Transcriptome Analysis of Cultivated and Wild Ginseng in Different Growth Years Revealed the Regulatory Mechanism of Ginsenosides

Background: As a famous Chinese medicine, ginseng has been used in the world for nearly 5,000 years. Wild ginseng is endangered due to environmental damage. Thus, cultivated ginseng is developed to replace wild ginseng. The morphological and physiological characteristics of both wild ginseng and cultivated ginseng change during growth, and the mechanism of this change is not yet understood. Results: This study performed transcriptome sequencing on the roots, stems and leaves of cultivated ginseng and wild ginseng with different growth years, exploring the effect of growth years on gene expression in ginseng. The number of DEGs in cultivated ginseng is more than that in wild ginseng. Based on the weighted gene co-expression network analysis, we found that the growth years significantly affected the gene expression of MAPK signaling pathway - plant and terpenoid backbone biosynthesis pathway in cultivated ginseng, but had no effects in wild ginseng. Furthermore, the growth years had significant effects on the genes related to ginsenoside synthesis in cultivated ginseng, and the effects were different in the roots, stems and leaves. However, it had little influence on the expression of genes related to ginsenoside synthesis in wild ginseng and no effect on leaves. These results showed wild ginseng was less affected by growth years than cultivated ginseng. Furthermore, HMGR, SS, DXS, DS, IspF, AACT, CYP450 and UGTs were related with MYB, NAC, AP2/ERF, bHLH and WRKY transcription factors. Growth years may regulate genes for ginsenoside synthesis by influencing these transcription factors, thereby affecting the content of ginsenosides. Conclusions: This study complemented the gaps in the genetic information of wild ginseng in different growth periods and different tissues and provided a new insight into the mechanism of ginsenoside regulation.

Transcriptome Analysis of Cultivated and Wild Ginseng in Different Growth Years Revealed the Regulatory Mechanism of Ginsenosides

Background: As a famous Chinese medicine, ginseng has been used in the world for nearly 5,000 years. Wild ginseng is endangered due to environmental damage. Thus, cultivated ginseng is developed to replace wild ginseng. The morphological and physiological characteristics of both wild ginseng and cultivated ginseng change during growth, and the mechanism of this change is not yet understood. Results: This study performed transcriptome sequencing on the roots, stems and leaves of cultivated ginseng and wild ginseng with different growth years, exploring the effect of growth years on gene expression in ginseng. The number of DEGs in cultivated ginseng is more than that in wild ginseng. Based on the weighted gene co-expression network analysis, we found that the growth years significantly affected the gene expression of MAPK signaling pathway - plant and terpenoid backbone biosynthesis pathway in cultivated ginseng, but had no effects in wild ginseng. Furthermore, the growth years had significant effects on the genes related to ginsenoside synthesis in cultivated ginseng, and the effects were different in the roots, stems and leaves. However, it had little influence on the expression of genes related to ginsenoside synthesis in wild ginseng and no effect on leaves. These results showed wild ginseng was less affected by growth years than cultivated ginseng. Furthermore, HMGR, SS, DXS, DS, IspF, AACT, CYP450 and UGTs were related with MYB, NAC, AP2/ERF, bHLH and WRKY transcription factors. Growth years may regulate genes for ginsenoside synthesis by influencing these transcription factors, thereby affecting the content of ginsenosides.Conclusions: This study complemented the gaps in the genetic information of wild ginseng in different growth periods and different tissues and provided a new insight into the mechanism of ginsenoside regulation.

Genome-Wide Identification and Analysis of the WRKY Gene Family and Cold Stress Response in Acer truncatum

WRKY transcription factors constitute one of the largest gene families in plants and are involved in many biological processes, including growth and development, physiological metabolism, and the stress response. In earlier studies, the WRKY gene family of proteins has been extensively studied and analyzed in many plant species. However, information on WRKY transcription factors in Acer truncatum has not been reported. In this study, we conducted genome-wide identification and analysis of the WRKY gene family in A. truncatum, 54 WRKY genes were unevenly located on all 13 chromosomes of A. truncatum, the highest number was found in chromosomes 5. Phylogenetic relationships, gene structure, and conserved motif identification were constructed, and the results affirmed 54 AtruWRKY genes were divided into nine subgroup groups. Tissue species analysis of AtruWRKY genes revealed which were differently exhibited upregulation in flower, leaf, root, seed and stem, and the upregulation number were 23, 14, 34, 18, and 8, respectively. In addition, the WRKY genes expression in leaf under cold stress showed that more genes were significantly expressed under 0, 6 and 12 h cold stress. The results of this study provide a new insight the regulatory function of WRKY genes under abiotic and biotic stresses.

