Tag: BGCs

How to perform fungal mutagenesis?

How to DNA sequence a yeast?3 answersDNA sequencing of yeast can be done using various methods. One protocol involves preparing yeast DNA by digesting the cell wall and lysing the resulting spheroplasts with SDS. This method yields several micrograms of yeast DNA that can be cleaved by restriction enzymes and…

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Whole genome sequencing provides evidence for Bacillus velezensis SH-1471 as a beneficial rhizosphere bacterium in plants

Inhibition effect of strain SH-1471 on plant pathogenic fungi The results of the plate confrontation experiment showed that B. velezensis SH-1471 had good inhibitory effects on various pathogenic microorganisms (Fig. 1). Specifically, our experiment showed that its inhibition rates on Sclerotinia scrotiorum, Phoma mateuciicola, and Fusarium oxysporum were 93.5%, 90.3%, and…

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A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources

40,039 MAGs reconstructed from large-scale genome-resolved metagenomics To reconstruct previously unexplored bacterial and archaeal genomes, we performed a large-scale single-sample metagenomic assembly on 3304 soil metagenomes across the globe (Fig. 1a), including 363 metagenomes from the in-house dataset and 2941 from publicly available metagenomes. The soil samples were mainly collected from…

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facing Issue while runing the CORASON command line

facing Issue while runing the CORASON command line 0 I want to use the CORASON command line to derive the phylogenetic tree for one of the selected secondary metabolite from bacterial genomes. I previously ran antiSMASH to get the BGCs from bacterial genomes and used BiG-SCAPE to get the gene…

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The leaderless communication peptide (LCP) class of quorum-sensing peptides is broadly distributed among Firmicutes

Leaderless communication peptide (LCP) system is broadly distributed To assess the distribution of SIP-like LCP-based qs systems across bacteria, we employed a large-scale search strategy that includes: (i) search for RopB homologs across a dataset of 129,001 bacterial genomes and 9,421 reference metagenomics-assembled genomes (MAGs), (ii) probing the genomic vicinity…

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Science: Metagenome sequencing reveals pathogen-mediated plant endophytes

Yi Gene|Science: Metagenome sequencing reveals pathogenic bacteria-mediated activation of plant endophyte disease-suppressive function Using metagenomics techniques of plant endophytes, researchers such as Carrión of the Netherlands Institute for Ecology have shown that certain “resident” bacteria can protect plant roots from fungal infection. It is revealed that microorganisms living inside plant…

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Input format for BiG-SLiCE

Input format for BiG-SLiCE 0 Hi, I have used the antiSMASH program to derive the biosynthetic gene cluster (BGC) from analyzing bacterial genome. At present, I want to use BiG-SLiCE program to cluster the homologous BGCs into Gene Cluster Families (GCFs). I would like to know if anyone can help…

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Metagenomics reveals the habitat specificity of biosynthetic potential of secondary metabolites in global food fermentations

Background: Fermented foods are considered to be beneficial for human health. Secondary metabolites determined by biosynthetic gene clusters (BGCs) are precious bioactive compounds with various biological activities. However, the diversity and distribution of the biosynthetic potential of secondary metabolites in global food fermentations remain largely unknown. In this study, we…

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Metagenomics Helps Reveal Microbial Pathogenic Mechanisms

Metagenomics is a new generation of high-throughput sequencing (NGS) technology that takes the microbial population genome in a specific environment as the research object. Based on the analysis of microbial diversity, population structure and evolutionary relationship, it can further explore the functional activity of microbial population, the relationship between mutual…

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Ancient Bacterial Natural Products Revived from Neanderthal Tooth Tartar

Researchers headed by teams at the Leibniz Institute for Natural Product Research and Infection Biology at the Max Planck Institute for Evolutionary Anthropology, and at Harvard University, have reconstructed the bacterial genomes of previously unknown bacteria, from the calcified dental plaque of human and Neanderthal remains. Using these genetic blueprints,…

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Scientists Reconstruct Pleistocene Bacterial Metabolites to Revive Natural Products

Reconstructing the bacterial genomes recovered from the calcified plaque of human and Neanderthal remains has offered new insights into previously undescribed Pleistocene bacterial metabolites, researchers report. The approach expands researchers ability to study microbial natural products, which has otherwise been mostly limited to studying living bacteria. Bioactive small molecules produced…

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JoF | Free Full-Text | Genome Sequencing and Analysis Reveal Potential High-Valued Metabolites Synthesized by Lasiodiplodia iranensis DWH-2

Lasiodiplodia belongs to the fungal family Botryosphaeriaceae, which thrives on a wide range of monocotyledonous, dicotyledonous, and gymnosperm hosts, on woody branches, herbaceous leaves, and grasses, causing die-back and canker diseases in numerous woody hosts [1], such as Mangifera indica [2], Prunus persica [3], Saccharum officinarum [4], and Vitis vinifera…

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Adaptations of Pseudoxylaria towards a comb-associated lifestyle in fungus-farming termite colonies

Genome reduction is associated with a termite comb-associated lifestyle For our studies, we collected fungus comb samples originating from mounds of Macrotermes natalensis, Odontotermes spp., and Microtermes spp. termites and were able to obtain seven viable Pseudoxylaria cultures (X802 [Microtermes sp.], Mn132, Mn153, X187, X3-2 [Macrotermes natalensis], and X167, X170LB [Odontotermes…

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A first insight into the Polish Bochnia Salt Mine metagenome

Sequencing statistics NGS was used across the V3-V4 region of the 16S rRNA gene to sequence 24 environmental samples. The mean number of ASVs per sample obtained after DADA2 was 72,050 ± 31,480, ranging from 22,568 to 143,267. From a total of 1,729,209 contigs remaining after quality control and removal of chimeras,…

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Scripts for BGC analysis in large MAGs and results of their application to soil metagenomes within Chernevaya Taiga RSF-funded project

This repository include scripts for analysis of biosynthetic gene clusters (BGCs) in large metagenome assemblies. All scripts were created within the Chernevaya Taiga project funded by the Russian Science Foundation (grant 19-16-00049). The repository also contains results of the scripts application to four hybrid (illumina + ONT) assemblies of various…

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Bacterial endosymbionts protect beneficial soil fungus from nematode attack

A healthy soil nourishes plants and animals, purifies water and air, and promotes sustainable agriculture. Characteristic for highly complex and competitive soil ecosystems are the frequent and direct interactions between all soil-dwelling microorganisms, animals, and plants (1, 2), all of which need to be provided with minerals and carbon sources….

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antiSMASH output

antiSMASH output 0 Hello. Can someone help me to interpret the antiSMASH output and the count number of BGCs by using command line. It would be great to receive your help. Thank you RESULTS antiSMASH • 65 views Login before adding your answer. Source link

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