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

Area of Science:

• Genomics
• Plant Science
• Molecular Biology

Background:

• The International Rice Genome Sequencing Project (IRGSP) established the initial high-quality rice reference genome in 2005.
• Genomic-enabled research in rice relies on accurate reference genome sequences.

Purpose of the Study:

• To update and validate the genome assembly and sequence of the Nipponbare cultivar of Oryza sativa.
• To provide a unified and improved reference genome for the rice research community.

Main Methods:

• Optical mapping was used to revise and validate the minimal tiling path of clones in the Nipponbare genome assembly.
• Re-sequencing using Illumina Genome Analyzer II/IIx and Roche 454 pyrosequencing platforms identified and corrected sequencing errors and insertions/deletions.
• Manual curation and comparison of sequences from three different Nipponbare individuals were performed.

Main Results:

• A revised genome assembly, Os-Nipponbare-Reference-IRGSP-1.0, was generated with a low error rate (0.15 per 10,000 nucleotides).
• 4,886 sequencing errors were identified and corrected across 321 Mb of the assembled genome.
• Allelic differences were identified between the original IRGSP individual and two re-sequenced individuals, highlighting genetic variation.

Conclusions:

• A validated, error-corrected Nipponbare rice genome assembly (Os-Nipponbare-Reference-IRGSP-1.0) has been produced.
• This improved assembly will significantly facilitate ongoing and future rice research.
• The study underscores the importance of considering allelic variation in rice diversity studies.