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

Olivier Garsmeur, Gaetan Droc, Rudie Antonise, Jane Grimwood, Bernard Potier, Karen Aitken, Jerry Jenkins, Guillaume Martin, Carine Charron, Catherine Hervouet, Laurent Costet, Nabila Yahiaoui, Adam Healey, David Sims, Yesesri Cherukuri, Avinash Sreedasyam, Andrzej Kilian, Agnes Chan, Marie-Anne Sluys, Kankshita Swaminathan, Christopher Town, Hélène Bergès, Blake Simmons, Jean Christophe Glaszmann, Edwin Vossen, Robert Henry, Jeremy Schmutz and Angélique D’Hont ()
Additional contact information
Olivier Garsmeur: UMR AGAP
Gaetan Droc: UMR AGAP
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
Carine Charron: UMR AGAP
Catherine Hervouet: UMR AGAP
Laurent Costet: CIRAD, UMR PVBMT
Nabila Yahiaoui: UMR AGAP
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
Edwin Vossen: KEYGENE N.V.
Robert Henry: University of Queensland
Jeremy Schmutz: HudsonAlpha Institute for Biotechnology
Angélique D’Hont: UMR AGAP

Nature Communications, 2018, vol. 9, issue 1, 1-10

Abstract: 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.

Date: 2018
References: Add references at CitEc
Citations: View citations in EconPapers (2)

Downloads: (external link)
https://www.nature.com/articles/s41467-018-05051-5 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-05051-5

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-018-05051-5

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().