Genome-Wide Sequence and Expression Analysis of Functional Genes in the Genome of Jilin Ginseng, Panax ginseng CA Mey

Ginseng, Panax ginseng CA Mey., is known as the top medicinal herb in China and eastern Asia, while Jilin ginseng contributes to 65% of the world’s ginseng production. Nevertheless, ginseng research, especially in genomics, remains very limited. In this study, 14 tissues of Jilin ginseng cv. Damaya were used to sequence, characterize and profile the expressions of all genes expressed in the species. A total of 198.95 million 100-bp clean reads were obtained from the 14 tissues, representing a total of 19.9 Gb sequences and >6.2 x of the 3.2-Gb ginseng genome. From the sequences, 248,992 unigenes were assembled, with an N50 of 1,572 bp and an average length of 936 bp. Of the unigenes, 109,781 (44.09%) could be annotated and were assigned to 716,067 GO terms grouped into 36 GO subcategories. Pathway analysis assigned 29,321 of them to 35,819 enzymes (EC) involved in 138 metabolic pathways. Of the pathways, four have been considered to significantly contribute to the biosynthesis of ginseng’s major medically active component – ginsenosides. Moreover, the expression profiles of all 248,992 unigenes in the 14 tissues were determined, of which 20.55% expressed in one of the 14 tissues; 60.88% expressed in 2 – 13 of the 14 tissues and 11.08% expressed in all 14 tissues studied, indicating that most of Jilin ginseng’s genes expressed in one or a few of tissues; only a small portion is housekeeping genes. Finally, 155 unigenes that are likely involved in ginsenoside biosynthesis were isolated. Analysis revealed that they formed a single interaction network that may be responsible for ginsenoside biosynthesis. These results suggest that the genes involved in ginsenoside biosynthesis may regulate the process in a gene group coordinative manner in different tissues. These findings have provided not only knowledge, but also gene resources, including sequences and expression profiles, neccesary for advanced studies and applications of economical genes in ginseng breeding and production.