Efficiently Constructing Complete Genomes with CycloneSEQ to Fill Gaps in Bacterial Draft Assemblies DOI Creative Commons
Hewei Liang, Mengmeng Wang, Tongyuan Hu

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 7, 2024

Abstract Background Current microbial sequencing relies on short-read platforms like Illumina and DNBSEQ, favored for their low cost high accuracy. However, these methods often produce fragmented draft genomes, hindering comprehensive bacterial function analysis. CycloneSEQ, a novel long-read platform developed by BGI-Research, its performance assembly improvements has been evaluated. Findings Using CycloneSEQ sequencing, the type strain produced long reads with an average length of 11.6 kbp quality score 14.4. After hybrid short data, assembled genome exhibited error rate only 0.04 mismatches 0.08 indels per 100 compared to reference genome. This method was validated across 9 diverse species, successfully assembling complete circular genomes. Hybrid significantly enhances completeness using fill gaps accurately assemble multi-copy rRNA genes, which unable be achieved solely. Through data subsampling, we found that over 500 Mbp combined can result in high-quality assembly. Additionally, effectively improves genomes from mixed communities. Conclusions CycloneSEQ’s read is sufficient but base needs improvement. Integrating DNBSEQ improved accuracy, resulting accurate assemblies. efficient approach widely applied sequencing.

Language: Английский

Pangenome mining of the Streptomyces genus redefines species’ biosynthetic potential DOI Creative Commons
Omkar S. Mohite, Tue Sparholt Jørgensen, Thomas Booth

et al.

Genome biology, Journal Year: 2025, Volume and Issue: 26(1)

Published: Jan. 14, 2025

Background Streptomyces is a highly diverse genus known for the production of secondary or specialized metabolites with wide range applications in medical and agricultural industries. Several thousand complete nearly genome sequences are now available, affording opportunity to deeply investigate biosynthetic potential within these organisms advance natural product discovery initiatives. Results We perform pangenome analysis on 2371 genomes, including approximately 1200 assemblies. Employing data-driven approach based similarities, was classified into 7 primary 42 Mash-clusters, forming basis comprehensive mining. A refined workflow grouping gene clusters (BGCs) redefines their diversity across different Mash-clusters. This also reassigns 2729 BGC families only 440 families, reduction caused by inaccuracies boundary detections. When genomic location BGCs included analysis, conserved structure, synteny, among becomes apparent species synteny suggests that vertical inheritance major factor diversification BGCs. Conclusions Our dataset at scale thousands genomes refines predictions using Mash-clusters as analysis. The observed conservation order BGCs’ locations shows vertically inherited. presented in-depth pave way large-scale investigations enhance our understanding genus.

Language: Английский

Citations

1
Enabling Access to Novel Bacterial Biosynthetic Potential From ONT Draft Genomic Data DOI Creative Commons
Marco A. Campos‐Magaña, Vítor A. P. Martins dos Santos, Luis Garcia Morales

et al.

Microbial Biotechnology, Journal Year: 2025, Volume and Issue: 18(3)

Published: March 1, 2025

Natural products comprise a wide diversity of compounds with range biological activities, including antibiotics, anti-inflammatory and anti-tumoral molecules. However, we can only access small portion these due to various technical difficulties. We have herein developed novel efficient approach for accessing biosynthetic gene clusters (BGCs) that encode natural from soil bacteria. The pipeline uses combination long-read sequencing, antiSMASH BGC identification Transformation-associated recombination (TAR) cloning the BGCs. hypothesized genome assembly using Oxford Nanopore Technology (ONT) sequencing could facilitate detection large BGCs at relatively fast low-cost DNA sequencing. Despite relative low accuracy sequence mistakes high GC content repetitions frequently found in containing bacteria, demonstrate ONT are effective identifying enabling TAR isolate desired vector. applied this on previously non-sequenced myxobacteria Aetherobacter fasciculatus SBSr002. Our enabled us clone unknown into engineering-ready vector, illustrating capabilities powerful cost-effective strategy.

