skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: 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:
ORCiD logo [1]; ORCiD logo [1];  [2];  [3]; ORCiD logo [4];  [5];  [3]; ORCiD logo [1]; ORCiD logo [1];  [1]; ORCiD logo [6];  [1];  [3];  [3];  [3];  [3];  [7];  [8]; ORCiD logo [9];  [3] more »; ORCiD logo [8];  [10]; ORCiD logo [11];  [1];  [2]; ORCiD logo [12];  [13];  [1] « less
  1. CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), Montpellier (France); Univ. Montpellier, Montpellier (France)
  2. KEYGENE N.V., Wageningen (The Netherlands)
  3. HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
  4. SASRI (South African Sugarcane Research Institute), Mount Edgecombe (South Africa)
  5. CSIRO (Commonwealth Scientific and Industrial Research Organisation), St. Lucia (Australia)
  6. CIRAD, La Reunion (France)
  7. Diversity Arrays Technology, Yarralumla (Australia)
  8. J. Craig Venter Institute, Rockville, MD (United States)
  9. Univ. de Sao Paulo, Sao Paulo (Brazil)
  10. INRA-CNRGV, Castanet-Tolosan (France)
  11. JBEI Joint BioEnergy Inst., Emeryville, CA (United States)
  12. Univ. of Queensland, St. Lucia (Australia)
  13. 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
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. 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, and D’Hont, Angélique. Fri . "A mosaic monoploid reference sequence for the highly complex genome of sugarcane". United States. doi: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 = {2018},
month = {7}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 27 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

The Sorghum bicolor genome and the diversification of grasses
journal, January 2009

  • Paterson, Andrew H.; Bowers, John E.; Bruggmann, Rémy
  • Nature, Vol. 457, Issue 7229
  • DOI: 10.1038/nature07723

Comparative Analysis of Miscanthus and Saccharum Reveals a Shared Whole-Genome Duplication but Different Evolutionary Fates
journal, June 2014


Sequence polymorphism from EST data in sugarcane: a fine analysis of 6-phosphogluconate dehydrogenase genes
journal, December 2001


Island species radiation and karyotypic stasis in Pachycladon allopolyploids
journal, January 2010

  • Mandáková, Terezie; Heenan, Peter B.; Lysak, Martin A.
  • BMC Evolutionary Biology, Vol. 10, Issue 1
  • DOI: 10.1186/1471-2148-10-367

De Novo Assembly and Transcriptome Analysis of Contrasting Sugarcane Varieties
journal, February 2014

  • Cardoso-Silva, Claudio Benicio; Costa, Estela Araujo; Mancini, Melina Cristina
  • PLoS ONE, Vol. 9, Issue 2
  • DOI: 10.1371/journal.pone.0088462

A putative major gene for rust resistance linked with a RFLP marker in sugarcane cultivar ‘R570’
journal, June 1996

  • Daugrois, J. H.; Grivet, L.; Roques, D.
  • Theoretical and Applied Genetics, Vol. 92, Issue 8
  • DOI: 10.1007/BF00224049

Genome wide association mapping of agro-morphological and disease resistance traits in sugarcane
journal, November 2014


Molecular investigation of the genetic base of sugarcane cultivars
journal, July 1999

  • Jannoo, N.; Grivet, L.; Seguin, M.
  • Theoretical and Applied Genetics, Vol. 99, Issue 1-2
  • DOI: 10.1007/s001220051222

Studies in Saccharum spontaneum Distribution and Geographical Association of Chromosome Numbers
journal, January 1960


Genome size variation in three Saccharum species
journal, March 2012


Differential chromosome pairing affinities at meiosis in polyploid sugarcane revealed by molecular markers
journal, August 2004


Genetic control of yield related stalk traits in sugarcane
journal, August 2008


Circos: An information aesthetic for comparative genomics
journal, June 2009


Sequence-based physical mapping of complex genomes by whole genome profiling
journal, February 2011


Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL.
journal, September 1996

  • Gaut, B. S.; Morton, B. R.; McCaig, B. C.
  • Proceedings of the National Academy of Sciences, Vol. 93, Issue 19
  • DOI: 10.1073/pnas.93.19.10274

Cytogenetics of modern sugar canes
journal, April 1963


The Diversification of Plant NBS-LRR Defense Genes Directs the Evolution of MicroRNAs That Target Them
journal, August 2016

  • Zhang, Yu; Xia, Rui; Kuang, Hanhui
  • Molecular Biology and Evolution, Vol. 33, Issue 10
  • DOI: 10.1093/molbev/msw154

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic
journal, November 2014

  • Sonnhammer, Erik L. L.; Östlund, Gabriel
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1203

A comprehensive genetic map of sugarcane that provides enhanced map coverage and integrates high-throughput Diversity Array Technology (DArT) markers
journal, January 2014


Genetic dissection of a modern sugarcane cultivar (Saccharum spp.). I. Genome mapping with AFLP markers
journal, July 2001

  • Hoarau, J. -Y.; Offmann, B.; D’Hont, A.
  • Theoretical and Applied Genetics, Vol. 103, Issue 1
  • DOI: 10.1007/s001220000390

Genetic mapping in sugarcane, a high polyploid, using bi-parental progeny: identification of a gene controlling stalk colour and a new rust resistance gene
journal, March 2006

  • Raboin, L. -M.; Oliveira, K. M.; Lecunff, L.
  • Theoretical and Applied Genetics, Vol. 112, Issue 7
  • DOI: 10.1007/s00122-006-0240-3

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997

  • Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A.
  • Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402
  • DOI: 10.1093/nar/25.17.3389

Characterisation of the double genome structure of modern sugarcane cultivars (
journal, January 1996

  • D’Hont, Angélique; Grivet, Laurent; Feldmann, Philippe
  • MGG Molecular & General Genetics, Vol. 250, Issue 4
  • DOI: 10.1007/s004380050092

Determination of basic chromosome numbers in the genus Saccharum by physical mapping of ribosomal RNA genes
journal, April 1998

  • D'Hont, Angélique; Ison, David; Alix, Karine
  • Genome, Vol. 41, Issue 2
  • DOI: 10.1139/g98-023

CD-HIT: accelerated for clustering the next-generation sequencing data
journal, October 2012


A major quantitative trait allele for resistance to the Sugarcane yellow leaf virus ( Luteoviridae ) : Major QTA for resistance to the
journal, July 2012


Prospecting sugarcane resistance to Sugarcane yellow leaf virus by genome-wide association
journal, June 2014


Problems in breeding and cytology of sugar cane
journal, March 1961


Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species
journal, August 2011


Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph
journal, October 2008


Building the sugarcane genome for biotechnology and identifying evolutionary trends
journal, January 2014

  • de Setta, Nathalia; Monteiro-Vitorello, Cláudia; Metcalfe, Cushla
  • BMC Genomics, Vol. 15, Issue 1
  • DOI: 10.1186/1471-2164-15-540

High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane
journal, October 2010


Genomic distribution and characterization of EST-derived resistance gene analogs (RGAs) in sugarcane
journal, May 2003


Centromere retention and loss during the descent of maize from a tetraploid ancestor
journal, November 2012

  • Wang, H.; Bennetzen, J. L.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 51
  • DOI: 10.1073/pnas.1218668109

Associations between DNA markers and resistance to diseases in sugarcane and effects of population substructure
journal, October 2006

  • Wei, Xianming; Jackson, Phillip A.; McIntyre, C. Lynne
  • Theoretical and Applied Genetics, Vol. 114, Issue 1
  • DOI: 10.1007/s00122-006-0418-8

Construction of a composite sorghum genome map and comparison with sugarcane, a related complex polyploid
journal, March 1997

  • Dufour, P.; Deu, M.; Grivet, L.
  • Theoretical and Applied Genetics, Vol. 94, Issue 3-4
  • DOI: 10.1007/s001220050430

Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize
journal, December 1997

  • Guimaraes, C. T.; Sills, G. R.; Sobral, B. W. S.
  • Proceedings of the National Academy of Sciences, Vol. 94, Issue 26
  • DOI: 10.1073/pnas.94.26.14261

Identification of a major quantitative trait locus (QTL) for yellow spot (Mycovellosiella koepkei) disease resistance in sugarcane
journal, November 2006


The Sugarcane Genome Challenge: Strategies for Sequencing a Highly Complex Genome
journal, June 2011

  • Souza, Glaucia Mendes; Berges, Helene; Bocs, Stephanie
  • Tropical Plant Biology, Vol. 4, Issue 3-4
  • DOI: 10.1007/s12042-011-9079-0

Genetic dissection of a modern sugarcane cultivar (Saccharum spp.).II. Detection of QTLs for yield components
journal, November 2002


Analysis of genome-wide linkage disequilibrium in the highly polyploid sugarcane
journal, January 2008

  • Raboin, Louis-Marie; Pauquet, Jérôme; Butterfield, Mike
  • Theoretical and Applied Genetics, Vol. 116, Issue 5
  • DOI: 10.1007/s00122-007-0703-1

QTL Analysis in a Complex Autopolyploid: Genetic Control of Sugar Content in Sugarcane
journal, November 2001


Sugarcane genomics: depicting the complex genome of an important tropical crop
journal, April 2002


Evolution of F-box genes in plants: Different modes of sequence divergence and their relationships with functional diversification
journal, January 2009

  • Xu, Guixia; Ma, Hong; Nei, Masatoshi
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 3
  • DOI: 10.1073/pnas.0812043106

A molecular approach to unraveling the genetics of sugarcane, a complex polyploid of the Andropogoneae tribe
journal, April 1994

  • D'Hont, Angélique; Lu, Yun-Hai; León, Diego González de
  • Genome, Vol. 37, Issue 2
  • DOI: 10.1139/g94-031

Experimental assessment of the accuracy of genomic selection in sugarcane
journal, August 2013

  • Gouy, M.; Rousselle, Y.; Bastianelli, D.
  • Theoretical and Applied Genetics, Vol. 126, Issue 10
  • DOI: 10.1007/s00122-013-2156-z

A bacterial artificial chromosome library for sugarcane
journal, August 1999

  • Tomkins, J. P.; Yu, Y.; Miller-Smith, H.
  • Theoretical and Applied Genetics, Vol. 99, Issue 3-4
  • DOI: 10.1007/s001220051252

The detection and estimation of linkage in polyploids using single-dose restriction fragments
journal, January 1992

  • Wu, K. K.; Burnquist, W.; Sorrells, M. E.
  • Theoretical and Applied Genetics, Vol. 83, Issue 3
  • DOI: 10.1007/BF00224274

Molecular cytogenetic investigation of chromosome composition and transmission in sugarcane
journal, June 2010

  • Piperidis, George; Piperidis, Nathalie; D’Hont, Angélique
  • Molecular Genetics and Genomics, Vol. 284, Issue 1
  • DOI: 10.1007/s00438-010-0546-3

Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes
journal, January 2010


A combination of AFLP and SSR markers provides extensive map coverage and identification of homo(eo)logous linkage groups in a sugarcane cultivar
journal, February 2005

  • Aitken, K. S.; Jackson, P. A.; McIntyre, C. L.
  • Theoretical and Applied Genetics, Vol. 110, Issue 5
  • DOI: 10.1007/s00122-004-1813-7

A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome
journal, January 2012

  • Figueira, Thais Rezende; Okura, Vagner; Rodrigues da Silva, Felipe
  • BMC Research Notes, Vol. 5, Issue 1
  • DOI: 10.1186/1756-0500-5-185

Analysis and Functional Annotation of an Expressed Sequence Tag Collection for Tropical Crop Sugarcane
journal, December 2003


    Works referencing / citing this record:

    Genetic dissection of a modern sugarcane cultivar (Saccharum spp.).II. Detection of QTLs for yield components
    journal, November 2002


    A combination of AFLP and SSR markers provides extensive map coverage and identification of homo(eo)logous linkage groups in a sugarcane cultivar
    journal, February 2005

    • Aitken, K. S.; Jackson, P. A.; McIntyre, C. L.
    • Theoretical and Applied Genetics, Vol. 110, Issue 5
    • DOI: 10.1007/s00122-004-1813-7

    Genetic mapping in sugarcane, a high polyploid, using bi-parental progeny: identification of a gene controlling stalk colour and a new rust resistance gene
    journal, March 2006

    • Raboin, L. -M.; Oliveira, K. M.; Lecunff, L.
    • Theoretical and Applied Genetics, Vol. 112, Issue 7
    • DOI: 10.1007/s00122-006-0240-3

    Associations between DNA markers and resistance to diseases in sugarcane and effects of population substructure
    journal, October 2006

    • Wei, Xianming; Jackson, Phillip A.; McIntyre, C. Lynne
    • Theoretical and Applied Genetics, Vol. 114, Issue 1
    • DOI: 10.1007/s00122-006-0418-8

    Analysis of genome-wide linkage disequilibrium in the highly polyploid sugarcane
    journal, January 2008

    • Raboin, Louis-Marie; Pauquet, Jérôme; Butterfield, Mike
    • Theoretical and Applied Genetics, Vol. 116, Issue 5
    • DOI: 10.1007/s00122-007-0703-1

    Genetic control of yield related stalk traits in sugarcane
    journal, August 2008


    Experimental assessment of the accuracy of genomic selection in sugarcane
    journal, August 2013

