title: De novo assembly and transcriptome analysis of contrasting sugarcane varieties.
abstract: Sugarcane is an important crop and a major source of sugar and alcohol. In this study, we performed de novo assembly and transcriptome annotation for six sugarcane genotypes involved in bi-parental crosses. The de novo assembly of the sugarcane transcriptome was performed using short reads generated using the Illumina RNA-Seq platform. We produced more than 400 million reads, which were assembled into 72,269 unigenes. Based on a similarity search, the unigenes showed significant similarity to more than 28,788 sorghum proteins, including a set of 5,272 unigenes that are not present in the public sugarcane EST databases; many of these unigenes are likely putative undescribed sugarcane genes. From this collection of unigenes, a large number of molecular markers were identified, including 5,106 simple sequence repeats (SSRs) and 708,125 single-nucleotide polymorphisms (SNPs). This new dataset will be a useful resource for future genetic and genomic studies in this species.
authors: Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil.
authors: Claudio Benicio
authors: CB
authors: Cardoso-Silva
authors: Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil.
authors: Estela Araujo
authors: EA
authors: Costa
authors: Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil.
authors: Melina Cristina
authors: MC
authors: Mancini
authors: Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil.
authors: Thiago Willian Almeida
authors: TW
authors: Balsalobre
authors: Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil.
authors: Lucas Eduardo Costa
authors: LE
authors: Canesin
authors: Centro Avançado da Pesquisa Tecnológica do Agronegócio de Cana (IAC/Apta), Ribeirão Preto, SP, Brazil.
authors: Luciana Rossini
authors: LR
authors: Pinto
authors: Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos, Araras, SP, Brazil.
authors: Monalisa Sampaio
authors: MS
authors: Carneiro
authors: Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brazil.
authors: Antonio Augusto Franco
authors: AA
authors: Garcia
authors: Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil ; Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil.
authors: Anete Pereira
authors: AP
authors: de Souza
authors: Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil.
authors: Renato
authors: R
authors: Vicentini
mesh_terms: D016000:Cluster Analysis; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D017343:Genes, Plant; D005819:Genetic Markers / Q000235:genetics; D005838:Genotype; D018895:Microsatellite Repeats; D016366:Open Reading Frames; D020641:Polymorphism, Single Nucleotide; D031786:Saccharum / Q000737:chemistry* / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013395:Sucrose / Q000737:chemistry*; D059467:Transcriptome
chemical_list: D005819:Genetic Markers; D013395:Sucrose