De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and SSR Marker identification in sweet potato (Ipomoea batatas)

In this study, we present a global characterization of root transcriptome of sweet potato using Illumina paired-end sequencing technology. In a single lane, we generated 59,233,468 sequencing reads, which were assembled into 56,516 unique sequences with N50 length of 765bp after stringent quality check and data filtering. Based on sequence similarity search with known proteins, a total of 35,051 (62.02%) assembled sequences were annotated with a cut-off E-value above 10-5, which represented 20,755 genes with unique protein accession numbers. Assembled sequences were assigned to gene ontology and clusters of orthologous group terms to classify the functions of the predicted genes, and also mapped to specific pathways by the Kyoto Encyclopedia of Genes and Genomes to identify the biological pathways that are active in sweet potato root. In addition, we located and characterized 4,114 simple sequence repeats as potential molecular markers. One hundred pairs of high quality PCR primers were designed, and a large number of these were amplified successfully in initial screening.