IC4R006-Genome-2014-25064006

Project Title

• The genome sequence of African rice (Oryza glaberrima)and evidence for independent domestication

The Background of This Project

• The cultivation of rice in Africa dates back more than 3,000 years. Interestingly, African rice is not of the same origin as Asian rice (Oryza sativa L.) but rather is an entirely different species (i.e., Oryza glaberrima Steud.). Here we present a high-quality assembly and annotation of the O. glaberrima genome and detailed analyses of its evolutionary history of domestication and selection.

Plant Culture & Treatment

• The researchers sequenced the O. glaberrima genome (International Rice Germplasm Collection (IRGC) accession #96717, var. CG14) using a minimum tiling path (MTP) of 3,485 BAC clones selected from a BAC-based physical map aligned to the O. sativa ssp. japonica reference genome (RefSeq)10,11 with (i) a hybrid BAC pool (3,319 BACs) and whole genome shotgun approach using Roche/454GS-FLX Titanium sequencing technology for 11.5 chromosomes12 and(ii) a BAC-by-BAC (166 BACs) Sanger method for the short arm of chromosome 3 (Chr3S).

Research Findings

• The researchers evaluated the final assembly for accuracy and completeness using four previously Sanger-sequenced and finished BACs located on chromosomes 1 (1 BAC), 5 (1 BAC) and 6 (2 BACs). Overall, more than 98% of the query BAC sequences were detected and localized in the correct chromosomal locations (549,598 bp query/557,270 bp subject) with a sequence accuracy of 99.6%. The 7.7 kb of missing sequence was located across 23 sequence gaps in the pseudomolecules.The overall run statistics are summarized in Supplementary Table 1,The genome was assembled as outlined in Supplementary Figure 1

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• The researchers derived 33,164 gene models, including potential gene models and 701 tRNA genes (Fig. 1).
• The researchers found that transposable elements (TEs)represented 104 Mb (i.e., 34.25%) in the O. glaberrima genome assembly (Fig. 1).

Figure 1 The O. glaberrima genome(CG14 v1). Concentric circles show structural,functional and evolutionary aspects of the genome: A, chromosome number; B, heat map view of genes; C, repeat (RNA and DNA TEs without MITEs) density in 200-kb windows(red, average +1 s.d.; blue, average −1 s.d.; yellow, gene and repeat density between red and blue); and D paralogous relationships between O. glaberrima chromosomes.

Labs working on this Project

• Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA.
• Plant Genome and Systems Biology, Helmholtz Center Munich,Neuherberg, Germany.
• Dow AgroSciences, Indianapolis, Indiana, USA.
• Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA.
• Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy.
• DuPont Pioneer, Johnston, Iowa, USA. 7Department of Agriculture, Food and Environment,University of Pisa, Pisa, Italy.
• State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing,China.
• US Arid Land Agricultural Research Center, Maricopa, Arizona, USA.
• Africa Rice Center, Cotonou, Benin. 11Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA.
• Department of Geography, Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA.
• Laboratoire Génome et Développement des Plantes, UMR CNRS/Institut de Recherche pour le Développement/l’Université de Perpignan Via Domitia, Université de Perpignan, Perpignan, France.
• Institute of Plant Biology, University of Zurich, Zurich, Switzerland. 15Department of Biology, University of Maryland, College Park,Maryland, USA. 16These authors contributed equally to this work.

Corresponding Author

• Rod A Wing:(rwing@mail.arizona.edu) & Mingsheng Chen (mschen@genetics.ac.cn) & Klaus F X Mayer(k.mayer@helmholtz-muenchen.de) & Steve Rounsley (steve.rounsley@gmail.com).