AI Article Synopsis
- Sugarcane is a vital crop for sugar and alcohol production, and this study focused on analyzing six sugarcane genotypes through de novo assembly and transcriptome annotation.
- Over 400 million short reads from the Illumina RNA-Seq platform were used to assemble 72,269 unigenes, with many showing significant similarities to sorghum proteins and revealing potentially new sugarcane genes not in existing databases.
- Additionally, the research identified numerous molecular markers, including over 5,100 simple sequence repeats (SSRs) and over 700,000 single-nucleotide polymorphisms (SNPs), providing valuable resources for future genetic studies.
Article 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.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3921171 | PMC |
| http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0088462 | PLOS |
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