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.
Highlights
Sugarcane belongs to the grass family (Poaceae), which is an economically important seed plant family that includes maize, wheat, rice, sorghum and many types of grasses
We further investigated the functional role of the remaining unigenes and putative long non-coding RNA (lncRNA) by searching for three indirect indications of functionality: we examined the stability of the secondary structure using the Vienna package [38], normalized to the Z-score index [39]; we mapped the small RNAs [40] against sugarcane unigenes; and we analyzed the sequence similarities between the unigenes and S. bicolor expressed sequence tag (EST) (BLASTN, E-value #1e25)
Considering the N50 values, the values for the sugarcane unigenes were greater than those for rubber trees (592 bp), bamboo (1,132 bp) and chili pepper (1,076 bp) [46], which were assembled using short reads generated by the Illumina platform
Summary
Sugarcane belongs to the grass family (Poaceae), which is an economically important seed plant family that includes maize, wheat, rice, sorghum and many types of grasses. The sugarcane crop is the main source of both sugar and alcohol, accounting for two-thirds of the world’s sugar production [1]. It is estimated that approximately 653.81 million tons of sugarcane will be produced during the 2013/2014 harvest in Brazil, surpassing the production of the last harvest [2]. Modern sugarcane varieties are derived from interspecific hybridization between Saccharum officinarum and Saccharum spontaneum, resulting in highly polyploid and aneuploid plants. Modern varieties of sugarcane typically exhibit more than eight homologous copies of each basic chromosome from S. officinarum and several copies of the homologous chromosomes from S. spontaneum [3]. Sugarcane cultivars are highly heterozygous, presenting several different alleles at each locus, and this high level of genetic complexity creates challenges during conventional and molecular breeding programs
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