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A mosaic monoploid reference sequence for the highly complex genome of sugarcane

Author

Listed:
  • Olivier Garsmeur

    (UMR AGAP
    Montpellier SupAgro)

  • Gaetan Droc

    (UMR AGAP
    Montpellier SupAgro)

  • Rudie Antonise

    (KEYGENE N.V.)

  • Jane Grimwood

    (HudsonAlpha Institute for Biotechnology)

  • Bernard Potier

    (SASRI (South African Sugarcane Research Institute))

  • Karen Aitken

    (CSIRO (Commonwealth Scientific and Industrial Research Organisation))

  • Jerry Jenkins

    (HudsonAlpha Institute for Biotechnology)

  • Guillaume Martin

    (UMR AGAP
    Montpellier SupAgro)

  • Carine Charron

    (UMR AGAP
    Montpellier SupAgro)

  • Catherine Hervouet

    (UMR AGAP
    Montpellier SupAgro)

  • Laurent Costet

    (CIRAD, UMR PVBMT)

  • Nabila Yahiaoui

    (UMR AGAP
    Montpellier SupAgro)

  • Adam Healey

    (HudsonAlpha Institute for Biotechnology)

  • David Sims

    (HudsonAlpha Institute for Biotechnology)

  • Yesesri Cherukuri

    (HudsonAlpha Institute for Biotechnology)

  • Avinash Sreedasyam

    (HudsonAlpha Institute for Biotechnology)

  • Andrzej Kilian

    (Diversity Arrays Technology)

  • Agnes Chan

    (J. Craig Venter Institute)

  • Marie-Anne Sluys

    (Universidade de Sao Paulo)

  • Kankshita Swaminathan

    (HudsonAlpha Institute for Biotechnology)

  • Christopher Town

    (J. Craig Venter Institute)

  • Hélène Bergès

    (INRA-CNRGV)

  • Blake Simmons

    (JBEI Joint BioEnergy Institute)

  • Jean Christophe Glaszmann

    (UMR AGAP
    Montpellier SupAgro)

  • Edwin Vossen

    (KEYGENE N.V.)

  • Robert Henry

    (University of Queensland)

  • Jeremy Schmutz

    (HudsonAlpha Institute for Biotechnology
    Joint Genome Institute)

  • Angélique D’Hont

    (UMR AGAP
    Montpellier SupAgro)

Abstract

Sugarcane (Saccharum spp.) is a major crop for sugar and bioenergy production. Its highly polyploid, aneuploid, heterozygous, and interspecific genome poses major challenges for producing a reference sequence. We exploited colinearity with sorghum to produce a BAC-based monoploid genome sequence of sugarcane. A minimum tiling path of 4660 sugarcane BAC that best covers the gene-rich part of the sorghum genome was selected based on whole-genome profiling, sequenced, and assembled in a 382-Mb single tiling path of a high-quality sequence. A total of 25,316 protein-coding gene models are predicted, 17% of which display no colinearity with their sorghum orthologs. We show that the two species, S. officinarum and S. spontaneum, involved in modern cultivars differ by their transposable elements and by a few large chromosomal rearrangements, explaining their distinct genome size and distinct basic chromosome numbers while also suggesting that polyploidization arose in both lineages after their divergence.

Suggested Citation

  • Olivier Garsmeur & Gaetan Droc & Rudie Antonise & Jane Grimwood & Bernard Potier & Karen Aitken & Jerry Jenkins & Guillaume Martin & Carine Charron & Catherine Hervouet & Laurent Costet & Nabila Yahia, 2018. "A mosaic monoploid reference sequence for the highly complex genome of sugarcane," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-05051-5
    DOI: 10.1038/s41467-018-05051-5
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    Cited by:

    1. Yixue Bao & Qing Zhang & Jiangfeng Huang & Shengcheng Zhang & Wei Yao & Zehuai Yu & Zuhu Deng & Jiaxin Yu & Weilong Kong & Xikai Yu & Shan Lu & Yibin Wang & Ru Li & Yuhan Song & Chengwu Zou & Yuzhi Xu, 2024. "A chromosomal-scale genome assembly of modern cultivated hybrid sugarcane provides insights into origination and evolution," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    2. 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.

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