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Open Access Highly Accessed Research article

Building the sugarcane genome for biotechnology and identifying evolutionary trends

Nathalia de Setta12, Cláudia Barros Monteiro-Vitorello3, Cushla Jane Metcalfe1, Guilherme Marcelo Queiroga Cruz1, Luiz Eduardo Del Bem4, Renato Vicentini4, Fábio Tebaldi Silveira Nogueira5, Roberta Alvares Campos6, Sideny Lima Nunes6, Paula Cristina Gasperazzo Turrini1, Andreia Prata Vieira1, Edgar Andrés Ochoa Cruz1, Tatiana Caroline Silveira Corrêa1, Carlos Takeshi Hotta6, Alessandro de Mello Varani3, Sonia Vautrin7, Adilson Silva da Trindade8, Mariane de Mendonça Vilela4, Carolina Gimiliani Lembke6, Paloma Mieko Sato6, Rodrigo Fandino de Andrade6, Milton Yutaka Nishiyama6, Claudio Benicio Cardoso-Silva4, Katia Castanho Scortecci8, Antônio Augusto Franco Garcia3, Monalisa Sampaio Carneiro9, Changsoo Kim10, Andrew H Paterson10, Hélène Bergès7, Angélique D’Hont11, Anete Pereira de Souza4, Glaucia Mendes Souza6, Michel Vincentz4, João Paulo Kitajima12 and Marie-Anne Van Sluys1*

Author Affiliations

1 Departamento de Botânica – Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo 05508-090, SP, Brazil

2 Universidade Federal do ABC, Rua Santa Adélia, 166, Santo André, 09210-170, Brazil

3 Escola Superior de Agricultura Luiz de Queiroz, Departamento de Genética, Universidade de São Paulo, Av. Padua Dias, 11, Agronomia 13418-900, Piracicaba, SP, Brasil

4 Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Cândido Rondon, 400, 13083-875 Campinas, Brazil

5 Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista, campus de Botucatu, Distrito de Rubião Jr., s/n, 18618-000, Botucatu, Brazil

6 Departamento de Bioquímica, Instituto de Química, Av. Prof. Lineu Prestes, 748, São Paulo 05508-900, SP, Brazil

7 INRA – CNRGV, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet Tolosan Cedex, France

8 Departamento de Biologia Celular e Genética – UFRN, Campus Universitário s/n, Natal, RN 59072-970, Brazil

9 Centro de Ciências Agrárias, Universidade Federal de São Carlos, Araras, SP, Brazil

10 Departments of Plant Biology, Crop and Soil Science, and Genetics, University of Georgia, 111 Riverbend Rd, Athens, GA 30602, USA

11 CIRAD, UMR1096, TA40/03 Avenue Agropolis, 34398, Montpellier Cedex 5, France

12 Mendelics Genomic Analysis, Rua Cubatão 86, São Paulo, SP, Brazil

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BMC Genomics 2014, 15:540  doi:10.1186/1471-2164-15-540

Published: 30 June 2014

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.

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.

Keywords:
Saccharum; Bacterial artificial chromosome sequencing; Polyploidy; Genome; Genetics; Grasses