De Novo Transcriptome Sequencing of the Orange-Fleshed Sweet Potato and Analysis of Differentially Expressed Genes Related to Carotenoid Biosynthesis

Abstract

Sweet potato, Ipomoea batatas (L.) Lam., is an important food crop worldwide. The orange-fleshed sweet potato is considered to be an important source of beta-carotene. In this study, the transcriptome profiles of an orange-fleshed sweet potato cultivar "Weiduoli" and its mutant "HVB-3" with high carotenoid content were determined by using the high-throughput sequencing technology. A total of 13,767,387 and 9,837,090 high-quality reads were produced from Weiduoli and HVB-3, respectively. These reads were de novo assembled into 58,277 transcripts and 35,909 unigenes with an average length of 596 bp and 533 bp, respectively. In all, 874 differentially expressed genes (DEGs) were obtained between Weiduoli and HVB-3, 401 of which were upregulated and 473 were downregulated in HVB-3 compared to Weiduoli. Of the 697 DEGs annotated, 316 DEGs had GO terms and 62 DEGs were mapped onto 50 pathways. The 22 DEGs and 31 transcription factors involved in carotenoid biosynthesis were identified between Weiduoli and HVB-3. In addition, 1,725 SSR markers were detected. This study provides the genomic resources for discovering the genes involved in carotenoid biosynthesis of sweet potato and other plants.

Figure 1

Overview of the sweet potato transcriptome assembly. (a) Size distribution of contigs; (b) size distribution of transcripts; and (c) size distribution of unigenes.

Figure 2

Species distribution of the top BlastX hits for each unigene in the Nr database.

Figure 3

Comparative analysis of gene expression in Weiduoli and HVB-3. (a) A scatter plot of RPKM logarithmic values in libraries of Weiduoli and HVB-3. Each dot represents the RPKM value of a specific gene. The greater deviation from the diagonal slope shows a greater expression level of the gene in the corresponding material. (b) A scatter plot of the ratio of RPKM logarithmic numerical values of genes in Weiduoli and HVB-3. This plot graphically represents genes differentially expressed between Weiduoli and HVB-3. Blue dots represent genes that had significant difference and red dots represent genes where no significant difference was observed between Weiduoli and HVB-3.

Figure 4

GO classification of unigenes in transcriptomes of Weiduoli and HVB-3. The red bars represent all the unigenes and the blue bars represent the DEGs.

Figure 5

COG-based functional classification of DEGs between Weiduoli and HVB-3.

Figure 6

KEGG-based functional classification of DEGs between Weiduoli and HVB-3. Numbers beside each bar represent the actual number of DEGs classified in that descriptive term.