De novo characterization of the Lycium chinense Mill. leaf transcriptome and analysis of candidate genes involved in carotenoid biosynthesis

Lycium chinense Mill. (Chinese wolfberry), enriching in carotenoids, is an important Chinese herbal medicine. However, studies on the functional genomics research, especially the carotenoid biosynthesis and accumulation, are limited because of insufficiently available datasets. RNA-Seq was performed by the Illumina sequencing platform. Approximately 26 million clean reads were generated after filtering. Clean reads were assembled by SOAPdenovo and subsequently annotated. Among all 61,595 unigenes, 37,816 (61.39%), 25,266 (41.02%), and 17,598 (28.57%) unigenes were annotated in NCBI non-redundant protein, Swiss-Prot, and Kyoto Encyclopedia of Genes and Genomes (KEGG) database, respectively. A total of 16,073 and 11,394 unigenes were assigned to Gene Ontology and Cluster of Orthologous Group, respectively. Furthermore, the majority of genes encoding the enzymes in the carotenoid biosynthesis pathway were identified in the unigene datasets. We first found several genes related to L. chinense carotenoid biosynthesis. The expression levels and the biological functions of these genes involved in carotenoid biosynthesis in the leaf and the green ripening fruit were further confirmed by qPCR and high performance liquid chromatography (HPLC). In the present study, we first characterized the transcriptome of L. chinense leaf, which may provide useful data for functional genomics investigations in L. chinense in the future. And essential genes involved in the carotenoid biosynthesis pathway may contribute to elucidate the expression patterns in different stages of development and fruit ripening and the specific mechanisms of carotenoid biosynthesis/accumulation in L. chinense.