Building the sugarcane genome for biotechnology and identifying evolutionary trends
Contribuinte(s) |
Universidade Estadual Paulista (UNESP) |
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Data(s) |
18/03/2015
18/03/2015
30/06/2014
|
Resumo |
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) Processo FAPESP: 08/52074-0 Processo FAPESP: 10/05591-9 Processo FAPESP: 08/58031-0 Processo FAPESP: 08/52197-4 Processo FAPESP: 08/52146-0 Processo FAPESP: 09/51632-1 Processo FAPESP: 09/09217-7 Processo FAPESP: 08/58243-8 Processo FAPESP: 09/09116-6 Processo FAPESP: 11/05317-7 Processo FAPESP: 08/54201-9 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. |
Formato |
17 |
Identificador |
http://dx.doi.org/10.1186/1471-2164-15-540 Bmc Genomics. London: Biomed Central Ltd, v. 15, 17 p., 2014. 1471-2164 http://hdl.handle.net/11449/117308 10.1186/1471-2164-15-540 WOS:000339583200001 WOS000339583200001.pdf |
Idioma(s) |
eng |
Publicador |
Biomed Central Ltd |
Relação |
Bmc Genomics |
Direitos |
openAccess |
Palavras-Chave | #Saccharum #Bacterial artificial chromosome sequencing #Polyploidy #Genome #Genetics #Grasses |
Tipo |
info:eu-repo/semantics/article |