Artigo
Building the sugarcane genome for biotechnology and identifying evolutionary trends
Registro en:
Bmc Genomics. London: Biomed Central Ltd, v. 15, 17 p., 2014.
1471-2164
10.1186/1471-2164-15-540
WOS:000339583200001
WOS000339583200001.pdf
Autor
Setta, Nathalia de
Monteiro-Vitorello, Claudia Barros
Metcalfe, Cushla Jane
Queiroga Cruz, Guilherme Marcelo
Del Bem, Luiz Eduardo
Vicentini, Renato
Silveira Nogueira, Fabio Tebaldi [UNESP]
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
Trindade, Adilson Silva da
Vilela, Mariane de Mendonca
Lembke, Carolina Gimiliani
Sato, Paloma Mieko
Andrade, Rodrigo Fandino de
Nishiyama, Milton Yutaka
Cardoso-Silva, Claudio Benicio
Scortecci, Katia Castanho
Franco Garcia, Antonio Augusto
Carneiro, Monalisa Sampaio
Kim, Changsoo
Paterson, Andrew H.
Berges, Helene
D'Hont, Angelique
Souza, Anete Pereira de
Souza, Glaucia Mendes
Vincentz, Michel
Kitajima, Joao Paulo
Van Sluys, Marie-Anne
Resumen
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. 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 Univ Sao Paulo, Inst Biociencias, Dept Bot, BR-05508090 Sao Paulo, Brazil Univ Fed ABC, BR-09210170 Santo Andre, Brazil Univ Sao Paulo, Dept Genet, Escola Super Agr Luiz de Queiroz, BR-13418900 Piracicaba, SP, Brazil Univ Estadual Campinas, Ctr Biol Mol & Engn Genet, BR-13083875 Campinas, SP, Brazil Univ Estadual Paulista, Inst Biociencias, Dept Genet, BR-18618000 Botucatu, SP, Brazil Inst Quim, Dept Bioquim, BR-05508900 Sao Paulo, SP, Brazil INRA CNRGV, F-31326 Castanet Tolosan, France Dept Biol Celular & Genet UFRN, BR-59072970 Natal, RN, Brazil Univ Fed Sao Carlos, Ctr Ciencias Agr, Araras, SP, Brazil Univ Georgia, Dept Plant Biol, Athens, GA 30602 USA Univ Georgia, Dept Crop & Soil Sci, Athens, GA 30602 USA Univ Georgia, Dept Genet, Athens, GA 30602 USA CIRAD, UMR1096, F-34398 Montpellier 5, France Mendel Genom Anal, Sao Paulo, Brazil Univ Estadual Paulista, Inst Biociencias, Dept Genet, BR-18618000 Botucatu, SP, Brazil 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