title: Building the sugarcane genome for biotechnology and identifying evolutionary trends.
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.
  
  
  CONCLUSIONS
  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.
authors.forename: Nathalia
authors.initials: N
authors.lastname: de Setta
authors.forename: Cláudia Barros
authors.initials: CB
authors.lastname: Monteiro-Vitorello
authors.forename: Cushla Jane
authors.initials: CJ
authors.lastname: Metcalfe
authors.forename: Guilherme Marcelo Queiroga
authors.initials: GM
authors.lastname: Cruz
authors.forename: Luiz Eduardo
authors.initials: LE
authors.lastname: Del Bem
authors.forename: Renato
authors.initials: R
authors.lastname: Vicentini
authors.forename: Fábio Tebaldi Silveira
authors.initials: FT
authors.lastname: Nogueira
authors.forename: Roberta Alvares
authors.initials: RA
authors.lastname: Campos
authors.forename: Sideny Lima
authors.initials: SL
authors.lastname: Nunes
authors.forename: Paula Cristina Gasperazzo
authors.initials: PC
authors.lastname: Turrini
authors.forename: Andreia Prata
authors.initials: AP
authors.lastname: Vieira
authors.forename: Edgar Andrés
authors.initials: EA
authors.lastname: Ochoa Cruz
authors.forename: Tatiana Caroline Silveira
authors.initials: TC
authors.lastname: Corrêa
authors.forename: Carlos Takeshi
authors.initials: CT
authors.lastname: Hotta
authors.forename: Alessandro
authors.initials: A
authors.lastname: de Mello Varani
authors.forename: Sonia
authors.initials: S
authors.lastname: Vautrin
authors.forename: Adilson Silva
authors.initials: AS
authors.lastname: da Trindade
authors.forename: Mariane
authors.initials: M
authors.lastname: de Mendonça Vilela
authors.forename: Carolina Gimiliani
authors.initials: CG
authors.lastname: Lembke
authors.forename: Paloma Mieko
authors.initials: PM
authors.lastname: Sato
authors.forename: Rodrigo Fandino
authors.initials: RF
authors.lastname: de Andrade
authors.forename: Milton Yutaka
authors.initials: MY
authors.lastname: Nishiyama
authors.forename: Claudio Benicio
authors.initials: CB
authors.lastname: Cardoso-Silva
authors.forename: Katia Castanho
authors.initials: KC
authors.lastname: Scortecci
authors.forename: Antônio Augusto Franco
authors.initials: AA
authors.lastname: Garcia
authors.forename: Monalisa Sampaio
authors.initials: MS
authors.lastname: Carneiro
authors.forename: Changsoo
authors.initials: C
authors.lastname: Kim
authors.forename: Andrew H
authors.initials: AH
authors.lastname: Paterson
authors.forename: Hélène
authors.initials: H
authors.lastname: Bergès
authors.forename: Angélique
authors.initials: A
authors.lastname: D'Hont
authors.forename: Anete Pereira
authors.initials: AP
authors.lastname: de Souza
authors.forename: Glaucia Mendes
authors.initials: GM
authors.lastname: Souza
authors.forename: Michel
authors.initials: M
authors.lastname: Vincentz
authors.forename: João Paulo
authors.initials: JP
authors.lastname: Kitajima
authors.affiliation: Departamento de Botânica - Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo 05508-090, SP, Brazil. mavsluys@usp.br.
authors.forename: Marie-Anne
authors.initials: MA
authors.lastname: Van Sluys
mesh_terms: D001483:Base Sequence; D005075:Biological Evolution; D001709:Biotechnology; D022202:Chromosomes, Artificial, Bacterial; D020440:Gene Duplication; D015723:Gene Library; D018745:Genome, Plant; D006239:Haplotypes; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008969:Molecular Sequence Data; D010744:Phosphoric Monoester Hydrolases / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics; D011123:Polyploidy; D012313:RNA / Q000235:genetics / Q000378:metabolism; D031786:Saccharum / Q000235:genetics*; D017423:Sequence Analysis, RNA; D045868:Sorghum / Q000235:genetics
chemical_list: D010940:Plant Proteins; D012313:RNA; D010744:Phosphoric Monoester Hydrolases