Language: Английский

Citations

0
Integrative metabolo-genomics suggests a biosynthetic pathway for tetrangulol in Streptomyces sp. KL110A DOI Creative Commons
Luisa M. Trejo-Alarcon, Carolina Cano‐Prieto, Ana Calheiros de Carvalho

et al.

World Journal of Microbiology and Biotechnology, Journal Year: 2025, Volume and Issue: 41(3)

Published: March 1, 2025

Natural products (NPs) of microbial origin are highly valued for their diverse bioactive properties. Among bacteria, Streptomyces stands out as a prolific source NPs with applications in medicine and agriculture. Recent advances metabolomics, bioinformatics well the abundance genomic data have revolutionized study NPs, enabling rapid connection biosynthetic pathways metabolites. However, discovering novel compounds from large pools genomes strains is cumbersome. Metabolo-genomics approaches promising strategies that can save time resources at initial stages natural product discovery pipeline by rapidly linking molecules genes. Here, we present characterization metabolomic profiling sp. KL110A, strain isolated rainforest soils Calakmul, Campeche Mexico. Using genome mining tools LC-MS/MS identified characterized known gene clusters (BGCs) proposed mechanism biosynthesis benz(a)anthraquinone tetrangulol. Our findings underscore relevance integrating elucidating pathways, positively contributing to field research.

Language: Английский

Citations

0
Exploring new natural products by utilizing untapped secondary metabolic pathways in actinomycetes DOI
Shotaro Hoshino

Journal of Natural Medicines, Journal Year: 2025, Volume and Issue: unknown

Published: April 4, 2025

Language: Английский

Citations

0
Genomic characteristics, virulence potential, antimicrobial resistance profiles, and phylogenetic insights into Nocardia cyriacigeorgica DOI Creative Commons
Yang Chen, Yuan Zheng,

Hong-Yi Gu

et al.

Annals of Clinical Microbiology and Antimicrobials, Journal Year: 2025, Volume and Issue: 24(1)

Published: April 5, 2025

Nocardia cyriacigeorgica, an opportunistic pathogen, is increasingly implicated in human infections. This pathogen predominantly causes pulmonary infections, leading to acute, subacute, or chronic necrotizing suppurative lesions, severe cases, may progress disseminated Effective clinical diagnosis, prevention, and treatment strategies require a thorough understanding of its biological characteristics pathogenic mechanisms. However, despite the rising incidence nocardial diseases, research on pathogenicity N. cyriacigeorgica remains limited, primarily focusing case reports epidemiological studies. study aimed provide comprehensive analysis genomic features, phylogenetic relationships, antimicrobial resistance profiles, candidate virulence factors strains inform future investigations into pathogenesis. Whole-genome sequencing was conducted five isolated from patients with infection at our hospital. utilized combination second-generation Illumina HiSeq third-generation PacBio technologies. Additionally, publicly available data 58 National Center Biotechnology Information database were integrated, resulting dataset 63 genomes. These genomes subjected comparative analyses, including reconstruction, pan-genome evaluation, gene distribution assessments. Phylogenetic identified major clades within cyriacigeorgica. ANI further subdivided clade B distinct subgroups. Pan-genome revealed clade-specific orthogroups genes assigned Clusters Orthologous Groups, A containing highest number families. Comparative uncovered several potential host cell invasion, phagosomal maturation arrest, intracellular survival macrophages, which conserved across all analyzed strains. Notable differences enterobactin-encoding observed among clades. The mce3C also displayed variable distributions clades; however, no correlation established between presence strain source. Among strains, 27 found harbor both mce4F genes, categorized patterns. Furthermore, antibiotic VanSO, VanRO, erm(O)-Irm, srmB, ermH, bcl, bla1, cmIR, demonstrated Notably, ermH associated isolation origin provides evaluation characteristics, factors, relationships findings offer valuable insights mechanisms underlying survival, replication pathogen-host interactions results establish foundation for pathogenesis management

Language: Английский

Citations

0
Efficiently constructing complete genomes with CycloneSEQ to fill gaps in bacterial draft assemblies DOI Creative Commons
Hewei Liang, Yuanqiang Zou,

Mengmeng Wang

et al.

