De Novo Assembly and Transcriptome Analysis of Contrasting Sugarcane Varieties

Autor(es)

Cardoso-Silva, Claudio Benicio ^[1] ; Costa, Estela Araujo ^[1] ; Mancini, Melina Cristina ^[1] ; Almeida Balsalobre, Thiago Willian ^[1] ; Costa Canesin, Lucas Eduardo ^[1] ; Pinto, Luciana Rossini ^[2] ; Carneiro, Monalisa Sampaio ^[3] ; Franco Garcia, Antonio Augusto ^[4] ; de Souza, Anete Pereira ^{[5, 1]} ; Vicentini, Renato ^[1]

Afiliação do(s) autor(es)

^[1] Univ Campinas UNICAMP, Ctr Mol Biol & Genet Engn CBMEG, Campinas, SP - Brazil

^[2] Ctr Avancado Pesquisa Tecnol Agronegocio Cana IAC, Ribeirao Preto, SP - Brazil

^[3] Univ Fed Sao Carlos, Dept Biotecnol & Prod Vegetal & Anim, Ctr Ciencias Agr, Araras, SP - Brazil

^[4] Univ Sao Paulo, Dept Genet, Escola Super Agr Luiz de Queiroz, Piracicaba, SP - Brazil

^[5] Univ Estadual Campinas UNICAMP, Inst Biol, Dept Biol Vegetal, Campinas, SP - Brazil

• Tipo de documento: Artigo Científico
• Fonte: PLoS One; v. 9, n. 2 FEB 11 2014.
• Citações Web of Science: 39

Resumo

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. (AU)

• Processo FAPESP: 08/52197-4 - Genomic-assisted breeding of sugarcane: using molecular markers for understanding the genetic architecture of quantitative traits and to implement marker assisted selection
• Beneficiário: Anete Pereira de Souza
• Modalidade de apoio: Auxílio à Pesquisa - Programa BIOEN - Temático
• Processo FAPESP: 08/58031-0 - Equilíbrio energético da cana-de-açúcar: uma abordagem de sistemas para compreender a regulação do metabolismo da sacarose e a sinalização de açúcar
• Beneficiário: Renato Vicentini dos Santos
• Modalidade de apoio: Auxílio à Pesquisa - Programa BIOEN - Jovens Pesquisadores