Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data.

ABSTRACT:

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 ra

SUBMITTER: Kawahara Y 

PROVIDER: S-EPMC5395016 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature