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Building the sugarcane genome for biotechnology and identifying evolutionary trends
  • Universidade de São Paulo (USP)
  • Universidade Federal do ABC (UFABC)
  • Universidade Estadual de Campinas (UNICAMP)
  • Universidade Estadual Paulista (UNESP)
  • Inst Quim
  • Dept Biol Celular & Genet UFRN
  • Universidade Federal de São Carlos (UFSCar)
  • Univ Georgia
  • Mendel Genom Anal
  • Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
  • Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
  • Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
  • International Consortium for Sugarcane Biotechnology
  • Consortium for Plant Biotechnology Research
  • Univ. Georgia Office of the Vice President for Research
Sponsorship Process Number: 
  • FAPESP: 08/52074-0
  • FAPESP: 10/05591-9
  • FAPESP: 08/58031-0
  • FAPESP: 08/52197-4
  • FAPESP: 08/52146-0
  • FAPESP: 09/51632-1
  • FAPESP: 09/09217-7
  • FAPESP: 08/58243-8
  • FAPESP: 09/09116-6
  • FAPESP: 11/05317-7
  • FAPESP: 08/54201-9
  • International Consortium for Sugarcane Biotechnology24
  • Consortium for Plant Biotechnology ResearchDE-FG36-02GO12026
Background: Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome.Results: Three hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. One of the sucrose pathway genes, sucrose-6-phosphate phosphohydrolase, is duplicated in sugarcane and sorghum, but not in rice and maize. A diversity analysis of the s6pp duplication region revealed haplotype-structured sequence composition. Examination of hom(e)ologous loci indicate both sequence structural and sRNA landscape variation. A synteny analysis shows that the sugarcane genome has expanded relative to the sorghum genome, largely due to the presence of transposable elements and uncharacterized intergenic and intronic sequences.Conclusion: This release of sugarcane genomic sequences will advance our understanding of sugarcane genetics and contribute to the development of molecular tools for breeding purposes and gene discovery.
Issue Date: 
Bmc Genomics. London: Biomed Central Ltd, v. 15, 17 p., 2014.
Time Duration: 
Biomed Central Ltd
  • Saccharum
  • Bacterial artificial chromosome sequencing
  • Polyploidy
  • Genome
  • Genetics
  • Grasses
Access Rights: 
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Appears in Collections:Artigos, TCCs, Teses e Dissertações da Unesp

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