Comparative Transcriptome Analysis of Cultivated Sweet Potato (Ipomea batatas) and Wild Ancestor (I. trifida)

Sweet potato storage roots offer excellent nutrition and health benefits to humans by the presence of abundant vitamins, antioxidant micronutrients, minerals and dietary fibers. Although recent studies indicate that the tuberizing events result from the activation of cambium followed by cell proliferation, detailed molecular information on genes controlling tuber formation is lacking in sweet potato. In order to understand the mechanism of storage root formation, sweet potato root transcriptomes were generated using paired-end Illumina sequencing of cDNA libraries created from pooled samples of both fibrous and storage roots of cultivated species Ipomoea batatas cv. Beauregard and non-tuber forming immediate ancestral species Ipomoea trifida. Transcriptome sequencing (RNA-Seq) generated 416 (Sp1) and 400 (Sp2) million sequence reads. A reference transcriptome was developed by de novo assembly of these sequences, as there is limited sequence information that exists in sweet potato. We report progress on the annotation of the contigs using BLASTx, separately against TAIR, the cassava protein database, the non-redundant protein database (nr) from NCBI, and the sweet potato gene index. A unique list of tuber-forming genes, transcriptome derived simple sequence repeats (EST-SSRs), and single nucleotide polymorphisms (SNPs) were identified from the transcriptome data. The annotated contigs 21,777 (Sp1) and 57,415 (Sp2) were used for downstream analyses to find orthologs between Sp1 and Sp2, and paralogs within the species. A total of 5695 (Sp1) and 6289 (Sp2) contigs represent 4865 ortholog groups  that were identified between the species may possibly help in understanding gene networks involved in tuber formation.