Integrated transcriptome and microRNA profiles analysis reveals molecular mechanisms underlying the consecutive monoculture problem of Polygonatum odoratum
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Polygonatum odoratum is a historically traditional Chinese medicine plant. However, the consecutive monoculture problem (CMP) widespread in other Chinese medicine limiting their cultivation on a large scale. In this study, the physiological data showed the adverse effect of CMP on the growth of P. odoratum under the consecutive cropping (CC) compared with the first cropping (FC). Then the high-throughput sequencing of miRNA and mRNA libraries of leaves and roots from FC and CC P. odoratum plants identified 671 differentially expressed genes (DEGs) and 184 differentially expressed miRNAs and revealed that the DEGs and target genes of the miRNAs were mainly involved in starch and sucrose metabolism, phenylpropanoid and brassinosteroid biosynthesis. The KEGG analysis revealed that the DEGs between CC and FC roots were enriched in the plant-pathogen interaction pathway. This study provided the expression regulation of genes related to CMP of P. odoratum but also suggested that CMP may result in the serious damage of pathogens to roots and cause the slow growth in the consecutive cropping plants.Keywords:
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Phenylpropanoid
Monoculture
Although decades of research suggest that higher species richness improves ecosystem functioning and stability, planted forests are predominantly monocultures. To determine whether diversification of plantations would enhance aboveground carbon storage, we systematically reviewed over 11,360 publications, and acquired data from a global network of tree diversity experiments. We compiled a maximum dataset of 79 monoculture to mixed comparisons from 21 sites with all variables needed for a meta-analysis. We assessed aboveground carbon stocks in mixed-species planted forests vs. (a) the average of monocultures, (b) the best monoculture, and (c) commercial species monocultures, and examined potential mechanisms driving differences in carbon stocks between mixtures and monocultures. On average, we found that aboveground carbon stocks in mixed planted forests were 70% higher than the average monoculture, 77% higher than commercial monocultures, and 25% higher than the best performing monocultures, although the latter was not statistically significant. Overyielding was highest in four-species mixtures (richness range 2–6 species), but otherwise none of the potential mechanisms we examined (nitrogen-fixer present vs. absent; native vs. non-native/mixed origin; tree diversity experiment vs. forestry plantation) consistently explained variation in the diversity effects. Our results, predominantly from young stands, thus suggest that diversification could be a very promising solution for increasing the carbon sequestration of planted forests and represent a call to action for more data to increase confidence in these results and elucidate methods to overcome any operational challenges and costs associated with diversification.
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The KEGG database and analysis tools (https://www.kegg.jp) have been developed mostly for understanding genes and genomes of cellular organisms. The KO (KEGG Orthology) dataset, which is a collection of functional orthologs, plays the role of linking genes in the genome to pathways and other molecular networks, enabling KEGG mapping to uncover hidden features in the genome. Although viruses were part of KEGG for some time, they were not fully integrated in the KEGG analysis tools, because the KO assignment rate is very low for virus genes. To supplement KOs a new dataset named virus ortholog clusters (VOCs) is computationally generated, covering 90% of viral proteins in KEGG. VOCs can be used, in place of KOs, for taxonomy mapping to uncover relationships of sequence similarity groups and taxonomic groups and for identifying conserved gene orders in virus genomes. Furthermore, selected VOCs are used to define tentative KOs for characterizing protein functions. Here an overview of KEGG tools is presented focusing on these extensions for viral protein analysis.
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SUMMARY An analysis is suggested for an experiment investigating competition between different plant species when they are grown in monoculture and in mixed cultures with species not in equal proportions. tion. An analysis is now obtained for a similar experiment in which mixed cultures are grown with species in the ratio u: v, where u + v = 1 and u + 1. All p(p - 1) combinations of two are grown, as well as the monoculture plantings. If we investigate competition between several varieties of wheat at ratio -1: 2 (and thus also at ratio 3: 3) each variety is grown in monoculture, in ratio 1:2 with every other variety and in ratio 2:1 with every other variety. Since an analysis is straightforward for p = 2 we assume that p > 2 and that we have r1 replications of monoculture yields, r2 replications of mixed culture yields.
