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Open Access Publications from the University of California

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

  • Author(s): Garsmeur, Olivier
  • Droc, Gaetan
  • Antonise, Rudie
  • Grimwood, Jane
  • Potier, Bernard
  • Aitken, Karen
  • Jenkins, Jerry
  • Martin, Guillaume
  • Charron, Carine
  • Hervouet, Catherine
  • Costet, Laurent
  • Yahiaoui, Nabila
  • Healey, Adam
  • Sims, David
  • Cherukuri, Yesesri
  • Sreedasyam, Avinash
  • Kilian, Andrzej
  • Chan, Agnes
  • Van Sluys, Marie-Anne
  • Swaminathan, Kankshita
  • Town, Christopher
  • Bergès, Hélène
  • Simmons, Blake
  • Glaszmann, Jean Christophe
  • van der Vossen, Edwin
  • Henry, Robert
  • Schmutz, Jeremy
  • D'Hont, Angélique
  • et al.

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.

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