A mosaic monoploid reference sequence for the highly complex genome of sugarcane
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.
- Authors:
-
[1];
[1];
[4];
[1];
[1];
[6];
[9];
more »
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), Montpellier (France); Univ. Montpellier, Montpellier (France)
- KEYGENE N.V., Wageningen (The Netherlands)
- HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
- SASRI (South African Sugarcane Research Institute), Mount Edgecombe (South Africa)
- CSIRO (Commonwealth Scientific and Industrial Research Organisation), St. Lucia (Australia)
- CIRAD, La Reunion (France)
- Diversity Arrays Technology, Yarralumla (Australia)
- J. Craig Venter Institute, Rockville, MD (United States)
- Univ. de Sao Paulo, Sao Paulo (Brazil)
- INRA-CNRGV, Castanet-Tolosan (France)
- JBEI Joint BioEnergy Inst., Emeryville, CA (United States)
- Univ. of Queensland, St. Lucia (Australia)
- HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1543745
- Alternate Identifier(s):
- OSTI ID: 1615275
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Science & Technology; Other Topics
Citation Formats
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, and D’Hont, Angélique. A mosaic monoploid reference sequence for the highly complex genome of sugarcane. United States: N. p., 2018.
Web. doi:10.1038/s41467-018-05051-5.
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. A mosaic monoploid reference sequence for the highly complex genome of sugarcane. United States. https://doi.org/10.1038/s41467-018-05051-5
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, and D’Hont, Angélique. Fri .
"A mosaic monoploid reference sequence for the highly complex genome of sugarcane". United States. https://doi.org/10.1038/s41467-018-05051-5. https://www.osti.gov/servlets/purl/1543745.
@article{osti_1543745,
title = {A mosaic monoploid reference sequence for the highly complex genome of sugarcane},
author = {Garsmeur, Olivier and Droc, Gaetan and Antonise, Rudie and Grimwood, Jane and Potier, Bernard and Aitken, Karen and Jenkins, Jerry and Martin, Guillaume and Charron, Carine and Hervouet, Catherine and Costet, Laurent and Yahiaoui, Nabila and Healey, Adam and Sims, David and Cherukuri, Yesesri and Sreedasyam, Avinash and Kilian, Andrzej and Chan, Agnes and Van Sluys, Marie -Anne and Swaminathan, Kankshita and Town, Christopher and Bergès, Hélène and Simmons, Blake and Glaszmann, Jean Christophe and van der Vossen, Edwin and Henry, Robert and Schmutz, Jeremy and D’Hont, Angélique},
abstractNote = {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.},
doi = {10.1038/s41467-018-05051-5},
journal = {Nature Communications},
number = 1,
volume = 9,
place = {United States},
year = {Fri Jul 06 00:00:00 EDT 2018},
month = {Fri Jul 06 00:00:00 EDT 2018}
}
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