ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2014
Motif-independent prediction of a secondary metabolism gene cluster using comparative genomics: application to sequenced genomes of Aspergillus and ten other filamentous fungal species.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 51 citations in OpenAlex.
- Fungal production of kojic acid and its industrial applications.Applied microbiology and biotechnology · 2023Review
- Artificial intelligence in microbial natural product drug discovery: current and emerging role.Natural product reports · 2022Review
- How to Completely Squeeze a Fungus-Advanced Genome Mining Tools for Novel Bioactive Substances.Pharmaceutics · 2022Review
- Improving candidate Biosynthetic Gene Clusters in fungi through reinforcement learning.Bioinformatics (Oxford, England) · 2022Article
- Exploring Newer Biosynthetic Gene Clusters in Marine Microbial Prospecting.Marine biotechnology (New York, N.Y.) · 2022Review
- Navigating and expanding the roadmap of natural product genome mining tools.Beilstein journal of organic chemistry · 2022Article
- Metabolomics and genomics in natural products research: complementary tools for targeting new chemical entities.Natural product reports · 2021Review
- Genome-based engineering of ligninolytic enzymes in fungi.Microbial cell factories · 2021Review
- Advances in Genetic Engineering Technology and Its Application in the Industrial FungusFrontiers in microbiology · 2021Review
- An Integrated Approach to Determine the Boundaries of the Azaphilone Pigment Biosynthetic Gene Cluster ofFrontiers in microbiology · 2021Article
- TOUCAN: a framework for fungal biosynthetic gene cluster discovery.NAR genomics and bioinformatics · 2020Article
- The Integration of Genome Mining, Comparative Genomics, and Functional Genetics for Biosynthetic Gene Cluster Identification.Frontiers in genetics · 2020Article
- New Approaches to Detect Biosynthetic Gene Clusters in the Environment.Medicines (Basel, Switzerland) · 2019Review
- Bioinformatics tools for the identification of gene clusters that biosynthesize specialized metabolites.Briefings in bioinformatics · 2018Review
- Review
- Development of fungal cell factories for the production of secondary metabolites: Linking genomics and metabolism.Synthetic and systems biotechnology · 2017Review
- KdmB, a Jumonji Histone H3 Demethylase, Regulates Genome-Wide H3K4 Trimethylation and Is Required for Normal Induction of Secondary Metabolism in Aspergillus nidulans.PLoS genetics · 2016Article
- The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production.Synthetic and systems biotechnology · 2016Review
- Computational approaches to natural product discovery.Nature chemical biology · 2015Article
- Motif-independent de novo detection of secondary metabolite gene clusters-toward identification from filamentous fungi.Frontiers in microbiology · 2015Review
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite their biological importance, a significant number of genes for secondary metabolite biosynthesis (SMB) remain undetected due largely to the fact that they are highly diverse and are not expressed under a variety of cultivation conditions. Several software tools including SMURF and antiSMASH have been developed to predict fungal SMB gene clusters by finding core genes encoding polyketide synthase, nonribosomal peptide synthetase and dimethylallyltryptophan synthase as well as several others typically present in the cluster. In this work, we have devised a novel comparative genomics method to identify SMB gene clusters that is independent of motif information of the known SMB genes. The method detects SMB gene clusters by searching for a similar order of genes and their presence in nonsyntenic blocks. With this method, we were able to identify many known SMB gene clusters with the core genes in the genomic sequences of 10 filamentous fungi. Furthermore, we have also detected SMB gene clusters without core genes, including the kojic acid biosynthesis gene cluster of Aspergillus oryzae. By varying the detection parameters of the method, a significant difference in the sequence characteristics was detected between the genes residing inside the clusters and those outside the clusters.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.