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The Sorghum bicolor genome and the diversification of grasses

Author

Listed:
  • 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
    College of Sciences, Hebei Polytechnic University, Tangshan, Hebei 063000, China)

  • 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
    Clemson University, Clemson, South Carolina 29631, 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
    Mississippi Genome Exploration Laboratory, Mississippi State University, Starkville, Mississippi 39762, USA)

  • Mehboob-ur-Rahman

    (Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA
    National Institute for Biotechnology & Genetic Engineering (NIBGE))

  • Doreen Ware

    (Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
    USDA NAA Robert Holley Center for Agriculture and Health, Ithaca, New York 14853, 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
    Stanford Human Genome Center, Stanford University, Palo Alto, California 94304, USA)

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.

Suggested Citation

  • 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 S, 2009. "The Sorghum bicolor genome and the diversification of grasses," Nature, Nature, vol. 457(7229), pages 551-556, January.
    • Handle: RePEc:nat:nature:v:457:y:2009:i:7229:d:10.1038_nature07723
    DOI: 10.1038/nature07723
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    Cited by:

    1. Md. S. Islam & Per McCord & Quentin D. Read & Lifang Qin & Alexander E. Lipka & Sushma Sood & James Todd & Marcus Olatoye, 2022. "Accuracy of Genomic Prediction of Yield and Sugar Traits in Saccharum spp. Hybrids," Agriculture, MDPI, vol. 12(9), pages 1-22, September.
    2. Hongzeng Fan & Jibin Wang & Songhao Shen & Mingchong Yang & Suli Li & Bihong Feng & Ruimin Zhong & Chongjian Ma & Jihong Wang & Ruohan Xie & Lingqiang Wang, 2022. "High-Throughput Phenotyping of Cross-Sectional Morphology to Assess Stalk Mechanical Properties in Sorghum," Agriculture, MDPI, vol. 12(10), pages 1-13, October.
    3. Theivanayagam Maharajan & Thumadath Palayullaparambil Ajeesh Krishna & Neenthamadathil Mohandas Krishnakumar & Mani Vetriventhan & Himabindu Kudapa & Stanislaus Antony Ceasar, 2024. "Role of Genome Sequences of Major and Minor Millets in Strengthening Food and Nutritional Security for Future Generations," Agriculture, MDPI, vol. 14(5), pages 1-28, April.
    4. Taikui Zhang & Weichen Huang & Lin Zhang & De-Zhu Li & Ji Qi & Hong Ma, 2024. "Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages," Nature Communications, Nature, vol. 15(1), pages 1-27, December.
    5. Veronika DUMALASOVÁ & Leona SVOBODOVÁ & Alena HANZALOVÁ, 2012. "Differentially expressed gene transcripts in wheat and barley leaves upon leaf spot infection," Czech Journal of Genetics and Plant Breeding, Czech Academy of Agricultural Sciences, vol. 48(3), pages 108-119.
    6. Yong-Pei Wu & Yu-Chi Chang & Su-Chen Kuo & Dah-Jing Liao & Ting-Yu Shen & Hsin-I Kuo & Sheng-Wen Wang & Yu-Chien Tseng, 2023. "The Breeding of Waxy Sorghum Using Traditional Three-Line Method and Marker-Assisted Selection," Agriculture, MDPI, vol. 13(11), pages 1-14, October.
    7. Peng Xie & Sanyuan Tang & Chengxuan Chen & Huili Zhang & Feifei Yu & Chao Li & Huimin Wei & Yi Sui & Chuanyin Wu & Xianmin Diao & Yaorong Wu & Qi Xie, 2022. "Natural variation in Glume Coverage 1 causes naked grains in sorghum," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    8. Katrien M. Devos & Peng Qi & Bochra A. Bahri & Davis M. Gimode & Katharine Jenike & Samuel J. Manthi & Dagnachew Lule & Thomas Lux & Liliam Martinez-Bello & Thomas H. Pendergast & Chris Plott & Dipnar, 2023. "Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    9. Katia A. Figueroa-Rodríguez & Francisco Hernández-Rosas & Benjamín Figueroa-Sandoval & Joel Velasco-Velasco & Noé Aguilar Rivera, 2019. "What Has Been the Focus of Sugarcane Research? A Bibliometric Overview," IJERPH, MDPI, vol. 16(18), pages 1-15, September.
    10. Liang Ma & Ke-Wei Liu & Zhen Li & Yu-Yun Hsiao & Yiying Qi & Tao Fu & Guang-Da Tang & Diyang Zhang & Wei-Hong Sun & Ding-Kun Liu & Yuanyuan Li & Gui-Zhen Chen & Xue-Die Liu & Xing-Yu Liao & Yu-Ting Ji, 2023. "Diploid and tetraploid genomes of Acorus and the evolution of monocots," Nature Communications, Nature, vol. 14(1), pages 1-18, December.

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