Genome-wide characterization and analysis of WRKY transcription factors in Panax ginseng

Background Panax ginseng is a well-known medicinal plant worldwide. As an herbal medicine, ginseng is also known for its long lifecycle, which can reach several decades. WRKY proteins play regulatory roles in many aspects of biological processes in plants, such as responses to biotic or abiotic stress, plant development, and adaptation to environmental challenges. Genome-wide analyses of WRKY genes in P. ginseng have not been reported. Results In this study, 137 PgWRKY genes were identified from the ginseng genome. Phylogenetic analysis showed that the PgWRKYs could be clustered into three primary groups and five subgroups. Most of the PgWRKY gene promoters contained several kinds of hormone- and stress-related cis-regulatory elements. The expression patterns of PgWRKY genes in 14 different tissues were analyzed based on the available public RNA-seq data. The responses of the PgWRKY genes to heat, cold, salt and drought treatment were also investigated. Most of the PgWRKY genes were expressed differently after heat treatment, and expression trends changed significantly under drought and cold treatment but only slightly under salt treatment. The coexpression analysis of PgWRKY genes with the ginsenoside biosynthesis pathway genes identified 11 PgWRKYs that may have a potential regulatory role in the biosynthesis process of ginsenoside. Conclusions This work provides insights into the evolution, modulation and distribution of the WRKY gene family in ginseng and extends our knowledge of the molecular basis along with modulatory mechanisms of WRKY transcription factors in ginsenoside biosynthesis.

Virus-Induced Gene Silencing of SlWRKY79 Attenuates Salt Tolerance in Tomato Plants

Previous studies have shown that WRKY transcription factors play important roles in abiotic stress responses. Thus, virus-induced gene silencing (VIGS) was used to identify the function of SlWRKY79 in the salt tolerance of tomato plants by downregulating the expression of the SlWRKY79 gene. Under the same salt treatment conditions, the SlWRKY79-silenced plants showed faster stem wilting and more severe leaf shrinkage than the control plants, and the bending degree of the stem of the SlWRKY79-silenced plants was also greater than that of the control plants. Physiological analyses showed that considerably higher levels of hydrogen peroxide (H2O2), superoxide anion (O2−), and abscisic acid (ABA) accumulated in the leaves of the SlWRKY79-silenced plants than in those of the controls after salt treatment. Taken together, our results suggested that SlWRKY79 plays a positive regulatory role in salt tolerance in tomato plants.

Dynamic differential evolution schemes of WRKY transcription factors in domesticated and wild rice

WRKY transcription factors play key roles in stress responses, growth, and development. We previously reported on the evolution of WRKYs from unicellular green algae to land plants. To address recent evolution events, we studied three domesticated and eight wild species in the genus Oryza, an ideal model due to its long history of domestication, economic importance, and central role as a model system. We have identified prevalence of Group III WRKYs despite differences in breeding of cultivated and wild species. Same groups of WRKY genes tend to cluster together, suggesting recent, multiple duplication events. Duplications followed by divergence may result in neofunctionalizations of co-expressed WRKY genes that finely tune the regulation of target genes in a same metabolic or response pathway. WRKY genes have undergone recent rearrangements to form novel genes. Group Ib WRKYs, unique to AA genome type Oryza species, are derived from Group III genes dated back to 6.76 million years ago. Gene tree reconciliation analysis with the species tree revealed details of duplication and loss events in the 11 genomes. Selection analysis on single copy orthologs reveals the highly conserved nature of the WRKY domain and clusters of fast evolving sites under strong positive selection pressure. Also, the numbers of single copy orthologs under positive or negative selection almost evenly split. Our results provide valuable insights into the preservation and diversification of an important gene family under strong selective pressure for biotechnological improvements of the world’s most valued food crop.