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Gene clusters

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Divergence of metabolites in three phylogenetically close Monascus species (M. pilosus, M. ruber, and M. purpureus) based on secondary metabolite biosynthetic gene clusters

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Furthermore, to evaluate the clusters of the enzymes related with the secondary metabolic pathways we ana- lyzed their genome sequences using antiSMASH 4.0 [31], and we obtained 24 gene clusters for M. scores of the 92 gene clusters (Fig. 4), obtaining 22 groups with multiple gene clusters and 32 singletons.. Gene clusters with identical gene organization were merged into a single group. We also obtained 54 groups of gene clusters (Table 1) that are displayed as Venn diagrams (Fig.

Genome mining and UHPLC–QTOF–MS/MS to identify the potential antimicrobial compounds and determine the specificity of biosynthetic gene clusters in Bacillus subtilis NCD-2

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Secondary metabolite biosynthetic gene clusters in strain NCD-2. The secondary metabolite biosynthetic gene clusters in the genome of strain NCD-2 were predicted using anti- SMASH [31]. 1 Circular genome of strain NCD-2 with specific features. From outside to inside: circle 1, the size of the complete genome.

Characterization of plant growth-promoting rhizobacteria from perennial ryegrass and genome mining of novel antimicrobial gene clusters

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Characterization of plant growth-promoting rhizobacteria from perennial ryegrass and genome mining of novel antimicrobial gene clusters. In this study, we expand the view to the food chain of grass-ruminant-human. Results: We screened 90 bacterial strains from the rhizosphere of healthy Dutch perennial ryegrass and characterized seven strains (B. Genome-mining of the seven strains discovered abundant BGCs, with some known, but also several potential novel ones.

A detailed in silico analysis of secondary metabolite biosynthesis clusters in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum

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Genes in both intracellular and extracellular siderophore clusters were downregulated in planta relative to in vitro, with the exception of homologues of NRPS2 in the B.. There are four nonreducing Type I PKSs encoded in the S.. For example, in the fungal species A. Prediction of secondary metabolite biosynthesis gene clusters in the Sclerotinia sclerotiorum genome. Homology analysis of Sclerotinia sclerotiorum secondary metabolite clusters. nearest repeat sequence for each gene in the S.

Novel heavy metal resistance gene clusters are present in the genome of Cupriavidus neocaledonicus STM 6070, a new species of Mimosa pudica microsymbiont isolated from heavy-metal-rich mining site soil

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STM 6070 HME gene products from clusters A, C, E, F, G and H displayed highest identity (93 to 100%) with corresponding proteins of C. Synteny analysis indicated that the specific STM 6070 HMR clusters B, D, I and J were absent from all other analysed Cupriavidus genomes, although some of the HMR genes within these clusters had orthologues (35 to 89% of encoded protein identity) in the genomes of the other Cupriavidus strains.

Genomic and transcriptomic survey of an endophytic fungus Calcarisporium arbuscula NRRL 3705 and potential overview of its secondary metabolites

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Among them, 23 and 12 gene clusters containing genes encoding polyketide synthases (PKS) and non-ribosomal peptides synthases (NRPS), respectively, were identified. In addition, there are gene clusters for terpenes, PKS/NRPS hybrids, indoles and other types of natural products (Additional file 8). Some of these gene clusters are highly similar to known gene clusters (Table 2)..

Human gene expression variability and its dependence on methylation and aging

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Overall, the func- tional annotations of the age-regulated Hyper-Variable gene clusters suggest that population EV is one outcome of age-dependent gene expression changes.. We next investigated a possible impact of methylation status on gene expression in the Up- and Down- regulated Hyper-Variable genes. 6 Hierarchical clustering of Hyper-Variable genes by age in (A) cerebellum tissue, and (B) frontal cortex tissue. gene expression and gene methylation for each gene.

Genome-wide identification of the restorerof-fertility-like (RFL) gene family in Brassica napus and expression analysis in Shaan2A cytoplasmic male sterility

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Genome-wide identification of the restorer- of-fertility-like ( RFL ) gene family in Brassica napus and expression analysis in Shaan2A cytoplasmic male sterility. Most of the Rf genes encode pentatricopeptide repeat (PPR) proteins.. While most of the BnRFL genes were distributed on 10 of the 19 chromosomes, gene clusters were identified on chromosomes A9 and C8.

Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium

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Biosynthetic gene clusters for secondary metabolites of strain CN732. Terpene biosynthesis related clusters were the most abundant type of clusters observed in the CN732 genome. Out of the 22 potential biosynthetic clusters, 15 Table 1 General genomic features of Streptomyces yeochonensis CN732 and other species used in this study. However, the levels of similarity were fairly low in most cases, which suggests the novelty of the possible metabolites from those pre- dicted gene clusters..

