De novo assembly and transcriptome analysis of contrasting sugarcane varieties

• Grant number: 14/01771-3
• Support Opportunities: Regular Research Grants - Publications - Scientific article
• Start date: March 01, 2014
• End date: August 31, 2014
• Field of knowledge: Agronomical Sciences - Agronomy - Crop Science
• Principal Investigator: Anete Pereira de Souza
• Grantee: Anete Pereira de Souza
• Host Institution: Centro de Biologia Molecular e Engenharia Genética (CBMEG). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil

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 Illumina RNA-Seq short reads. We produced more than 400 million reads that were assembled into 72,269 unigenes. Through 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; it is likely that many of these unigenes are putative undescribed sugarcane genes. From this collection of unigenes, a large number of molecular markers were determined, 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 on this species. (AU)