title: The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication.
abstract: 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. Population genomics analyses of 20 O. glaberrima and 94 Oryza barthii accessions support the hypothesis that O. glaberrima was domesticated in a single region along the Niger river as opposed to noncentric domestication events across Africa. We detected evidence for artificial selection at a genome-wide scale, as well as with a set of O. glaberrima genes orthologous to O. sativa genes that are known to be associated with domestication, thus indicating convergent yet independent selection of a common set of genes during two geographically and culturally distinct domestication processes.
authors: 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2].
authors: Muhua
authors: M
authors: Wang
authors: 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2].
authors: Yeisoo
authors: Y
authors: Yu
authors: 1] Plant Genome and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany. [2].
authors: Georg
authors: G
authors: Haberer
authors: 1] Dow AgroSciences, Indianapolis, Indiana, USA. [2].
authors: Pradeep Reddy
authors: PR
authors: Marri
authors: 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2] Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA.
authors: Chuanzhu
authors: C
authors: Fan
authors: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA.
authors: Jose Luis
authors: JL
authors: Goicoechea
authors: Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.
authors: Andrea
authors: A
authors: Zuccolo
authors: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA.
authors: Xiang
authors: X
authors: Song
authors: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA.
authors: Dave
authors: D
authors: Kudrna
authors: 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2] DuPont Pioneer, Johnston, Iowa, USA.
authors: Jetty S S
authors: JS
authors: Ammiraju
authors: Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy.
authors: Rosa Maria
authors: RM
authors: Cossu
authors: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA.
authors: Carlos
authors: C
authors: Maldonado
authors: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
authors: Jinfeng
authors: J
authors: Chen
authors: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA.
authors: Seunghee
authors: S
authors: Lee
authors: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA.
authors: Nick
authors: N
authors: Sisneros
authors: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA.
authors: Kristi
authors: K
authors: de Baynast
authors: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA.
authors: Wolfgang
authors: W
authors: Golser
authors: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA.
authors: Marina
authors: M
authors: Wissotski
authors: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA.
authors: Woojin
authors: W
authors: Kim
authors: 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2] US Arid Land Agricultural Research Center, Maricopa, Arizona, USA.
authors: Paul
authors: P
authors: Sanchez
authors: Africa Rice Center, Cotonou, Benin.
authors: Marie-Noelle
authors: MN
authors: Ndjiondjop
authors: Africa Rice Center, Cotonou, Benin.
authors: Kayode
authors: K
authors: Sanni
authors: Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA.
authors: Manyuan
authors: M
authors: Long
authors: Department of Geography, Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA.
authors: Judith
authors: J
authors: Carney
authors: 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.
authors: Olivier
authors: O
authors: Panaud
authors: Institute of Plant Biology, University of Zurich, Zurich, Switzerland.
authors: Thomas
authors: T
authors: Wicker
authors: Department of Biology, University of Maryland, College Park, Maryland, USA.
authors: Carlos A
authors: CA
authors: Machado
authors: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
authors: Mingsheng
authors: M
authors: Chen
authors: Plant Genome and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany.
authors: Klaus F X
authors: KF
authors: Mayer
authors: Dow AgroSciences, Indianapolis, Indiana, USA.
authors: Steve
authors: S
authors: Rounsley
authors: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA.
authors: Rod A
authors: RA
authors: Wing
mesh_terms: D000349:Africa; D000595:Amino Acid Sequence; D001483:Base Sequence; D018556:Crops, Agricultural / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D014644:Genetic Variation; D005828:Genetics, Population / Q000379:methods; D018745:Genome, Plant; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D018744:DNA, Plant