Comparative genomic analysis of eutherian fibroblast growth factor genes

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The most comprehensive curated eutherian FGF third-party data gene data set was deposited in European Nucleotide Archive under accessions: LR130242-LR . The present study first described 8 superclusters FGF1–8 including 22 major gene clusters of eutherian FGF genes, proposing their updated nomenclature (Fig.. The eutherian FGF genes included ei- ther 5 coding exons (5 major gene clusters FGF1A-D.

Genome-wide analysis and prediction of genes involved in the biosynthesis of polysaccharides and bioactive secondary metabolites in high-temperature-tolerant wild Flammulina filiformis

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(Table 3).. 3 Identification of the 13 putative gene clusters for terpene and two polyketides gene clusters (PKS) in F. filiformis A total of 119 genes of 13 terpenoid clusters were di- vided into 10 clades according to their expression levels in different developmental stages of the wild strain or cultivar strains (Additional file 8: Fig.

The global gene expression outline of the bovine blastocyst: Reflector of environmental conditions and predictor of developmental capacity

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CVO) and between non-competent in vivo derived embryos and non- competent in vitro derived embryos (NVT vs. 3 Gene clusters significantly enriched in in vivo derived competent embryos (CVO) compared to none competent (NVO) ones. The transcriptome profile comparison between non- competent in vitro (NVT) and non-competent in vivo.

Precursor peptide-targeted mining of more than one hundred thousand genomes expands the lanthipeptide natural product family

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Bacteroidetes were found to encode a large number of these biosynthetic gene clusters, despite making up a relatively small portion of the genomes in this dataset. Additionally, examination of the biosynthetic gene clusters revealed that enzymes installing secondary post-translational modifications are more widespread than initially thought..

A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms

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Transcription factors involved in the genetic control of flower development, such as the PISTILLATA genes (Cp4.1LG02g03120 and. 4 a Hierarchical clustering of eigengenes of the co-expressed gene clusters found by weighted gene coexpression network analysis. b Heatmap of the relationship among gene clusters (measured as the eigenge adjacency). Cp4.1LG06g06100), were upregulated in flowers and less expressed in the three earliest fruit stages..

Weighted gene co-expression network analysis unveils gene networks associated with the Fusarium head blight resistance in tetraploid wheat

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It is likely that genes of the FHB-M2 module contribute to the transgressive expression of resistance in R. 0.05) enriched gene clusters for the modules significantly correlated with FHB resistance. Defense-related hub genes of modules correlated with FHB resistance. 2 The size (number of genes) and module eigengenes (ME) expression of gene networks correlated with Type II FHB resistance. Error bars indicate standard deviations of the mean of three biological replicates.

Prediction and analysis of metagenomic operons via MetaRon: A pipeline for prediction of Metagenome and wholegenome opeRons

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Of the 822 proximal clusters, a third of the clusters demonstrated binary configuration, followed by proxi- mons of length three (19.7. At this point, it is imperative to highlight that no Transcription Unit Boundary (TUB) is defined in the proximal gene clusters. The operonic gene clusters contains a promoter upstream of the first and downstream of the last operonic gene. These results corroborate with the fact that most of the operons in E.

Antimicrobial activity screening of rhizosphere soil bacteria from tomato and genome-based analysis of their antimicrobial biosynthetic potential

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EDO6, which in turn consists of four trans-AT PKs genes and one trans-AT PKs-NRPs hybrid gene.. 4 Novel Biosynthetic Gene Clusters (BGCs) identified from the isolated Bacillus and Paenibacillus strains. b a Type I PKs-NRPs hybrid BGC found in B. c, d two trans-AT PKs-NRPs hybrid BGCs harboered by Paenibacillus sp.

Mechanisms of gene rearrangement in 13 bothids based on comparison with a newly completed mitogenome of the threespot flounder, Grammatobothus polyophthalmus (Pleuronectiformes: Bothidae)

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One such representative case was the mitochondrial gene rearrangement in the blue flounder, Crossorhombus azureus [14]. The order of these genes in these two clusters was maintained as in the non-rearranged mitogenome of fish, except for the novel location of tRNA-D. Furthermore, un- like the typical position of the CR in fish, the CR of this species is located between tRNA-D and tRNA-Q, thus separating the two gene clusters on the H-strand and L- strand..

Linking genotype to phenotype in multiomics data of small sample

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Due to the large number of genes, and thus the many obtained gene clusters, group lasso regression can be performed on gene clusters and phenotypes.. Additional details are provided in the Supplementary Information.. Most clustering algorithms perform well Table 1 PS values of the top 20 pathways. According to the analysis of Jiang et al. SNP clusters corresponding to the selected gene clusters can be identified by eQTL data.

Genome sequencing, assembly, and annotation of the self-flocculating microalga Scenedesmus obliquus AS-6-11

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clusters with 14,576 orthologous clusters and 1303 single-copy gene clusters (Fig. obliquus AS-6-11 has the most gene clusters and singletons (defined as the single- ton genes for which no orthologs could be found in any of the other species [25.