    • Gouy, M.; Rousselle, Y.; Bastianelli, D.
    • Theoretical and Applied Genetics, Vol. 126, Issue 10
    • DOI: 10.1007/s00122-013-2156-z

    Prospecting sugarcane resistance to Sugarcane yellow leaf virus by genome-wide association
    journal, June 2014


    Genetic dissection of a modern sugarcane cultivar (Saccharum spp.). I. Genome mapping with AFLP markers
    journal, July 2001

    • Hoarau, J. -Y.; Offmann, B.; D’Hont, A.
    • Theoretical and Applied Genetics, Vol. 103, Issue 1
    • DOI: 10.1007/s001220000390

    Construction of a composite sorghum genome map and comparison with sugarcane, a related complex polyploid
    journal, March 1997

    • Dufour, P.; Deu, M.; Grivet, L.
    • Theoretical and Applied Genetics, Vol. 94, Issue 3-4
    • DOI: 10.1007/s001220050430

    Molecular investigation of the genetic base of sugarcane cultivars
    journal, July 1999

    • Jannoo, N.; Grivet, L.; Seguin, M.
    • Theoretical and Applied Genetics, Vol. 99, Issue 1-2
    • DOI: 10.1007/s001220051222

    A bacterial artificial chromosome library for sugarcane
    journal, August 1999

    • Tomkins, J. P.; Yu, Y.; Miller-Smith, H.
    • Theoretical and Applied Genetics, Vol. 99, Issue 3-4
    • DOI: 10.1007/s001220051252

    Genomic distribution and characterization of EST-derived resistance gene analogs (RGAs) in sugarcane
    journal, May 2003


    Molecular cytogenetic investigation of chromosome composition and transmission in sugarcane
    journal, June 2010

    • Piperidis, George; Piperidis, Nathalie; D’Hont, Angélique
    • Molecular Genetics and Genomics, Vol. 284, Issue 1
    • DOI: 10.1007/s00438-010-0546-3

    Characterisation of the double genome structure of modern sugarcane cultivars (
    journal, January 1996

    • D’Hont, Angélique; Grivet, Laurent; Feldmann, Philippe
    • MGG Molecular & General Genetics, Vol. 250, Issue 4
    • DOI: 10.1007/s004380050092

    Genome size variation in three Saccharum species
    journal, March 2012


    Genome wide association mapping of agro-morphological and disease resistance traits in sugarcane
    journal, November 2014


    Identification of a major quantitative trait locus (QTL) for yellow spot (Mycovellosiella koepkei) disease resistance in sugarcane
    journal, November 2006


    The Sugarcane Genome Challenge: Strategies for Sequencing a Highly Complex Genome
    journal, June 2011

    • Souza, Glaucia Mendes; Berges, Helene; Bocs, Stephanie
    • Tropical Plant Biology, Vol. 4, Issue 3-4
    • DOI: 10.1007/s12042-011-9079-0

    The Sorghum bicolor genome and the diversification of grasses
    journal, January 2009

    • Paterson, Andrew H.; Bowers, John E.; Bruggmann, Rémy
    • Nature, Vol. 457, Issue 7229
    • DOI: 10.1038/nature07723

    Differential chromosome pairing affinities at meiosis in polyploid sugarcane revealed by molecular markers
    journal, August 2004


    Evolution of F-box genes in plants: Different modes of sequence divergence and their relationships with functional diversification
    journal, January 2009

    • Xu, Guixia; Ma, Hong; Nei, Masatoshi
    • Proceedings of the National Academy of Sciences, Vol. 106, Issue 3
    • DOI: 10.1073/pnas.0812043106

    Centromere retention and loss during the descent of maize from a tetraploid ancestor
    journal, November 2012

    • Wang, H.; Bennetzen, J. L.
    • Proceedings of the National Academy of Sciences, Vol. 109, Issue 51
    • DOI: 10.1073/pnas.1218668109

    Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL.
    journal, September 1996

    • Gaut, B. S.; Morton, B. R.; McCaig, B. C.
    • Proceedings of the National Academy of Sciences, Vol. 93, Issue 19
    • DOI: 10.1073/pnas.93.19.10274

    Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize
    journal, December 1997

    • Guimaraes, C. T.; Sills, G. R.; Sobral, B. W. S.
    • Proceedings of the National Academy of Sciences, Vol. 94, Issue 26
    • DOI: 10.1073/pnas.94.26.14261

    CD-HIT: accelerated for clustering the next-generation sequencing data
    journal, October 2012


