The initial release of the Oryza glaberrima genome from the Arizona Genomics Institute and the Rounsley Lab

June 6, 2014

Oryza glaberrima genome sequence release announcement

We are pleased to announce the initial release of the Oryza glaberrima genome from the Arizona Genomics Institute and the Rounsley Lab. O. glaberrima is a west African species of cultivated rice that was domesticated independently of Asian rice (O. sativa ssp. japonica and indica) about 3,500 years ago.O. glaberrima contains many important adaptive traits for cultivation in African soils and climates. The specific strain sequenced (IRGC accession # 96717 [variety name CG14]) is the parent used for the development of the new rice for African (NERICA) lines that revolutionized rice cultivation in Africa.

The O. glaberrima genome was sequenced using a hybrid BAC pooling/ whole genome shotgun approach with Roche GSFLX/454 Titanium sequencing technology. Sequences were assembled and combined with a subset of previously sequenced BAC clones to produce a whole genome assembly.

Three sources of DNA were used for the O. glaberrima sequencing project:

1. Individual BAC clones: 155 bacterial artificial chromosome (BAC) clones were shotgun Sanger sequenced and manually finished, including the entire short arm of chromosome 3 (Chr3S);
2. BAC pools: We selected a minimum tiling path of 3,321 BAC clones from the OG_BBa BAC library (Details here) across the O. glaberrima genome (except Chr3S). DNA from each BAC was purified, quantified and pooled (~28 BAC DNA preps/pool) to produce a total of 115 3Mb pools. 3Mb or chromosome arm pools were Roche GSFLX/454 sequenced using either Titanium shotgun or Titanium paired-end libraries, respectively;
3. Genomic DNA from O. glaberrima seedlings (accession # 96717 [variety name CG14]) was purified from nuclei and GSFLX/454 sequenced using a Titanium shotgun library.

The assembly is available from for downloading and Genbank (GenomeProject ID #47325). The assembly consists of 5,309 scaffolds with a Scaffold N50 of 230.6kb resulting in a total length of 316.1Mb for the genome with 4% gaps. 85% of the genome is in scaffolds larger than 50kb. 90% of the genome (Scaffold N50: 255kb) can be unambiguously ordered and oriented based on the O. sativa ssp. japonica genome sequence. The sequences from these regions are numbered sequentially from the top to bottom of each chromosome. While the remaining 10% of the genome (Scaffold N50: 50.5kb) cannot be ordered and oriented with precision, the BAC-pooling strategy allows placement in a single 3Mb region on the physical map map. These general locations are described in the comment for each unplaced sequence.

A preliminary annotation is now underway at MIPS led by Klaus Mayer and will be available for browsing and BLAST analysis shortly.

The O. glaberrima genome sequencing project was funded by the National Science Foundation Plant Genome Research Program (#082224) to R. Wing, S. Rounsley and Y. Yu.


Muhua Wang, Yeisoo Yu, Georg Haberer, Pradeep Reddy Marri, Chuanzhu Fan, Jose Luis Goicoechea, Andrea Zuccolo, Xiang Song, Dave Kudrna, Jetty S S Ammiraju, Rosa Maria Cossu, Carlos Maldonado, Jinfeng Chen, Seunghee Lee, Nick Sisneros, Kristi de Baynast, Wolfgang Golser, Marina Wissotski, Woojin Kim, Paul Sanchez, Marie-Noelle Ndjiondjop, Kayode Sanni, Manyuan Long, Judith Carney, Olivier Panaud, Thomas Wicker, Carlos A Machado, Mingsheng Chen, Klaus F X Mayer, Steve Rounsley & Rod A Wing. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. 2014. Nature Genetics - doi:10.1038/ng.3044

Download the complete Oryza glaberrima genome here.