PLoS ONE (Jan 2014)

De novo assembly and transcriptome analysis of contrasting sugarcane varieties.

  • Claudio Benicio Cardoso-Silva,
  • Estela Araujo Costa,
  • Melina Cristina Mancini,
  • Thiago Willian Almeida Balsalobre,
  • Lucas Eduardo Costa Canesin,
  • Luciana Rossini Pinto,
  • Monalisa Sampaio Carneiro,
  • Antonio Augusto Franco Garcia,
  • Anete Pereira de Souza,
  • Renato Vicentini

DOI
https://doi.org/10.1371/journal.pone.0088462
Journal volume & issue
Vol. 9, no. 2
p. e88462

Abstract

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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.