Panax ginseng C.A. Meyer is one of the most highly valued medicinal plants in the world. To analyze the transcriptome of P. ginseng and discover the genes involved in ginsenoside biosynthesis, cDNAs derived from the total RNA of 11-year-old, wood-grown P. ginseng roots were analyzed by 454 sequencing. A total of 217,529 high quality reads (expressed sequence tags, ESTs), with an average length of 409 bases, were generated from a one-quarter run to yield 31,741 unique sequences. The majority (20,198; 63.6%) of the unique sequences were annotated using BLAST similarity searches. A total of 16,810 and 16,577 unique sequences were assigned to functional classifications and biochemical pathways based on Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes assignment, respectively. Nine genes involved in the biosynthesis of ginsenoside skeletons and many candidate genes putatively responsible for modification of the skeletons, including 133 cytochrome P450s and 235 glycosyltransferases, were identified. From these candidates, six transcripts encoding UDP-glycosyltransferases that were most likely to be involved in ginsenoside biosynthesis were selected. These results open a new avenue by which to explore and exploit biosynthetic and biochemical properties that may lead to drug improvement. These 454 ESTs will provide the foundation for further functional genomic research into the traditional herb P. ginseng or its closely related species.

Fruit length is a prominent agricultural trait during cucumber (Cucumis sativus) domestication and diversifying selection; however, the regulatory mechanisms of fruit elongation remain elusive. We identified two alleles of the FRUITFULL (FUL)-like MADS-box gene CsFUL1 with 3393 C/A Single Nucleotide Polymorphism variation among 150 cucumber lines. Whereas CsFUL1 A was specifically enriched in the long-fruited East Asian type cucumbers (China and Japan), the CsFUL1 C allele was randomly distributed in cucumber populations, including wild and semiwild cucumbers. CsFUL1 A knockdown led to further fruit elongation in cucumber, whereas elevated expression of CsFUL1 A resulted in significantly shorter fruits. No effect on fruit elongation was detected when CsFUL1 C expression was modulated, suggesting that CsFUL1 A is a gain-of-function allele in long-fruited cucumber that acts as a repressor during diversifying selection of East Asian cucumbers. Furthermore, CsFUL1 A binds to the CArG-box in the promoter region of SUPERMAN, a regulator of cell division and expansion, to repress its expression. Additionally, CsFUL1 A inhibits the expression of auxin transporters PIN-FORMED1 (PIN1) and PIN7, resulting in decreases in auxin accumulation in fruits. Together, our work identifies an agriculturally important allele and suggests a strategy for manipulating fruit length in cucumber breeding that involves modulation of CsFUL1 A expression.

Flower opening is essential for pollination and thus successful sexual reproduction; however, the underlying mechanisms of its timing control remain largely elusive. We identify a unique cucumber (Cucumis sativus) line '6457' that produces normal ovaries when nutrients are under-supplied, and super ovaries (87%) with delayed corolla opening when nutrients are oversupplied. Corolla opening in both normal and super ovaries is divided into four distinct phases, namely the green bud, green-yellow bud, yellow bud, and flowering stages, along with progressive color transition, cytological tuning, and differential expression of 14,282 genes. In the super ovary, cell division and cell expansion persisted for a significantly longer period of time; the expressions of genes related to photosynthesis, protein degradation, and signaling kinases were dramatically upregulated, whereas the activities of most transcription factors and stress-related genes were significantly down-regulated; concentrations of cytokinins (CKs) and gibberellins were higher in accordance with reduced cytokinin conjugation and degradation and increased expression of gibberellin biosynthesis genes. Exogenous CK application was sufficient for the genesis of super ovaries, suggesting a decisive role of CKs in controlling the timing of corolla opening. Furthermore, 194 out of 11,127 differentially expressed genes identified in pairwise comparisons, including critical developmental, signaling, and cytological regulators, contained all three types of cis-elements for CK, nitrate, and phosphorus responses in their promoter regions, indicating that the integration of hormone modulation and nutritional regulation orchestrated the precise control of corolla opening in cucumber. Our findings provide a valuable framework for dissecting the regulatory pathways for flower opening in plants.The flower is the most distinguishing organ in higher plants, and artists and scientists have been attracted to explore the mystery of flower structure and origin for decades. The evolution of flowering plants was greatly accelerated approximately 100 million years ago with the development of flowers, which were essential for recruiting animals to help distribute pollen and seeds (Danielson and Frommer, 2013). Flowers are produced from a specialized structure in the shoot tip called the shoot apical meristem, which consists of a pool of stem cells that continuously divide and replenish themselves (Fletcher et al., 1999). Morphologically, flowers are comprised of four basic structures arranged in concentric whorls: sepals in the outermost whorl 1, petals in whorl 2, stamens in whorl 3, and carpels in the innermost whorl 4. Bisexual flowers possess all four basic structures, while unisexual flowers lack one or more structures, usually the male organ stamen or the female organ carpel (Dellaporta and Calderon-Urrea, 1993). In flowering plants, approximately 90% species produce bisexual flowers, 6% species are dioecious with male and female flowers on separate plants, and 4% species a...

No abstract