Adaptive evolution of polyploid ginseng (Panax ginseng) revealed by genome annotation and comparative transcriptomes

Abstract

and that unprecedented retention of chlorophyll a/b binding protein genes enables efficient photosynthesis under low light. Furthermore, eleven novel candidates UDP-glucuronosyltransferase (UGTs) were identified through integrated transcriptome and metabolome data. Heat and light stress poses an important threat to the growth and sustainable production of ginseng. Efforts have been made to study the effects of high temperature on ginseng physiology, but knowledge of the molecular responses to heat stress is still limited. Thus, in the second chapter, I have compared the transcriptomes (RNA-Seq) of two ginseng cultivars, Chungpoong (CP) and Yunpoong (YP), which are sensitive and resistant to heat stress, respectively, after 1- and 3-week heat treatments. Differential gene expression (DEG) and gene ontology (GO) enrichment along with profiled chlorophyll contents were performed. CP is more sensitive to heat stress than YP, and exhibited a lower chlorophyll content than YP. Moreover, heat stress reduced the chlorophyll content more rapidly in CP compared to YP. A total of 329 heat-responsive genes were identified. Intriguingly, genes encoding chlorophyll ab binding (CAB) proteins, WRKY transcription factors, and fatty acid desaturase (FAD) were predominantly responsive during heat stress and appeared to inhibit photosynthesis. In addition, a genome-wide scan of photosynthetic and sugar metabolic genes revealed reduced transcript levels for ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) under heat stress, especially in CP, possibly attributable to elevated levels of soluble sugars. Long noncoding RNAs (lncRNAs) have been implicated with diverse biological roles including genome regulation, various developmental processes and diseases. In the third chapter, through a systematic pipeline using ~104 billion sequencing RNA reads from various tissues, stages of growth and abiotic stress treatments of P. ginseng, I catalogued 19,495 and identified more than 100 candidate lncRNAs involved in abiotic stress responses to drought, salt, cold, heat and methyl jasmonate (MeJA) and 2,607 involved in specialized unknown function in specific tissues and growth stages of P. ginseng. Further, transposons might have been the contributor for the functional potential of lncRNAs in ginseng. Having realized the importance of this plant to humans, an integrated omics resource becomes indispensable to facilitate genomic research, molecular breeding and pharmacological study of this herb. In the fourth chapter, using the draft genome, transcriptome, and functional annotation datasets of P. ginseng, I developed the Ginseng Genome Database http://ginsengdb.snu.ac.kr/, the first open-access platform to provide comprehensive P. ginseng genomic resources. The current version of this database provides the latest draft genome sequence along with the structural and functional annotations of genes and digital expression of genes based on transcriptome data from different tissues, growth stages and treatments. In addition, tools for visualization and analysis of genomic data are provided. All data in the database were manually curated and integrated within a user-friendly query page. Overall, this study will enable us to develop new cultivars carrying resistant to biotic/abiotic stresses, tolerant to direct sun light, and improving medicinal values of ginseng either through genomics-assisted breeding or metabolic engineering.

Panax ginseng C. A. Meyer, reputed as the king of medicinal herbs, has slow growth, long generation time, low seed production, and complicated genome structure that hamper its study. Furthermore, the knowledge of molecular responses to various abiotic stresses is still limited in P. ginseng. To facilitate its functional genomics, metabolomics and breeding in P. ginseng, I have performed four independent studies or chapters. With advent of sequencing technologies, the ginseng genome project was initiated in 2011 and the first draft genome assembly was completed in 2016. In first chapter, I annotated a total of 59,352 protein coding genes in tetraploid P. ginseng. Of them, 97% of the genes got functional descriptions. A total of 3, 588 transcription factors and 851 transcription regulators were identified and grouped into 94 families. Functional and evolutionary analyses suggest that production of pharmacologically important dammarane type ginsenosides originated in Panax and are produced largely in shoot tissues and transported to roots

that newly evolved P. ginseng fatty acid desaturases increase freezing tolerance