Gigabyte, Journal Year: 2025, Volume and Issue: 2025

Published: April 25, 2025

Current microbial sequencing relies on short-read platforms like Illumina and DNBSEQ, which are cost-effective accurate but often produce fragmented draft genomes. Here, we used CycloneSEQ for long-read of ATCC BAA-835, producing long-reads with an average length 11.6 kbp quality score 14.4. Hybrid assembly short-reads data resulted in error rate only 0.04 mismatches 0.08 indels per 100 compared to the reference genome. This method, validated across nine species, successfully assembled complete circular significantly enhances genome completeness by using fill gaps accurately assembling multi-copy rRNA genes, unlike alone. Data subsampling showed that combining over 500 Mbp yields high-quality assemblies. improves genomes from mixed communities; however, its base needs improving. Integrating DNBSEQ improved accuracy, resulting

Language: Английский

Citations

0
Regulation of daptomycin biosynthesis in Streptomyces roseosporus: new insights from genomic analysis and synthetic biology to accelerate lipopeptide discovery and commercial production DOI
Richard H. Baltz

Natural Product Reports, Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 1, 2024

Complex regulatory mechanisms govern daptomycin biosynthesis in Streptomyces roseosporus . Ten genes modulate transcription of biosynthetic from a single promoter, and translation is coordinated by translational coupling.

Language: Английский

Citations

1
The chemical ecology and physiological functions of type I polyketide natural products: the emerging picture DOI
R François,

Jean-Malo Massicard,

Kira J. Weissman

et al.

Natural Product Reports, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 18, 2024

Covering: up to 2024.For many years, the value of complex polyketides lay in their medical properties, including antibiotic and antifungal activities, with little consideration paid native functions. However, more recent evidence gathered from study inter-organismal interactions has revealed influence these metabolites upon ecological adaptation distribution hosts, as well modes communication. The increasing number sequenced genomes associated transcriptomes also unveiled widespread occurrence underlying biosynthetic enzymes across all kingdoms life, important contributions they make physiological events specific each organism. This review depicts diversity roles fulfilled by type I polyketides, particularly light studies carried out during last decade, providing an initial overall picture diverse

Language: Английский

Citations

1
Efficiently Constructing Complete Genomes with CycloneSEQ to Fill Gaps in Bacterial Draft Assemblies DOI Creative Commons
Hewei Liang, Mengmeng Wang, Tongyuan Hu

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 7, 2024

Abstract Background Current microbial sequencing relies on short-read platforms like Illumina and DNBSEQ, favored for their low cost high accuracy. However, these methods often produce fragmented draft genomes, hindering comprehensive bacterial function analysis. CycloneSEQ, a novel long-read platform developed by BGI-Research, its performance assembly improvements has been evaluated. Findings Using CycloneSEQ sequencing, the type strain produced long reads with an average length of 11.6 kbp quality score 14.4. After hybrid short data, assembled genome exhibited error rate only 0.04 mismatches 0.08 indels per 100 compared to reference genome. This method was validated across 9 diverse species, successfully assembling complete circular genomes. Hybrid significantly enhances completeness using fill gaps accurately assemble multi-copy rRNA genes, which unable be achieved solely. Through data subsampling, we found that over 500 Mbp combined can result in high-quality assembly. Additionally, effectively improves genomes from mixed communities. Conclusions CycloneSEQ’s read is sufficient but base needs improvement. Integrating DNBSEQ improved accuracy, resulting accurate assemblies. efficient approach widely applied sequencing.

Language: Английский

Citations

0