Sweetpotato, Ipomoea batatas L., Convolvulaceae, rich in starch, is a major staple economically important root crop worldwide. Limited functional genomics resources and whole genome studies could be improved through the development of next-generation sequencing technologies. Illumina sequencing of three sweetpotato varieties, Xushu 18, Xu 781 and Xushu 25, including de novo transcriptome assembly, functional annotation, and differential expression of potential starch biosynthesis-related genes are described. A total of 2508, 1807 and 3169 Mb clean reads were generated for Xushu 18, Xu 781 and Xushu 25, and were assembled into 32,112, 35,788 and 36,955 unigenes with an average length of 787, 802 and 824 bp, respectively. BLAST against the NCBI non-redundant protein, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Gene Ontology (GO) databases have classified these unigenes into functional categories for understanding gene functions and regulation pathways. The proportion of up-regulated DEGs was lower than that of the down-regulated DEGs among three sweetpotato cultivars. The similar proportion of the up/down-regulated gene number was presented between Xushu 25 and one of its parents (Xushu18 and Xu 781). Moreover, 14 unigenes related to starch biosynthesis in Xushu 18 and Xu 781were searched out from the transcriptome sequencing data. Furthermore, gene expression of these genes in storage root during different developing stages was also investigated, 6 types of gene expression patterns were summarized. The novel sequence dataset developed in this study will be helpful for the further genetic characterization and studies of starch biosynthesis in sweetpotato.

甘薯，番薯，旋花科富含淀粉，是世界范围内一种主要的主要经济上重要的根系作物。下一代测序技术的发展可以改善有限的功能基因组学资源和整个基因组研究。描述了三个甘薯品种，Xushu 18，Xu 781和Xushu 25的Illumina测序，包括从头转录组装配，功能注释和潜在的淀粉生物合成相关基因的差异表达。分别对Xushu 18，Xu 781和Xushu 25生成了2508、1807和3169 Mb的干净读取，并被组装成32,112、35,788和36,955个单基因，平均长度分别为787、802和824 bp。针对NCBI非冗余蛋白的BLAST，京都基因与基因组百科全书（KEGG）和基因本体论（GO）数据库已将这些单基因分类为功能类别，以了解基因功能和调控途径。在三个甘薯品种中，DEGs上调的比例低于DEGs的下调。在Xushu 25和它的一个亲本（Xushu18和Xu 781）之间出现了类似比例的上/下调基因数。此外，从转录组测序数据中检索到徐树18号和徐781号中与淀粉生物合成有关的14个单基因。此外，还研究了这些基因在不同发育阶段在贮藏根中的基因表达，总结了6种类型的基因表达模式。