Building the sugarcane genome for biotechnology and identifying evolutionary trends

BMC Genomics

Marie-Anne Van Sluys⁹  João Paulo Kitajima^1,11  Michel Vincentz³  Glaucia Mendes Souza⁷  Anete Pereira de Souza³  Angélique D’Hont^1,12  Hélène Bergès¹  Andrew H Paterson⁴  Changsoo Kim⁴  Monalisa Sampaio Carneiro⁵  Antônio Augusto Franco Garcia^1,10  Katia Castanho Scortecci⁶  Claudio Benicio Cardoso-Silva³  Milton Yutaka Nishiyama⁷  Rodrigo Fandino de Andrade⁷  Paloma Mieko Sato⁷  Carolina Gimiliani Lembke⁷  Mariane de Mendonça Vilela³  Adilson Silva da Trindade⁶  Sonia Vautrin¹  Alessandro de Mello Varani^1,10  Carlos Takeshi Hotta⁷  Tatiana Caroline Silveira Corrêa⁹  Edgar Andrés Ochoa Cruz⁹  Andreia Prata Vieira⁹  Paula Cristina Gasperazzo Turrini⁹  Sideny Lima Nunes⁷  Roberta Alvares Campos⁷  Fábio Tebaldi Silveira Nogueira²  Renato Vicentini³  Luiz Eduardo Del Bem³  Guilherme Marcelo Queiroga Cruz⁹  Cushla Jane Metcalfe⁹  Cláudia Barros Monteiro-Vitorello^1,10  Nathalia de Setta⁸ 

[1] INRA – CNRGV, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet Tolosan Cedex, France;Departamento de Genética, Instituto de Biociências, Universidade Estadual Paulista, campus de Botucatu, Distrito de Rubião Jr., s/n, 18618-000, Botucatu, Brazil;Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Cândido Rondon, 400, 13083-875 Campinas, Brazil;Departments of Plant Biology, Crop and Soil Science, and Genetics, University of Georgia, 111 Riverbend Rd, Athens, GA 30602, USA;Centro de Ciências Agrárias, Universidade Federal de São Carlos, Araras, SP, Brazil;Departamento de Biologia Celular e Genética – UFRN, Campus Universitário s/n, Natal, RN 59072-970, Brazil;Departamento de Bioquímica, Instituto de Química, Av. Prof. Lineu Prestes, 748, São Paulo 05508-900, SP, Brazil;Universidade Federal do ABC, Rua Santa Adélia, 166, Santo André, 09210-170, Brazil;Departamento de Botânica – Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo 05508-090, SP, Brazil;Escola Superior de Agricultura Luiz de Queiroz, Departamento de Genética, Universidade de São Paulo, Av. Padua Dias, 11, Agronomia 13418-900, Piracicaba, SP, Brasil;Mendelics Genomic Analysis, Rua Cubatão 86, São Paulo, SP, Brazil;CIRAD, UMR1096, TA40/03 Avenue Agropolis, 34398, Montpellier Cedex 5, France

关键词: Grasses;    Genetics;    Genome;    Polyploidy;    Bacterial artificial chromosome sequencing;    Saccharum;   

Others  :  1216544
DOI  :  10.1186/1471-2164-15-540

 received in 2013-12-17, accepted in 2014-06-19,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 de Setta et al.; licensee BioMed Central Ltd.

【 图 表 】

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