Building the sugarcane genome for biotechnology and identifying evolutionary trends. de Setta, N.; Monteiro-Vitorello, C., B.; Metcalfe, C., J.; Cruz, G., M., Q.; Del Bem, L., E.; Vicentini, R.; Nogueira, F., T., S.; Campos, R., A.; Nunes, S., L.; Turrini, P., C., G.; Vieira, A., P.; Ochoa Cruz, E., A.; Corrêa, T., C., S.; Hotta, C., T.; de Mello Varani, A.; Vautrin, S.; da Trindade, A., S.; de Mendonça Vilela, M.; Lembke, C., G.; Sato, P., M.; de Andrade, R., F.; Nishiyama, M., Y.; Cardoso-Silva, C., B.; Scortecci, K., C.; Garcia, A., A., F.; Carneiro, M., S.; Kim, C.; Paterson, A., H.; Bergès, H.; D'Hont, A.; de Souza, A., P.; Souza, G., M.; Vincentz, M.; Kitajima, J., P.; and Van Sluys, M. BMC genomics, 15:540, 2014.
Building the sugarcane genome for biotechnology and identifying evolutionary trends. [pdf]Paper  abstract   bibtex   
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.\n\nRESULTS: 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.\n\nCONCLUSION: 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.
@article{
 title = {Building the sugarcane genome for biotechnology and identifying evolutionary trends.},
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 year = {2014},
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 keywords = {bacterial artificial chromosome sequencing,br,correspondence,genetics,genome,grasses,mavsluys,polyploidy,saccharum,usp},
 pages = {540},
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 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.\n\nRESULTS: 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.\n\nCONCLUSION: 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.},
 bibtype = {article},
 author = {de Setta, Nathalia and Monteiro-Vitorello, Cláudia Barros and Metcalfe, Cushla Jane and Cruz, Guilherme Marcelo Queiroga and Del Bem, Luiz Eduardo and Vicentini, Renato and Nogueira, Fábio Tebaldi Silveira and Campos, Roberta Alvares and Nunes, Sideny Lima and Turrini, Paula Cristina Gasperazzo and Vieira, Andreia Prata and Ochoa Cruz, Edgar Andrés and Corrêa, Tatiana Caroline Silveira and Hotta, Carlos Takeshi and de Mello Varani, Alessandro and Vautrin, Sonia and da Trindade, Adilson Silva and de Mendonça Vilela, Mariane and Lembke, Carolina Gimiliani and Sato, Paloma Mieko and de Andrade, Rodrigo Fandino and Nishiyama, Milton Yutaka and Cardoso-Silva, Claudio Benicio and Scortecci, Katia Castanho and Garcia, Antônio Augusto Franco and Carneiro, Monalisa Sampaio and Kim, Changsoo and Paterson, Andrew H and Bergès, Hélène and D'Hont, Angélique and de Souza, Anete Pereira and Souza, Glaucia Mendes and Vincentz, Michel and Kitajima, João Paulo and Van Sluys, Marie-Anne},
 journal = {BMC genomics}
}
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