Draft genome sequence of Streptomyces tunisialbus DSM 105760T

Ayed, Ameni; Wibberg, Daniel; Euch, Imene Zendah El; Frese, Marcel; Limam, Férid; Sewald, Norbert

doi:10.1007/s00203-020-01913-z

Cited by 2 publications

(2 citation statements)

References 26 publications

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“…Recently, a draft genome was published ( 30 ) for Streptomyces tunisialbus , a new streptomycete isolated from the rhizospheric soil of lavender plants ( Lavandula officinalis ) in Tunisia ( 31 ). To showcase how BiG-FAM can be used to assess biosynthetic novelty and capture distant relationships of newly sequenced BGCs, we downloaded the assembled genome from ENA (accession: OKRJ01) and uploaded it to the antiSMASH web server ( http://antismash.secondarymetabolites.org/ ), returning a unique job id (‘bacteria/fungi-xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx’) which (after the run is done) can then directly be used to perform GCF analysis in BiG-FAM ( https://bigfam.bioinformatics.nl/query ) (Figure 4A ).…”

Section: Example Use Casesmentioning

confidence: 99%

BiG-FAM: the biosynthetic gene cluster families database

Kautsar

Blin

Shaw

et al. 2020

Nucleic Acids Research

169

129

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Computational analysis of biosynthetic gene clusters (BGCs) has revolutionized natural product discovery by enabling the rapid investigation of secondary metabolic potential within microbial genome sequences. Grouping homologous BGCs into Gene Cluster Families (GCFs) facilitates mapping their architectural and taxonomic diversity and provides insights into the novelty of putative BGCs, through dereplication with BGCs of known function. While multiple databases exist for exploring BGCs from publicly available data, no public resources exist that focus on GCF relationships. Here, we present BiG-FAM, a database of 29,955 GCFs capturing the global diversity of 1,225,071 BGCs predicted from 209,206 publicly available microbial genomes and metagenome-assembled genomes (MAGs). The database offers rich functionalities, such as multi-criterion GCF searches, direct links to BGC databases such as antiSMASH-DB, and rapid GCF annotation of user-supplied BGCs from antiSMASH results. BiG-FAM can be accessed online at https://bigfam.bioinformatics.nl.

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Section: Example Use Casesmentioning

confidence: 99%

BiG-FAM: the biosynthetic gene cluster families database

Kautsar

Blin

Shaw

et al. 2020

Nucleic Acids Research

169

129

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“…It has gained much attention among researchers because it produces various secondary metabolites. They can produce over 10,000 bioactive compounds, accounting for around 65% of the total microbial secondary metabolites identi ed (Ayed et al 2020). The members of the genus Streptomyces are considered essential in the pharmaceutical industry due to their tremendous contribution to the therapeutic and industrial segments (Antoraz et al 2015).…”

Section: Introductionmentioning

confidence: 99%

The whole-genome shotgun sequence of a chitinolytic actinomycete, Streptomyces californicus TBG-201, and the in-silico studies of its chitinase-19 genes

Sreela¹,

Salim

Satheesan

et al. 2023

Preprint

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Streptomyces species are reported to have family-19 chitinases, similar to plant chitinase-C. Streptomyces griseus HUT6037 is the first Streptomyces spp. found to produce family-19 chitinase. Chitinolytic Streptomyces have been reported to have antifungal activity against phytopathogenic fungi. Chitinase-19 (GH-19) has received much attention in recent decades because of its potential use in the biocontrol of phytopathogens like insects and fungi. According to reports, chitinase C has a significantly higher specific hydrolyzing activity than the common bacterial family-18 chitinases. This study presents the whole genome sequence of a chitinolytic isolate, S. californicus TBG-201. The genome is 7.99 Mb, with 72.60% G + C content, 6683 protein-coding genes, 31 rRNAs, 66 tRNAs, and 116 pseudogenes. Genome annotation using Glimmer, PGAP, and dbCAN provides insights into its chitinolytic activity. Multiple genes in the genome are involved in chitin degradation; based on this, a chitin degradation mechanism for S. californicus TBG-201 is presented. There are 35 biosynthetic gene clusters predicted from the whole genome sequence using the antiSMASH tool. The study further focused on the in-silico analysis of chitinase-19 genes, including phylogenetic analysis, physicochemical characterization, and functional studies. Homology modeling using the SWISS-MODEL server followed by docking studies has a better understood the enzyme structure and ligand binding features. The insights gathered from in-silico investigations would greatly assist in elucidating the in vitro characteristics of S. californicus chitinase-19.

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Draft genome sequence of Streptomyces tunisialbus DSM 105760T

Cited by 2 publications

References 26 publications

BiG-FAM: the biosynthetic gene cluster families database

BiG-FAM: the biosynthetic gene cluster families database

The whole-genome shotgun sequence of a chitinolytic actinomycete, Streptomyces californicus TBG-201, and the in-silico studies of its chitinase-19 genes

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