scholarly journals Whole-genome sequencing of two Streptomyces strains isolated from the sand dunes of Sahara

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Chahira Zerouki ◽  
Farid Bensalah ◽  
Suvi Kuittinen ◽  
Ari Pappinen ◽  
Ossi Turunen
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Uv Light ◽  
Sand Dunes ◽  
Gene Clusters ◽  
Extreme Environment ◽  
Climatic Conditions ◽  
Whole Genome ◽  
Protein Coding ◽  
Algerian Sahara

Abstract Background Sahara is one of the largest deserts in the world. The harsh climatic conditions, especially high temperature and aridity lead to unique adaptation of organisms, which could be a potential source of new metabolites. In this respect, two Saharan soils from El Oued Souf and Beni Abbes in Algeria were collected. The bacterial isolates were selected by screening for antibacterial, antifungal, and enzymatic activities. The whole genomes of the two native Saharan strains were sequenced to study desert Streptomyces microbiology and ecology from a genomic perspective. Results Strains Babs14 (from Beni Abbes, Algeria) and Osf17 (from El Oued Souf, Algeria) were initially identified by 16S rRNA sequencing as belonging to the Streptomyces genus. The whole genome sequencing of the two strains was performed using Pacific Biosciences Sequel II technology (PacBio), which showed that Babs14 and Osf17 have a linear chromosome of 8.00 Mb and 7.97 Mb, respectively. The number of identified protein coding genes was 6910 in Babs14 and 6894 in Osf17. No plasmids were found in Babs14, whereas three plasmids were detected in Osf17. Although the strains have different phenotypes and are from different regions, they showed very high similarities at the DNA level. The two strains are more similar to each other than either is to the closest database strain. The search for potential secondary metabolites was performed using antiSMASH and predicted 29 biosynthetic gene clusters (BGCs). Several BGCs and proteins were related to the biosynthesis of factors needed in response to environmental stress in temperature, UV light and osmolarity. Conclusion The genome sequencing of Saharan Streptomyces strains revealed factors that are related to their adaptation to an extreme environment and stress conditions. The genome information provides tools to study ecological adaptation in a desert environment and to explore the bioactive compounds of these microorganisms. The two whole genome sequences are among the first to be sequenced for the Streptomyces genus of Algerian Sahara. The present research was undertaken as a first step to more profoundly explore the desert microbiome.

scholarly journals Whole-genome Sequencing of Two Streptomyces Strains Isolated From Sand Dunes of Sahara

2020 ◽  
Author(s):  
Chahira Zerouki ◽  
Farid Bensalah ◽  
Suvi Kuittinen ◽  
Ari Pappinen ◽  
Ossi Turunen
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Uv Light ◽  
Sand Dunes ◽  
Gene Clusters ◽  
Extreme Environment ◽  
Whole Genome ◽  
16S Rrna Sequence ◽  
Algerian Sahara ◽  
Genome Duplications

Abstract Background. Sahara is one of the largest deserts in the world. The hard conditions especially high temperature and aridity lead to unique adaptation of organisms that could be a potential source of new metabolites. In this respect, two Saharan soils from El Oued Souf and Beni Abbes in Algeria were collected. The bacterial isolates were selected by screening the antibacterial, antifungal, and enzymatic activities. The whole genomes of the two native Saharan strains were sequenced to study the desert Streptomyces microbiology and ecology from genomic perspective. Results. The strains Babs14 (from Beni Abbes, Algeria) and Osf17 (from El Oued Souf, Algeria) were initially identified by 16S rRNA sequence as belonging to the Streptomyces genus. The whole genome sequencing of the two strains was performed by using Pacific Biosciences Sequel II technology (PacBio) and it showed that Babs14 and Osf17 have a linear chromosome of 8.00 Mb and 7.97 Mb, respectively. The number of identified proteins is 6910 in Babs14 and 6894 in Osf17. No plasmids were found in Babs14, whereas three plasmids were detected in Osf17 and no genome duplications were detected in the two strains. Although the strains have different phenotypes and are from different regions, they are slightly different from each other in protein sequence level but, differ more from their earlier published relatives. 29 biosynthetic gene clusters (BGCs) coding for secondary metabolites were predicted in each strain indicating antifungal, antibiotic, and other activities of Babs14 and Osf17. Moreover, many other BGCs were related to biosynthesis of factors needed in response to environmental stress in temperature, UV light and osmolarity. Conclusion. The genome sequencing of Saharan Streptomyces strains revealed factors that are related to their adaptation to an extreme environment and stress conditions. The genome information gives tools to study the ecological adaptation in desert environment and to explore the bioactive compounds of these microorganisms. The two whole genome sequences are among the first ones for the Streptomyces genus of Algerian Sahara. The present research was undertaken as a first step to explore more profoundly the desert microbiome.

scholarly journals Whole-genome sequencing of the endemic Antarctic fungus Antarctomyces pellizariae reveals an ice-binding protein, a scarce set of secondary metabolites gene clusters and provides insights on Thelebolales phylogeny

