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Data released on May 27, 2014

Genomic

The Rice 3000 Genomes Project Data.

The 3000 Rice Genomes Project (2014): The Rice 3000 Genomes Project Data. GigaScience Database. http://dx.doi.org/10.5524/200001 RIS BibTeX Text


Rice, Oryza sativa L., is the staple food for half the world’s population. By 2030, rice production must increase by at least 25% to keep pace with population growth. Accelerated genetic gains in rice improvement are needed to mitigate the effects of climate change and loss of arable land and to ensure global food supply.
Here, we include data from an international effort resequencing a core collection of 3,000 rice accessions from 89 countries as a global public good. The 3,000 sequenced rice genomes had an average sequencing depth of 14X, average genome coverage and mapping rates of 94.0% and 92.5%, respectively.
This data provides a foundation for large-scale discovery of novel alleles for important rice phenotypes using various bioinformatics and/or genetic approaches. It also serves to understand at a higher level of detail the genomic diversity within O. sativa. With the release of the sequencing data, the project calls for the global rice community to take advantage of this data as a foundation for establishing a global, public rice genetic/genomic database and information platform for advancing rice breeding technology for future rice improvement.
Keywords: Oryza sativa, genetic resources, genome diversity, next generation sequencing

The 3000 rice genomes sequence data are now completely uploaded into the INSDC databases (the Sequence Read Archives (SRA) at EBI, DDBJ and NCBI), and available for easy download from the links noted below, rather than from GigaDB. NB - the mapping of each file as previously stored in GigaDB to the relevant location on the EBI FTP server can be found in the file seq_file_mapping_to_SRA.txt.

Please choose the appropriate geographical location:

Europe: EBI - PRJEB6180

USA: NCBI - PRJEB6180

Asia: DDBJ - ERP005654


Any inquires can be directed to any /all of the following members of the consortium:
Gengyun Zhang BGI, Shenzhen, China
Zhikang Li Chinese Academy of Agricultural Sciences, Beijing, China
Tian-Qing Zheng Chinese Academy of Agricultural Sciences, Beijing, China
Kenneth L. McNally International Rice Research Institute, Metro Manila, Philippines

Related manuscripts:

doi:10.1186/2047-217X-3-8
doi:10.1186/2047-217X-3-7

Accessions (data included in GigaDB):

ENA: PRJEB6180

Projects:



Files (FTP site) (Aspera):Aspera user name: gigadb , password: gigadb Table Settings
Items per page:

File Name Sample ID File Type File Format Size Release Date

readme.txt

readme TEXT 1 4 18461.8 KB 2014-04-28

consortium_list.csv

Other TEXT 1 4 51405.02 KB 2014-04-28

seq_file_mapping_to_SRA.txt

TSV TEXT 2 8 2446456723.33 MB 2014-04-28

rice_line_metadata_20141029.xlsx

Other EXCEL 1 6 431436421.32 KB 2014-10-29

rice3K_sequence_data_at_EBI

UNKNOWN 1 1 00 KB 2014-10-29