Building the sugarcane genome for biotechnology and identifying evolutionary trends
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
BMC Genomics 2014, 15:540 doi:10.1186/1471-2164-15-540Published: 30 June 2014
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.
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.
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.