Gene identification using RNA-seq in two sweetpotato genotypes and the use of mining to analyze carotenoid biosynthesis

Abstract Sweetpotatoes are important food crops with high starch and high carotene content. However, studies concerning the molecular biology of these crops are limited. In this paper, we selected two varieties of sweetpotato (Zhengshu 20 and Luoxushu 8) for transcriptome analysis. De novo RNA sequencing of these sweetpotatoes (tuberous roots, stems and leaves) under field conditions was performed using an Illumina Hiseq 2500 platform with PE125. Approximately 34.4 G nucleotide bases were sequenced. Following assembly, 176,167 transcripts and 109,401 unigenes were identified. 41,729 (Nr), 21,004 (Nt), 12,524 (KO), 29,444 (SwissProt), 30,212 (PFAM), 31,304 (GO), and 14,349 (KOG) unigenes were functionally annotated using different databases, and a total of 47,749 annotated sequences were identified. Simple sequence repeats (SSRs) analyses revealed 9549 SSR loci on the 8334 unigenes. The KEGG analysis uncovered 55 and 78 unigenes involved in the carotenoid and terpenoid backbone biosynthesis pathways, respectively. Among these genes, 20 and 10 differentially expressed unigenes were observed in the Zhengshu 20 and Luoxushu 8, respectively. Eight differentially expressed unigenes were validated by qRT-PCR. Thus, we prepared and analyzed the transcriptome data of the two sweetpotato varieties, for which prior genomic information was limited. This new sequence information will improve the current knowledge in this important and healthy crop and provide valuable insight for further biological research.