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Niu Y.,Chinese Academy of Sciences | Luo H.,Chinese Academy of Sciences | Sun C.,Chinese Academy of Sciences | Yang T.-J.,Plant Genomics and Breeding Institute | And 4 more authors.
Gene | Year: 2014

Panax notoginseng (Burk) F. H. Chen, an economically significant medicinal plant with hemostatic and health tonic activities, has been used in Traditional Chinese Medicine (TCM) for more than 3000. years. Triterpene saponins are responsible for most of the pharmacological activities of P. notoginseng. Here, we cloned five cDNA sequences encoding the key enzymes involved in triterpene saponin biosynthesis, namely, PnFPS, PnSS, PnSE1, PnSE2, and PnDS, and analyzed the conserved domains and phylogenetics of their corresponding proteins. Their organ-specific expression patterns in four-year-old P. notoginseng were detected by real-time PCR, showing that they were all most highly expressed in flowers. In addition, four of the genes, excluding PnSE2, were upregulated in leaves following stimulation with methyl jasmonate. This study is the first comprehensive analysis of the expression patterns of pivotal genes for triterpene saponin biosynthesis in P. notoginseng and provides a basis to further elucidate the molecular mechanism for the biosynthesis of these medically important compounds. © 2013 Elsevier B.V. Source

Cho K.,John Innes Center | O'Neill C.M.,John Innes Center | Kwon S.,South Korean National Institute of Animal Science | Yang T.,Plant Genomics and Breeding Institute | And 3 more authors.
Plant Journal | Year: 2010

We conducted a sequence-level comparative analyses, at the scale of complete bacterial artificial chromosome (BAC) clones, between the genome of the most economically important Brassica species, Brassica napus (oilseed rape), and those of Brassica rapa, the genome of which is currently being sequenced, and Arabidopsis thaliana. We constructed a new B. napus BAC library and identified and sequenced clones that contain homoeologous regions of the genome including stearoyl-ACP desaturase-encoding genes. We sequenced the orthologous region of the genome of B. rapa and conducted comparative analyses between the Brassica sequences and those of the orthologous region of the genome of A. thaliana. The proportion of genes conserved (∼56%) is lower than has been reported previously between A. thaliana and Brassica (∼66%). The gene models for sets of conserved genes were used to determine the extent of nucleotide conservation of coding regions. This was found to be 84.2 ± 3.9% and 85.8 ± 3.7% between the B. napus A and C genomes, respectively, and that of A. thaliana, which is consistent with previous results for other Brassica species, and 97.5 ± 3.1% between the B. napus A genome and B. rapa, and 93.1 ± 4.9% between the B. napus C genome and B. rapa. The divergence of the B. napus genes from the A genome and the B. rapa genes was greater than anticipated and indicates that the A genome ancestor of the B. napus cultivar studied was relatively distantly related to the cultivar of B. rapa selected for genome sequencing. © 2009 The Authors. Journal compilation © 2009 Blackwell Publishing Ltd. Source

Hwang I.,Sunchon National University | Jung H.-J.,Sunchon National University | Park J.-I.,Sunchon National University | Yang T.-J.,Plant Genomics and Breeding Institute | Nou I.-S.,Sunchon National University
Genomics | Year: 2014

Plant bZIP transcription factors play crucial roles in biological processes. In this study, 136 putative bZIP transcription members were identified in Brassica rapa. The bZIP family can be divided into nine groups according to the specific amino acid rich domain in B. rapa and Arabidopsis thaliana. To screen the cold stress responsive BrbZIP genes, we evaluated whether the transcription patterns of the BrbZIP genes were enhanced by cold treatment in the inbred lines, Chiifu and Kenshin, by microarray data analysis and qRT-PCR. The expression level of six genes increased significantly in Kenshin, but these genes were unchanged in Chiifu. These findings suggest that the six genes that encoded proteins containing N-rich regions might be involved in cold stress response. The results presented herein provide valuable information regarding the molecular basis of the bZIP transcription factors and their potential function in regulation growth and development, particularly in cold stress response. © 2014 Elsevier Inc. Source