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Abstract Background The MetaCyc and KEGG projects have developed large metabolic pathway databases that are used for a variety of applications including genome analysis and metabolic engineering. We present a comparison of the compound, reaction, and pathway content of MetaCyc version 16.0 and a KEGG version downloaded on Feb-27-2012 to increase understanding of their relative sizes, their degree of overlap, and their scope. To assess their overlap, we must know the correspondences between compounds, reactions, and pathways in MetaCyc, and those in KEGG. We devoted significant effort to computational and manual matching of these entities, and we evaluated the accuracy of the correspondences. Results KEGG contains 179 module pathways versus 1,846 base pathways in MetaCyc; KEGG contains 237 map pathways versus 296 super pathways in MetaCyc. KEGG pathways contain 3.3 times as many reactions on average as do MetaCyc pathways, and the databases employ different conceptualizations of metabolic pathways. KEGG contains 8,692 reactions versus 10,262 for MetaCyc. 6,174 KEGG reactions are components of KEGG pathways versus 6,348 for MetaCyc. KEGG contains 16,586 compounds versus 11,991 for MetaCyc. 6,912 KEGG compounds act as substrates in KEGG reactions versus 8,891 for MetaCyc. MetaCyc contains a broader set of database attributes than does KEGG, such as relationships from a compound to enzymes that it regulates, identification of spontaneous reactions, and the expected taxonomic range of metabolic pathways. MetaCyc contains many pathways not found in KEGG, from plants, fungi, metazoa, and actinobacteria; KEGG contains pathways not found in MetaCyc, for xenobiotic degradation, glycan metabolism, and metabolism of terpenoids and polyketides. MetaCyc contains fewer unbalanced reactions, which facilitates metabolic modeling such as using flux-balance analysis. MetaCyc includes generic reactions that may be instantiated computationally. Conclusions KEGG contains significantly more compounds than does MetaCyc, whereas MetaCyc contains significantly more reactions and pathways than does KEGG, in particular KEGG modules are quite incomplete. The number of reactions occurring in pathways in the two DBs are quite similar.
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The term monoculture is widely used in the scientific literature concerning the agricultural sector. However, it is very difficult to find a clear and shared definition of this term. This study investigates the concept of monoculture in agricultural areas where high specialization in a specific crop is observed. Therefore, we refer to a territorial-level definition, which associates the idea of monoculture to the prevalent presence of a crop in a region including many farms. The objectives of the paper are: (i) to define indicators capable of verifying the existence of this condition; (ii) to test the ability of such indicators in identifying the effective presence of a monoculture. A set of Italian areas identified as monoculture in the recent literature were selected to carry out a quantitative analysis, assessing different indexes of monoculture. On the basis of the obtained results, such an analysis should help in comparing the monoculture indexes and fostering a discussion on their suitability and descriptive capacities.
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Mulberry sclerotiniose caused by Ciboria shiraiana is a devastating disease of mulberry (Morus alba L.) fruit in Northwest China. At present, no disease-resistant varieties are used in production, as the molecular mechanisms of this disease are not well understood. In this study, to explore new prevention methods and provide direction for molecular breeding, transcriptomic sequencing and un-targeted metabolomics were performed on healthy (CK), early-stage diseased (HB1), and middle-stage diseased (HB2) mulberry fruits. Functional annotation, gene ontology, a Kyoto encyclopedia of genes and genomes (KEGG) analysis, and a Mapman analysis of the differentially expressed genes revealed differential regulation of genes related to plant hormone signal transduction, transcription factors, and phenylpropanoid biosynthesis. A correspondence between the transcript pattern and metabolite profile was observed in the phenylpropanoid biosynthesis pathway. It should be noted that the log2 ratio of eugenol (isoeugenol) in HB1 and HB2 are 85 times and 23 times higher than CK, respectively. Our study shows that phenylpropanoid biosynthesis may play an essential role in response to sclerotiniose pathogen infection and eugenol(isoeugenol) enrichment in mulberry fruit, which may provide a novel method for mulberry sclerotiniose control.
