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Gene cluster

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The expression of the acarbose biosynthesis gene cluster in Actinoplanes sp. SE50/110 is dependent on the growth phase

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Interestingly, the proteins of the acarbose biosynthesis gene cluster are distributed over 5 different cluster (P5, P13, P15, P28 and P34), although the acb genes were found to be highly co-transcribed in transcriptomic clus- ters T31 and T32. The genes of the acarbose biosynthetic gene cluster are transcriptionally and post-transcriptionally regulated during filamentous growth.

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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Therefore, the fengycin biosynthetic gene cluster of strain NCD-2 was compared with that of B.

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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In the analysis of the monacolin K gene cluster, four M. ruber NBRC 4483 have a complete set of monacolin K gene clusters. ruber NBRC 4483 can produce monacolin K but lack a complete set of citrinin biosynthetic gene clusters.. purpureus may play an important role in the food in- dustry and industrial field through the improved utilization of Monascus species.

Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs

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The putative CNV maps to the type I Interferon (IFN) gene family cluster and, ac- cording to the canine RefSeq annotation [28], overlaps with the potential promoter, 5 ′ UTR and first protein coding co- dons of the IFNA7 gene..

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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Interestingly, a 26-bp middle portion of tRNA-N could form an O L -like structure (Fig. speculated that translocation of tRNA-D could have occurred either before (Fig. 1i-e) the DMNL process [14]. 1IV-B2), and the existence of one of the following four arrangements of CRs, tRNA-D and the 8- gene cluster (Q-A-C-Y-S 1 -ND6-E-P): D–CR–8-gene clus- ter, CR–5-gene cluster (Q-A-C-Y-S 1 )–D–3-gene cluster (ND6-E-P), CR1–5-gene cluster–D–3-gene cluster–CR2, and 5-gene cluster–D–3-gene cluster–CR..

Comparative transcriptomic analysis of global gene expression mediated by (p) ppGpp reveals common regulatory networks in Pseudomonas syringae

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Our results showed that (p) ppGpp suppressed 66 coen- zyme metabolism-related genes in both PstDC3000 and PssB728a, including the ribDEF gene cluster, which is in- volved in riboflavin biosynthesis [92–94], nadACD gene cluster (regulate niacin biosynthesis) and the hemACFHL gene cluster (Additional file 5: Table S12).

Dynamic network inference and association computation discover gene modules regulating virulence, mycotoxin and sexual reproduction in Fusarium graminearum

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Remarkably, our network in- ference yielded a 44-gene module (M46) capturing the majority (9 of 12) of the Tri-cluster genes and accurately predicted Tri6 and Tri10 as the top two regulators of this module (Fig. Most of the overlapped genes were Tri-cluster genes. 3 High accuracy of network inference highlighted by its capture of the trichothecene biosynthetic gene cluster. Diagram of the trichothecene biosynthetic gene cluster (Tri-cluster) in F.

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

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Schematic representation of the putative aurovertin gene cluster (cluster 23) and the description of each gene in a gene cluster.

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

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Identification and functional analysis of the fusaricidin biosynthetic gene of Paenibacillus polymyxa E681. Macrolactin is the polyketide biosynthesis product of the pks2 cluster of Bacillus amyloliquefaciens FZB42. Draft genome sequences of six Bacillus strains and one Brevibacillus strain isolated from the rhizosphere of perennial ryegrass (Lolium perenne).

Differential network analysis of bovine muscle reveals changes in gene coexpression patterns in response to changes in maternal nutrition

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Overall, the six unpreserved modules were considered as gene coexpression modules or subnet- works that were significantly perturbed by the maternal methionine diet.. c Tree plot of initial module eigengenes (MEs) in the maternal control diet using soft threshold = 24. 2 Gene coexpression networks. a Gene cluster dendrogram in the maternal control diet. b Gene cluster dendrogram in the maternal methionine diet.

