Building the sugarcane genome for biotechnology and identifying evolutionary trends
2014
de Setta, Nathalia | Monteiro-Vitorello, Claudia Barros | Metcalfe, Cushla Jane | Queiroga Cruz, Guilherme Marcelo | del Bem, Luiz Eduardo | Vicentini, Renato | Silveira Nogueira, Fabio Tebaldi | Campos, Roberta Alvares | Nunes, Sideny Lima | Gasperazzo Turrini, Paula Cristina | Vieira, Andreia Prata | Ochoa Cruz, Edgar Andres | Silveira Correa, Tatiana Caroline | Hotta, Carlos Takeshi | Varani, Alessandro de Mello | Vautrin, Sonia, S. | da Trindade, Adilson Silva | Vilela, Mariane de Mendonca | Lembke, Carolina Gimiliani | Sato, Paloma Mieko | de Andrade, Rodrigo Fandino | Nishiyama, Milton Yutaka | Cardoso-Silva, Claudio Benicio | Scortecci, Katia Castanho | Franco Garcia, Antonio Augusto | Carneiro, Monalisa Sampaio | Kim, Changsoo | Paterson, Andrew H. | Berges, Helene, H. | d'Hont, Angélique | de Souza, Anete Pereira | Souza, Glaucia Mendes | Vincentz, Michel | Kitajima, Joao Paulo | van Sluys, Marie-Anne | Universidade de São Paulo = University of São Paulo (USP) | Universidade Federal do ABC = Federal University of ABC = Université Fédérale de l'ABC [Brazil] (UFABC) | Universidade Estadual de Campinas = University of Campinas (UNICAMP) | Instituto de Biociências, Departamento de Genética ; Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP) | Univ Sao Paulo, Dept Genet, Escola Super Agr Luiz de Queiroz, BR-13418900 Piracicaba, SP, Brazil ; Partenaires INRAE | Centre National de Ressources Génomiques Végétales (CNRGV) ; Institut National de la Recherche Agronomique (INRA) | Universidade Federal do Rio Grande do Norte [Natal] (UFRN) | Centro de Ciências Agrárias ; Universidade Federal de Santa Catarina = Federal University of Santa Catarina [Florianópolis] (UFSC) | University of Georgia [USA] | Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro) | Mendelics Genomic Analysis ; Partenaires INRAE | FAPESP [MAVS- 2008/52074-0, CBMV- 2010/05591-9, RV- 2008/58031-0, APS 2008/52197-4, GMS 08/52146-0, 2009/51632-1, 2009/09217-7, 2008/58243-8, 2009/09116-6, 2011/05317-7, 2008/54201-9]; CNPq (MV- INCT BIOETHANOL); CAPES; International Consortium for Sugarcane Biotechnology [24]; Consortium for Plant Biotechnology Research [DE-FG36-02GO12026]; Univ. Georgia Office of the Vice President for Research
International audience
Afficher plus [+] Moins [-]anglais. 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.
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