%0 Journal Article
%T De Novo Assembly and Transcriptome Analysis of Contrasting Sugarcane Varieties
%A Claudio Benicio Cardoso-Silva
%A Estela Araujo Costa
%A Melina Cristina Mancini
%A Thiago Willian Almeida Balsalobre
%A Lucas Eduardo Costa Canesin
%A Luciana Rossini Pinto
%A Monalisa Sampaio Carneiro
%A Antonio Augusto Franco Garcia
%A Anete Pereira de Souza
%A Renato Vicentini
%J PLOS ONE
%D 2014
%I Public Library of Science (PLoS)
%R 10.1371/journal.pone.0088462
%X 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.
%U http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0088462