Genomics ◽  
2020 ◽  
Vol 112 (5) ◽  
pp. 2915-2921 ◽  
Author(s):  
Thiago Mafra Batista ◽  
Heron Oliveira Hilario ◽  
Gabriel Antônio Mendes de Brito ◽  
Rennan Garcias Moreira ◽  
Carolina Furtado ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Binding Protein ◽  
Protein A ◽  
Gene Clusters ◽  
Whole Genome ◽  
Ice Binding ◽  
Ice Binding Protein

scholarly journals Bacillus velezensis UTB96 Is an Antifungal Soil Isolate with a Reduced Genome Size Compared to That of Bacillus velezensis FZB42

2019 ◽  
Vol 8 (38) ◽  
Author(s):  
Maliheh Vahidinasab ◽  
Masoud Ahmadzadeh ◽  
Marius Henkel ◽  
Rudolf Hausmann ◽  
Kambiz Morabbi Heravi
Keyword(s):  
Antifungal Activity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Gene Clusters ◽  
Type I ◽  
Whole Genome ◽  
Bacillus Velezensis ◽  
Content Type ◽  
Reduced Genome ◽  
Soil Isolate

Bacillus velezensis UTB96 was isolated from soil based on its antifungal activity. Whole-genome sequencing of strain UTB96 provided further information about its secondary metabolite gene clusters. Compared to the well-known strain FZB42, UTB96 lacks an IS3 element and a type I restriction endonuclease.

scholarly journals Whole genome sequencing of four bacterial strains from South Shetland Trench revealing biosynthetic and environmental adaptation gene clusters

2020 ◽  
Vol 54 ◽  
pp. 100782 ◽  
Author(s):  
Wael M. Abdel-Mageed ◽  
Burhan Lehri ◽  
Scott A. Jarmusch ◽  
Kevin Miranda ◽  
Lamya H. Al-Wahaibi ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Gene Clusters ◽  
Environmental Adaptation ◽  
Whole Genome ◽  
Bacterial Strains ◽  
South Shetland Trench

Can multidrug-resistant organisms become resistant to ultraviolet (UV) light following serial exposures? Characterization of post-UV genomic changes using whole-genome sequencing

2021 ◽  
pp. 1-7
Author(s):  
Hosoon Choi ◽  
Piyali Chatterjee ◽  
Munok Hwang ◽  
Eileen M. Stock ◽  
Janell S. Lukey ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Uv Light ◽  
Multidrug Resistant ◽  
Uv Disinfection ◽  
Whole Genome ◽  
Uv Resistance ◽  
Kill Rate ◽  
Uv Lamp

Abstract Objectives: No-touch disinfection systems like xenon- or mercury-based ultraviolet (UV) are now commonly being used for hospital room disinfection. However, serial exposure to UV light can potentially lead to the development of bacterial resistance. We sought to determine whether UV resistance develops due to serial exposure to UV light using 3 epidemiologically important multidrug-resistant microbial strains. Methods: Methicillin-resistant Staphylococcus aureus (MRSA), carbapenemase–producing Klebsiella pneumoniae (KPC) and metallo-β-lactamase–producing Klebsiella pneumoniae (MBL) were serially exposed to 25 growth-irradiation cycles of UV produced by a xenon-based UV (Xe-UV) lamp for 5 minutes or a mercury-based UV (Hg-UV) lamp for 10 minutes. After each UV exposure cycle, the surviving colony-forming units (CFUs) were measured and compared with the initial inoculum of each cycle for each strain, respectively. Results: In each cycle, ˜1–10 million of MRSA, KPC, and MBL were used to test the effect of UV irradiation. Postexposure colony counts remained low (3–100 colonies) throughout the 25 serial exposures to both xenon- and mercury-based UV. The log-kill rate after each exposure showed no changes following UV disinfection by Xe-UV. The MRSA log-kill rate increased after repeated exposure to Hg-UV unlike KPC and MBL K. pneumoniae, which did not change. Whole-genome sequencing (WGS) analyses performed on these 3 strains demonstrated no significant genetic changes after multiple UV irradiation cycles. Conclusions: Exposure of multidrug-resistant bacteria to UV produced from 2 different UV sources did not engender UV resistance after 25 serial exposures, as demonstrated by WGS analysis; thus, UV disinfection is unlikely to generate UV-resistant hospital flora.

scholarly journals Secondary metabolites from hypocrealean entomopathogenic fungi: genomics as a tool to elucidate the encoded parvome

2020 ◽  
Vol 37 (9) ◽  
pp. 1164-1180 ◽  
Author(s):  
Liwen Zhang ◽  
Qun Yue ◽  
Chen Wang ◽  
Yuquan Xu ◽  
István Molnár
Keyword(s):  
Secondary Metabolites ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bioactive Compounds ◽  
Entomopathogenic Fungi ◽  
Gene Clusters ◽  
Whole Genome ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters

Whole genome sequencing allows the cataloguing of the parvome (secondary metabolome) of hypocrealean entomopathogenic fungi, uncovering biosynthetic gene clusters for known and novel bioactive compounds with ecological and pharmaceutical significance.

