The Sorghum bicolor genome and the diversification of grasses

Andrew H. Paterson (), John E. Bowers, Rémy Bruggmann, Inna Dubchak, Jane Grimwood, Heidrun Gundlach, Georg Haberer, Uffe Hellsten, Therese Mitros, Alexander Poliakov, Jeremy Schmutz, Manuel Spannagl, Haibao Tang, Xiyin Wang, Thomas Wicker, Arvind K. Bharti, Jarrod Chapman, F. Alex Feltus, Udo Gowik, Igor V. Grigoriev, Eric Lyons, Christopher A. Maher, Mihaela Martis, Apurva Narechania, Robert P. Otillar, Bryan W. Penning, Asaf A. Salamov, Yu Wang, Lifang Zhang, Nicholas C. Carpita, Michael Freeling, Alan R. Gingle, C. Thomas Hash, Beat Keller, Patricia Klein, Stephen Kresovich, Maureen C. McCann, Ray Ming, Daniel G. Peterson, Mehboob-ur-Rahman, Doreen Ware, Peter Westhoff, Klaus F. X. Mayer, Joachim Messing and Daniel S. Rokhsar
Additional contact information
Andrew H. Paterson: Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
John E. Bowers: Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
Rémy Bruggmann: Waksman Institute for Microbiology, Rutgers University, Piscataway, New Jersey 08854, USA
Inna Dubchak: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Jane Grimwood: Stanford Human Genome Center, Stanford University, Palo Alto, California 94304, USA
Heidrun Gundlach: MIPS/IBIS, Helmholtz Zentrum München, Inglostaedter Landstrasse 1, 85764 Neuherberg, Germany
Georg Haberer: MIPS/IBIS, Helmholtz Zentrum München, Inglostaedter Landstrasse 1, 85764 Neuherberg, Germany
Uffe Hellsten: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Therese Mitros: Center for Integrative Genomics, University of California, Berkeley, California 94720, USA
Alexander Poliakov: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Jeremy Schmutz: Stanford Human Genome Center, Stanford University, Palo Alto, California 94304, USA
Manuel Spannagl: MIPS/IBIS, Helmholtz Zentrum München, Inglostaedter Landstrasse 1, 85764 Neuherberg, Germany
Haibao Tang: Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
Xiyin Wang: Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
Thomas Wicker: Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
Arvind K. Bharti: Waksman Institute for Microbiology, Rutgers University, Piscataway, New Jersey 08854, USA
Jarrod Chapman: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
F. Alex Feltus: Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
Udo Gowik: Institut fur Entwicklungs und Molekularbiologie der Pflanzen, Heinrich-Heine-Universitat, Universitatsstrasse 1
Igor V. Grigoriev: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Eric Lyons: University of California, Berkeley, California 94720, USA
Christopher A. Maher: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
Mihaela Martis: MIPS/IBIS, Helmholtz Zentrum München, Inglostaedter Landstrasse 1, 85764 Neuherberg, Germany
Apurva Narechania: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
Robert P. Otillar: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Bryan W. Penning: Department of Biological Sciences,
Asaf A. Salamov: DOE Joint Genome Institute, Walnut Creek, California 94598, USA
Yu Wang: MIPS/IBIS, Helmholtz Zentrum München, Inglostaedter Landstrasse 1, 85764 Neuherberg, Germany
Lifang Zhang: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
Nicholas C. Carpita: Purdue University, West Lafayette, Indiana 47907, USA
Michael Freeling: University of California, Berkeley, California 94720, USA
Alan R. Gingle: Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
C. Thomas Hash: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)
Beat Keller: Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008 Zurich, Switzerland
Patricia Klein: Texas A&M University, College Station, Texas 77843, USA
Stephen Kresovich: Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
Maureen C. McCann: Department of Biological Sciences,
Ray Ming: University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
Daniel G. Peterson: Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
Mehboob-ur-Rahman: Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
Doreen Ware: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
Peter Westhoff: Institut fur Entwicklungs und Molekularbiologie der Pflanzen, Heinrich-Heine-Universitat, Universitatsstrasse 1
Klaus F. X. Mayer: MIPS/IBIS, Helmholtz Zentrum München, Inglostaedter Landstrasse 1, 85764 Neuherberg, Germany
Joachim Messing: Waksman Institute for Microbiology, Rutgers University, Piscataway, New Jersey 08854, USA
Daniel S. Rokhsar: DOE Joint Genome Institute, Walnut Creek, California 94598, USA

Nature, 2009, vol. 457, issue 7229, 551-556

Abstract: Abstract Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the ∼730-megabase Sorghum bicolor (L.) Moench genome, placing ∼98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the ∼75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization ∼70 million years ago, most duplicated gene sets lost one member before the sorghum–rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum’s drought tolerance.

Date: 2009
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DOI: 10.1038/nature07723

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