Building the sugarcane genome for biotechnology and identifying evolutionary trends

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

Building the sugarcane genome for biotechnology and identifying evolutionary trends

Arquivos

WOS000339583200001.pdf (1.8 MB)

Data

2014-06-30

Autores

Setta, Nathalia de

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

Editor

Biomed Central Ltd

Tipo

Artigo

Direito de acesso

Acesso aberto

Resumo

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.