    The Diversification of Plant NBS-LRR Defense Genes Directs the Evolution of MicroRNAs That Target Them
    journal, August 2016

    • Zhang, Yu; Xia, Rui; Kuang, Hanhui
    • Molecular Biology and Evolution, Vol. 33, Issue 10
    • DOI: 10.1093/molbev/msw154

    Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    journal, September 1997

    • Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A.
    • Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402
    • DOI: 10.1093/nar/25.17.3389

    InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic
    journal, November 2014

    • Sonnhammer, Erik L. L.; Östlund, Gabriel
    • Nucleic Acids Research, Vol. 43, Issue D1
    • DOI: 10.1093/nar/gku1203

    Circos: An information aesthetic for comparative genomics
    journal, June 2009


    Sequence-based physical mapping of complex genomes by whole genome profiling
    journal, February 2011


    Analysis and Functional Annotation of an Expressed Sequence Tag Collection for Tropical Crop Sugarcane
    journal, December 2003


    QTL Analysis in a Complex Autopolyploid: Genetic Control of Sugar Content in Sugarcane
    journal, November 2001


    Comparative Analysis of Miscanthus and Saccharum Reveals a Shared Whole-Genome Duplication but Different Evolutionary Fates
    journal, June 2014


    A major quantitative trait allele for resistance to the Sugarcane yellow leaf virus ( Luteoviridae ) : Major QTA for resistance to the
    journal, July 2012


    High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane
    journal, October 2010


    A molecular approach to unraveling the genetics of sugarcane, a complex polyploid of the Andropogoneae tribe
    journal, April 1994

    • D'Hont, Angélique; Lu, Yun-Hai; León, Diego González de
    • Genome, Vol. 37, Issue 2
    • DOI: 10.1139/g94-031

    Determination of basic chromosome numbers in the genus Saccharum by physical mapping of ribosomal RNA genes
    journal, April 1998

    • D'Hont, Angélique; Ison, David; Alix, Karine
    • Genome, Vol. 41, Issue 2
    • DOI: 10.1139/g98-023

    Island species radiation and karyotypic stasis in Pachycladon allopolyploids
    journal, January 2010

    • Mandáková, Terezie; Heenan, Peter B.; Lysak, Martin A.
    • BMC Evolutionary Biology, Vol. 10, Issue 1
    • DOI: 10.1186/1471-2148-10-367

    Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes
    journal, January 2010


    A comprehensive genetic map of sugarcane that provides enhanced map coverage and integrates high-throughput Diversity Array Technology (DArT) markers
    journal, January 2014


    Building the sugarcane genome for biotechnology and identifying evolutionary trends
    journal, January 2014

    • de Setta, Nathalia; Monteiro-Vitorello, Cláudia; Metcalfe, Cushla
    • BMC Genomics, Vol. 15, Issue 1
    • DOI: 10.1186/1471-2164-15-540

    A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome
    journal, January 2012

    • Figueira, Thais Rezende; Okura, Vagner; Rodrigues da Silva, Felipe
    • BMC Research Notes, Vol. 5, Issue 1
    • DOI: 10.1186/1756-0500-5-185

    Silencing of a BAHD acyltransferase in sugarcane increases biomass digestibility
    journal, May 2019

    • de Souza, Wagner Rodrigo; Pacheco, Thályta Fraga; Duarte, Karoline Estefani
    • Biotechnology for Biofuels, Vol. 12, Issue 1
    • DOI: 10.1186/s13068-019-1450-7

    Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph
    journal, October 2008


    De Novo Assembly and Transcriptome Analysis of Contrasting Sugarcane Varieties
    journal, February 2014

    • Cardoso-Silva, Claudio Benicio; Costa, Estela Araujo; Mancini, Melina Cristina
    • PLoS ONE, Vol. 9, Issue 2
    • DOI: 10.1371/journal.pone.0088462

    Studies in Saccharum spontaneum Distribution and Geographical Association of Chromosome Numbers
    journal, January 1960


    Genome-wide alternative splicing landscapes modulated by biotrophic sugarcane smut pathogen
    journal, June 2019


    Comparative analysis of glyoxalase pathway genes in Erianthus arundinaceus and commercial sugarcane hybrid under salinity and drought conditions
    journal, April 2019

    • Manoj, Vadakkancherry Mohanan; Anunanthini, Pushpanathan; Swathik, Peter Clarancia
    • BMC Genomics, Vol. 19, Issue S9
    • DOI: 10.1186/s12864-018-5349-7

    Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype
    journal, November 2019