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

Garsmeur Olivier, Droc Gaëtan, Antonise Rudie, Grimwood Jane, Potier Bernard, Aitken Karen S., Jenkins Jerry, Martin Guillaume, Charron Carine, Hervouet Catherine, Costet Laurent, Yahiaoui Nabila, Healey Adam, Sims David, Cherukuri Yesesri, Sreedasyam Avinash, Kilian Andrzej, Chan Agnes P., Van Sluys Marie-Anne, Swaminathan Kankshita, Town Christopher, Berges Hélène, Simmons Blake, Glaszmann Jean-Christophe, Van der Vossen Edwin, Henry Robert, Schmutz Jeremy, D'Hont Angélique. 2018. A mosaic monoploid reference sequence for the highly complex genome of sugarcane. Nature Communications, 9:2638, 10 p.

Journal article ; Article de recherche ; Article de revue à facteur d'impact
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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.

Mots-clés Agrovoc : Saccharum, Génome, Saccharum officinarum, Génétique, Variété, Amélioration des plantes, Saccharum spontaneum

Mots-clés géographiques Agrovoc : Réunion

Mots-clés libres : Canne à sucre, Réference génome sequence, Structure génome, Évolution génome, Saccharum

Classification Agris : F30 - Plant genetics and breeding

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • Garsmeur Olivier, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-8869-3689
  • Droc Gaëtan, CIRAD-BIOS-UMR AGAP (FRA)
  • Antonise Rudie, KeyGene (NLD)
  • Grimwood Jane, DOE-JGI (USA)
  • Potier Bernard, SASRI (ZAF)
  • Aitken Karen S., CSIRO (AUS)
  • Jenkins Jerry, HudsonAlpha Biotechnology Institute (USA)
  • Martin Guillaume, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-1801-7500
  • Charron Carine, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0003-0281-9936
  • Hervouet Catherine, CIRAD-BIOS-UMR AGAP (FRA)
  • Costet Laurent, CIRAD-BIOS-UMR PVBMT (REU) ORCID: 0000-0003-3199-2885
  • Yahiaoui Nabila, CIRAD-BIOS-UMR AGAP (FRA)
  • Healey Adam, HudsonAlpha Biotechnology Institute (USA)
  • Sims David, HudsonAlpha Biotechnology Institute (USA)
  • Cherukuri Yesesri, HudsonAlpha Biotechnology Institute (USA)
  • Sreedasyam Avinash, HudsonAlpha Biotechnology Institute (USA)
  • Kilian Andrzej, Diversity Arrays Technology (AUS)
  • Chan Agnes P., JCVI (USA)
  • Van Sluys Marie-Anne, Universidade de São Paulo (BRA)
  • Swaminathan Kankshita, HudsonAlpha Biotechnology Institute (USA)
  • Town Christopher, The J. Craig Venter Institute (USA)
  • Berges Hélène, INRA (FRA)
  • Simmons Blake, Joint Bioenergy Institute (USA)
  • Glaszmann Jean-Christophe, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-9918-875X
  • Van der Vossen Edwin, KeyGene (NLD)
  • Henry Robert, University of Queensland (AUS)
  • Schmutz Jeremy, DOE-JGI (USA)
  • D'Hont Angélique, CIRAD-BIOS-UMR AGAP (FRA) - auteur correspondant

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