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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Moreover, AtRFL2, AtRFL4 and AtRFL9 were located within the gene cluster on Arabidopsis chromosome 1 and partici- pated in the processing of the mitochondrial RNA [25–. 3), and the structural analysis showed that all of the BnRFLs and the known restorer genes in radish share a conserved motif (Fig.

GeneMates: An R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure

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It is, however, confined by limitations of short-read genome assembly, and its power will increase in the future as we are accumulating complete genomes and enhancing our ability in resolving repeats using sequencing data.. https://doi.org/10.. https://doi.org/. pCERC1, a Small, Globally Disseminated Plasmid Carrying the dfrA14 Cassette in the strA Gene of the sul2-strA-strB Gene Cluster. https://doi.org/10.1016/S . https://doi.org/10.1038/s .

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

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In contrast, cluster 2 from strain CN732 consisted of only three NRPS genes all of which differed from the lpm cluster of S. For example, in addition to the differences in the number of C-A-T do- mains, the epimerization (E) domains were absent in two of these NRPS enzymes that were present in two out of four NRPS enzymes from S. PKS-NRPS hybrid gene clusters.

Intra-specific comparison of mitochondrial genomes reveals host gene fragment exchange via intron mobility in Tremella fuciformis

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Evolutionary origins of the Fumonisin secondary metabolite gene cluster in Fusarium verticillioides and Aspergillus Niger. Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis.. Strand invasion structures in the inverted repeat of Candida albicans mitochondrial DNA reveal a role for homologous recombination in replication.

Comparative genomics of Alternaria species provides insights into the pathogenic lifestyle of Alternaria brassicae – a pathogen of the Brassicaceae family

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Genomic characterization of the conditionally dispensable chromosome in Alternaria arborescens provides evidence for horizontal gene transfer. Genomics, evolutionary history and diagnostics of the Alternaria alternata species group including apple and Asian pear pathotypes. Gene cluster involved in melanin biosynthesis of the filamentous fungus Alternaria alternata.

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

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A total of 766 probes associated with 700 gene tran- scripts were identified to be differentially expressed between competent in vivo derived embryos (CVO) and non-competent in vivo derived embryos (NVO), (Fig. Expression of gene cluster predicting the developmental capacity of in vivo derived bovine embryos.

Intra-species variation within Lactobacillus rhamnosus correlates to beneficial or harmful outcomes: Lessons from the oral cavity

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Identification of a gene cluster for the biosynthesis of a long, Galactose-rich exopolysaccharide in Lactobacillus rhamnosus GG and functional analysis of the priming Glycosyltransferase.. Comparative genomic and phenotypic analysis of the vaginal probiotic Lactobacillus rhamnosus GR-1. Comparative analysis of the exopolysaccharide biosynthesis gene clusters from four strains of Lactobacillus rhamnosus. A Genome- Based Species Taxonomy of the Lactobacillus Genus Complex..

Genomic dissection of the most prevalent Listeria monocytogenes clone, sequence type ST87, in China

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A ST87-specific gene cluster that harbored a type II restriction-modification (RM) system was identified and is present in all ST87 strains sequenced in this study (Fig. The GC content of the endonuclease gene, the methyltransferase gene and the whole gene cluster were and 33.78%, re- spectively, noticeably lower than the genome average of 38%.

Transcriptional response of Asarum heterotropoides Fr. Schmidt var. mandshuricum (Maxim.) Kitag. leaves grown under full and partial daylight conditions

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The first gene (Cluster was downregulated in Asarum leaves grown under full to 50%, full to 12, 50 to 12%, and 28 to 12% sunlight conditions.

Fuzzy Cluster Analysis with Cluster Repulsion

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In objective function based clustering usually each cluster is represented by a cluster prototype. This prototype consists of a cluster center (whose name already indicates its meaning) and maybe some additional information about the size and the shape of the cluster. The cluster center is an instantiation of the attributes used to describe the domain, just as the data points in the dataset to divide..