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Phenylpropanoid
Phytophthora infestans
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Secondary metabolism
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Catechol oxidase
Phenylalanine ammonia-lyase
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The large yellow croaker (Larimichthys crocea) is an economically important fish species in Chinese mariculture industry. To understand the molecular basis underlying the response to fasting, Illumina HiSeqTM 2000 was used to analyze the liver transcriptome of fasting large yellow croakers. A total of 54,933,550 clean reads were obtained and assembled into 110,364 contigs. Annotation to the NCBI database identified a total of 38,728 unigenes, of which 19,654 were classified into Gene Ontology and 22,683 were found in Kyoto Encyclopedia of Genes and Genomes (KEGG). Comparative analysis of the expression profiles between fasting fish and normal-feeding fish identified a total of 7,623 differentially expressed genes (P < 0.05), including 2,500 upregulated genes and 5,123 downregulated genes. Dramatic differences were observed in the genes involved in metabolic pathways such as fat digestion and absorption, citrate cycle, and glycolysis/gluconeogenesis, and the similar results were also found in the transcriptome of skeletal muscle. Further qPCR analysis confirmed that the genes encoding the factors involved in those pathways significantly changed in terms of expression levels. The results of the present study provide insights into the molecular mechanisms underlying the metabolic response of the large yellow croaker to fasting as well as identified areas that require further investigation.
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RNA-Seq
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The Asian citrus psyllid (ACP), Diaphorina citri Kuwayama, is the principal vector of the Candidatus Liberibacter asiaticus (CLas) bacterium that causes Huanglongbing (HLB) disease. The D. citri salivary glands (SG) is an important barrier to the transmission of CLas. Despite its importance, the transcriptome and proteome of SG defense against CLas are unstudied in D. citri. In the present study, we generated a comparative transcriptome dataset of the SG in infected and uninfected D. citri using an Illumina RNA-Seq technology. We obtained 407 differentially expressed genes (DEGs), including 159 upregulated DEGs and 248 downregulated DEGs. Functional categories showed that many DEGs were associated with the ribosome, the insecticide resistance, the immune response and the digestion in comparison with CLas-infected SG and CLas-free SG. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases confirmed that metabolism and immunity were important functions in the SG. Among the DEGs, 68 genes (35 upregulated and 33 downregulated) encoding putative-secreted proteins were obtained with a signal peptide, suggesting that these genes may play important roles in CLas infection. A total of 673 SG proteins were identified in uninfected D. citri by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) analysis, and 30 DEGs (15 upregulated and 15 downregulated) were found using the local tBLASTP programs. Among the 30 DEGs, many DEGs mainly involved in the metabolism and cellular processes pathways. This study provides basic transcriptome and proteome information for the SG in D. citri, and helps illuminate the molecular interactions between CLas and D. citri.
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Diaphorina citri
Proteome
RNA-Seq
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Phenylpropanoids are naturally occurring compounds that exert beneficial pharmacological effects on human health. Phenylpropanoids can act as antioxidants and are involved in resistance to ultraviolet light and cancer; these compounds possess anti-inflammatory, antiviral, and antibacterial activity, and aid in wound healing. The expression of genes involved in phenylpropanoid biosynthesis, and consequent accumulation of phenylpropanoids in wheat sprout under conditions of stress, have not been extensively studied. This is the first study to examine the effects of light-emitting diodes (LED) on the expression of genes involved in phenylpropanoid biosynthesis and accumulation of phenylpropanoids in wheat sprouts. Our results, obtained using qRT-PCR and HPLC analyses, indicate that white light (380 nm) was the optimal wavelength for epicatechin biosynthesis in wheat sprouts. Compared with the effects of white light, blue light (470 nm) enhanced the accumulation of gallic acid and quercetin, but decreased the levels of p-coumaric acid and epicatechin; red light (660 nm) increased the accumulation of ferulic acid at 8 day and p-coumaric acid at 12 day. Compared gene expression with phenylpropanoid content showed that TaPAL3, TaPAL4, and TaDFR maybe important genes in phenylpropanoid biosynthesis in wheat sprout. This study provides insights into the effects of led lights on phenylpropanoid production in wheat sprouts. This knowledge will help improve secondary metabolite production in wheat sprouts.
Phenylpropanoid
Secondary metabolite
Coumaric acid
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