Transcriptome analysis of field-grown Asian ginseng provides clues to environmental conditions and developmental mechanisms related to red skin root syndrome

Red skin root greatly decreases the quality and production of Asian ginseng (Panax ginseng). However, the molecular mechanisms of its origin and development are still obscure. The present study used Illumina high-throughput mRNA sequencing (RNA-seq) technology to conduct a comparative transcriptome analysis on field-sampled healthy and red skin root-affected ginseng fibrous roots. A total of 116,537 transcripts were assembled with an average length of 794 bp. Results of BLAST searches in the NCBI non-redundant protein database showed that the annotated transcripts were mostly enriched in plant species as well as the arbuscular mycorrhizae fungus Rhizophagus irregularis and the putative fungal pathogen Marssonina brunnea. With a cutoff of 1.5-fold (p < 0.01), the fibrous roots of red skin root-affected ginseng showed 1856 up-regulated genes and 1581 down-regulated genes compared with the healthy ginseng roots. In addition to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enriched analyses, the environmental stimuli and phenolic compound metabolism underlying the origin and development of red skin disease were also discussed. The present study provides molecular clues to understanding the occurrence mechanisms of red skin root in ginseng.