]
Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S, Childs KL, Davidson RM, Lin H, Quesada-Ocampo L, Vaillancourt B, Sakai H, Lee SS, Kim J, Numa H, Itoh T, Buell CR, Matsumoto T.

Background

Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group).

Results

The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community.

Conclusions

A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies.

Rice (N Y). 2013:6(1) | 724 Citations (from Europe PMC, 2022-07-02)

Ranking

All databases:
119/5381 (97.807%)
Raw bio-data:
12/505 (97.822%)
Gene genome and annotation:
50/1428 (96.569%)
119
Total Rank
724
Citations
80.444
z-index

Community reviews

Not Rated
Data quality & quantity:
Content organization & presentation
System accessibility & reliability:

Word cloud

Related Databases

Citing
Cited by

Record metadata

Created on: 2022-05-06
Curated by:
Zhang Zhang [2022-06-20]
Lina Ma [2022-06-01]
WANG XIAOTING [2022-05-06]