Lee J.,Konkuk University | Lee J.,Plant Genomics and Breeding Institute | Koh H.-J.,Plant Genomics and Breeding Institute
Proteome Science | Year: 2011

Background: Although a great deal of rice proteomic research has been conducted, there are relatively few studies specifically addressing the rice grain proteome. The existing rice grain proteomic researches have focused on the identification of differentially expressed proteins or monitoring protein expression patterns during grain filling stages.Results: Proteins were extracted from rice grains 10, 20, and 30 days after flowering, as well as from fully mature grains. By merging all of the identified proteins in this study, we identified 4,172 non-redundant proteins with a wide range of molecular weights (from 5.2 kDa to 611 kDa) and pI values (from pH 2.9 to pH 12.6). A Genome Ontology category enrichment analysis for the 4,172 proteins revealed that 52 categories were enriched, including the carbohydrate metabolic process, transport, localization, lipid metabolic process, and secondary metabolic process. The relative abundances of the 1,784 reproducibly identified proteins were compared to detect 484 differentially expressed proteins during rice grain development. Clustering analysis and Genome Ontology category enrichment analysis revealed that proteins involved in the metabolic process were enriched through all stages of development, suggesting that proteome changes occurred even in the desiccation phase. Interestingly, enrichments of proteins involved in protein folding were detected in the desiccation phase and in fully mature grain.Conclusion: This is the first report conducting comprehensive identification of rice grain proteins. With a label free shotgun proteomic approach, we identified large number of rice grain proteins and compared the expression patterns of reproducibly identified proteins during rice grain development. Clustering analysis, Genome Ontology category enrichment analysis, and the analysis of composite expression profiles revealed dynamic changes of metabolisms during rice grain development. Interestingly, we detected that proteins involved in glycolysis, TCA-cycle, lipid metabolism, and proteolysis accumulated at higher levels in fully mature grain compared to grain developing stages, suggesting that the accumulation of these proteins during the desiccation stage may be associated with the preparation of proteins required in germination. © 2011 Lee and Koh; licensee BioMed Central Ltd. Source

Kim H.-J.,Plant Genomics and Breeding Institute | Han J.-H.,Kangwon National University | Kim K.S.,Kangwon National University | Lee Y.-H.,Plant Genomics and Breeding Institute
Fungal Genetics and Biology | Year: 2014

The ascomycete fungus Magnaporthe oryzae is an economically important pathogen that causes rice blast disease worldwide. Accumulating evidence indicates that the fungal velvet genes are key regulators of a number of cellular processes, including development, pathogenicity and secondary metabolism, in many species of fungi. In this study, we identified and functionally characterized four genes (. MoVOSA, MoVELB, MoVEA, and MoVELC) from the genome of the fungal pathogen M. oryzae. These genes were homologous to the velvet gene family of Aspergillus nidulans. Deletions of MoVEA, MoVELB, and MoVELC resulted in a significant decrease in conidiation, indicating their roles as positive regulators thereof. The MoVELC gene was involved in development of conidial morphology, while MoVELB and MoVEA appeared necessary for conidial germination, MoVEA further being indispensable for appressorial development and modulation of reactive oxygen species in disease development. Deletion of MoVELC affected the cell wall integrity of appressoria, resulting in failure to penetrate host cells. Unexpectedly, MoVOSA appeared dispensable for the development and pathogenicity of M. oryzae, even though its homologs play specific roles in other fungal species. Taken together, our data demonstrate that the velvet genes are linked to M. oryzae infection-related development and pathogenicity, and the findings provide a framework for comparative studies of the conserved velvet gene family across a range of fungal taxa, which may provide new insight into fungal development and pathogenicity. © 2014 Elsevier Inc. Source

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