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Building the sugarcane genome for biotechnology and identifying evolutionary trends

de Setta Nathalia, Monteiro-Vitorello Cláudia, Metcalfe Cushla Jane, Cruz Guilherme Marcelo Queiroga, Del Bem Luiz Eduardo, Vicentini Renato, Tebaldi Silveira Nogueira Fábio, Alvares Campos Roberta, Lima Nunes Sideny, Gasperazzo Turrini Paula Crisina, Prata Vieira Andreia, Ochoa Cruz Edgar Andrés, Silveira Corrêa Tatiana Caroline, Takeshi Hotta Carlos, de Mello Varani Alessandro, Vautrin Sonia, Silva da Trindade Adilson, de Mendonça Vilela Marianne, Gimiliani Lembke Carolina, Mieko Sato Paloma, Fandino de Andrade Rodrigo, Yutaka Nishiyama Milton, Cardoso-Silva Claudio Benicio, Castanho Scortecci Katia, Garcia Antonio Augusto Franco, Sampaio Carneiro Monalisa, Kim Changsoo, Paterson Andrew H., Berges Hélène, D'Hont Angélique, Pereira de Souza Anete, Mendes Souza Glaucia, Vincentz Michel, Kitajima João Paulo, Van Sluys Marie-Anne. 2014. Building the sugarcane genome for biotechnology and identifying evolutionary trends. BMC Genomics, 15 (540), 18 p.

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Quartile : Q1, Sujet : BIOTECHNOLOGY & APPLIED MICROBIOLOGY / Quartile : Q1, Sujet : GENETICS & HEREDITY

Abstract : 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. (Résumé d'auteur)

Mots-clés Agrovoc : Saccharum officinarum, Saccharum spontaneum, Génome, Génie génétique, Polyploïdie, Séquence nucléotidique, Carte génétique, Métabolisme des glucides, Sorghum

Mots-clés complémentaires : Chromosome artificiel

Classification Agris : F30 - Plant genetics and breeding
F60 - Plant physiology and biochemistry

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • de Setta Nathalia, Universidade de São Paulo (BRA)
  • Monteiro-Vitorello Cláudia, ESALQ (BRA)
  • Metcalfe Cushla Jane, Universidade de São Paulo (BRA)
  • Cruz Guilherme Marcelo Queiroga, Universidade de São Paulo (BRA)
  • Del Bem Luiz Eduardo, UNICAMP (BRA)
  • Vicentini Renato, UNICAMP (BRA)
  • Tebaldi Silveira Nogueira Fábio, UNESP (BRA)
  • Alvares Campos Roberta, Instituto de Quimica de São Carlos (BRA)
  • Lima Nunes Sideny, Instituto de Quimica de São Carlos (BRA)
  • Gasperazzo Turrini Paula Crisina, Universidade de São Paulo (BRA)
  • Prata Vieira Andreia, Universidade de São Paulo (BRA)
  • Ochoa Cruz Edgar Andrés, Universidade de São Paulo (BRA)
  • Silveira Corrêa Tatiana Caroline, Universidade de São Paulo (BRA)
  • Takeshi Hotta Carlos, Universidade de São Paulo (BRA)
  • de Mello Varani Alessandro, ESALQ (BRA)
  • Vautrin Sonia, INRA (FRA)
  • Silva da Trindade Adilson, UFRJ (BRA)
  • de Mendonça Vilela Marianne, UFCG (BRA)
  • Gimiliani Lembke Carolina, Instituto de Quimica de São Carlos (BRA)
  • Mieko Sato Paloma, Instituto de Quimica de São Carlos (BRA)
  • Fandino de Andrade Rodrigo, Instituto de Quimica de São Carlos (BRA)
  • Yutaka Nishiyama Milton, Instituto de Quimica de São Carlos (BRA)
  • Cardoso-Silva Claudio Benicio, UNICAMP (BRA)
  • Castanho Scortecci Katia, UFRB (BRA)
  • Garcia Antonio Augusto Franco, Universidade de São Paulo (BRA)
  • Sampaio Carneiro Monalisa, Universidade Federal de São Carlos (BRA)
  • Kim Changsoo, University of Georgia (USA)
  • Paterson Andrew H., University of Georgia (USA)
  • Berges Hélène, INRA (FRA)
  • D'Hont Angélique, CIRAD-BIOS-UMR AGAP (FRA)
  • Pereira de Souza Anete, UNICAMP (BRA)
  • Mendes Souza Glaucia, Instituto de Quimica de São Carlos (BRA)
  • Vincentz Michel, UNICAMP (BRA)
  • Kitajima João Paulo, Mendelics Genomic Analysis (BRA)
  • Van Sluys Marie-Anne, Universidade de São Paulo (BRA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/577697/)

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