scholarly journals Whole-Genome Sequencing of Sinocyclocheilus maitianheensis Reveals Phylogenetic Evolution and Immunological Variances in Various Sinocyclocheilus Fishes

2021 ◽  
Vol 12 ◽  
Author(s):  
Ruihan Li ◽  
Xiaoai Wang ◽  
Chao Bian ◽  
Zijian Gao ◽  
Yuanwei Zhang ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Assembly ◽  
Genetic Resource ◽  
Whole Genome ◽  
Protein Coding ◽  
A Genome ◽  
Surface Dwelling ◽  
Phylogenetic Evolution ◽  
Comparative Phylogenetic Analysis

An adult Sinocyclocheilus maitianheensis, a surface-dwelling golden-line barbel fish, was collected from Maitian river (Kunming City, Yunnan Province, China) for whole-genome sequencing, assembly, and annotation. We obtained a genome assembly of 1.7 Gb with a scaffold N50 of 1.4 Mb and a contig N50 of 24.7 kb. A total of 39,977 protein-coding genes were annotated. Based on a comparative phylogenetic analysis of five Sinocyclocheilus species and other five representative vertebrates with published genome sequences, we found that S. maitianheensis is close to Sinocyclocheilus anophthalmus (a cave-restricted species with similar locality). Moreover, the assembled genomes of S. maitianheensis and other four Sinocyclocheilus counterparts were used for a fourfold degenerative third-codon transversion (4dTv) analysis. The recent whole-genome duplication (WGD) event was therefore estimated to occur about 18.1 million years ago. Our results also revealed a decreased tendency of copy number in many important genes related to immunity and apoptosis in cave-restricted Sinocyclocheilus species. In summary, we report the first genome assembly of S. maitianheensis, which provides a valuable genetic resource for comparative studies on cavefish biology, species protection, and practical aquaculture of this potentially economical fish.

scholarly journals Whole genome sequencing delineates regulatory and novel genic variants in childhood cardiomyopathy

2020 ◽  
Author(s):  
Robert Lesurf ◽  
Abdelrahman Said ◽  
Oyediran Akinrinade ◽  
Jeroen Breckpot ◽  
Kathleen Delfosse ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Disorder ◽  
Regulatory Elements ◽  
Whole Genome ◽  
Loss Of Function ◽  
Protein Coding ◽  
Human Cardiomyocytes ◽  
Regulatory Variants ◽  
Coding Variants

ABSTRACTCardiomyopathy (CMP) is a heritable genetic disorder. Protein-coding variants account for 20-30% of cases. The contribution of variants in non-coding DNA elements that regulate gene expression has not been explored. We performed whole-genome sequencing (WGS) of 228 unrelated CMP families. Besides pathogenic protein-coding variants in known CMP genes, 5% cases harbored rare loss-of-function variants in novel cardiac genes, with NRAP and FHOD3 being strong candidates. WGS also revealed a high burden of high-risk variants in promoters and enhancers of CMP genes in an additional 20% cases (Odds ratio 2.14, 95% CI 1.60-2.86, p=5.26×10−7 vs 1326 controls) with genes involved in α-dystroglycan glycosylation (FKTN, DTNA) and desmosomal signaling (DSC2, DSG2) specifically enriched for regulatory variants (False discovery rate <0.03). These findings were independently replicated in the Genomics England CMP cohort (n=1266). The functional effect of non-coding variants on transcription was functionally validated in patient myocardium and reporter assays in human cardiomyocytes, and that of novel gene variants in zebrafish knockouts. Our results show that functionally active variants in novel genes and in regulatory elements of CMP genes contribute strongly to the genomic etiology of childhood-onset CMP.

scholarly journals De Novo Mutation in an Enhancer of EBF3 in simplex autism

2020 ◽  
Author(s):  
Evin M. Padhi ◽  
Tristan J. Hayeck ◽  
Brandon Mannion ◽  
Sumantra Chatterjee ◽  
Marta Byrska-Bishop ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
De Novo ◽  
Neurodevelopmental Disorder ◽  
De Novo Mutation ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Enhancer Activity ◽  
Protein Coding

AbstractPrevious research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of de novo protein-coding variants within specific genes. The role of de novo noncoding variation has been observable as a general increase in genetic burden but has yet to be resolved to individual functional elements. In this study, we assessed whole-genome sequencing data in 2,671 families with autism, with a specific focus on de novo variation in enhancers with previously characterized in vivo activity. We identified three independent de novo mutations limited to individuals with autism in the enhancer hs737. These mutations result in similar phenotypic characteristics, affect enhancer activity in vitro, and preferentially occur in AAT motifs in the enhancer with predicted disruptions of transcription factor binding. We also find that hs737 is enriched for copy number variation in individuals with NDDs, is dosage sensitive in the human population, is brain-specific, and targets the NDD gene EBF3 that is genome-wide significant for protein coding de novo variants, demonstrating the importance of understanding all forms of variation in the genome.One Sentence SummaryWhole-genome sequencing in thousands of families reveals variants relevant to simplex autism in a brain enhancer of the well-established neurodevelopmental disorder gene EBF3.

Sign in / Sign up

Export Citation Format

Share Document