Fukuia kurodai ooyagii is a freshwater snail endemic to the Shimokita Peninsula, Japan, yet little is known about its mitochondrial genome or phylogenetic position. To address this, we sequenced the mitochondrial genomes of five individuals. The genomes ranged from 16,145 to 16,169 bp and included all 37 typical animal mitochondrial genes. Gene arrangement and nucleotide composition were consistent with other Truncatelloidea species. The control region featured long inverted repeats and AT-repeat regions. Phylogenetic analysis placed F. kurodai ooyagii within the Pomatiopsidae family, with moderate support for a closer relationship to Tricula hortensis than to Oncomelania species. These results provide the first complete mitochondrial genome sequences for this species, confirming its evolutionary stability within Pomatiopsidae. However, due to the lack of mitochondrial data for other Fukuia and Blanfordia species, its precise taxonomic status remains uncertain. This study offers a foundation for future comparative analyses and highlights the need for broader taxon sampling and additional genomic data to resolve phylogenetic relationships within this group.
{"title":"Mitochondrial genome sequencing and phylogenetic analysis of the freshwater snail Fukuia kurodai ooyagii (Pomatiopsidae)","authors":"Yuuki Ebata , Akira Ooyagi , Kazuo Umetsu , Takashi Kitano","doi":"10.1016/j.genrep.2025.102365","DOIUrl":"10.1016/j.genrep.2025.102365","url":null,"abstract":"<div><div><em>Fukuia kurodai ooyagii</em> is a freshwater snail endemic to the Shimokita Peninsula, Japan, yet little is known about its mitochondrial genome or phylogenetic position. To address this, we sequenced the mitochondrial genomes of five individuals. The genomes ranged from 16,145 to 16,169 bp and included all 37 typical animal mitochondrial genes. Gene arrangement and nucleotide composition were consistent with other Truncatelloidea species. The control region featured long inverted repeats and AT-repeat regions. Phylogenetic analysis placed <em>F. kurodai ooyagii</em> within the Pomatiopsidae family, with moderate support for a closer relationship to <em>Tricula hortensis</em> than to <em>Oncomelania</em> species. These results provide the first complete mitochondrial genome sequences for this species, confirming its evolutionary stability within Pomatiopsidae. However, due to the lack of mitochondrial data for other <em>Fukuia</em> and <em>Blanfordia</em> species, its precise taxonomic status remains uncertain. This study offers a foundation for future comparative analyses and highlights the need for broader taxon sampling and additional genomic data to resolve phylogenetic relationships within this group.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102365"},"PeriodicalIF":0.9,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145358389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Transposable elements (TEs) are mobile genetic elements that can disrupt genomic integrity, influencing gene regulation and contributing to various diseases, including cancer. The accurate identification and characterization of TEs in high-throughput sequencing data is essential for understanding their role in genomic instability and tumorigenesis. To streamline this process, we developed MeX_Docker, a pipeline that utilizes Docker containerization to overcome software dependency issues and ensure reproducibility across different computing environments. Docker provides a standardized, portable solution that allows researchers to deploy and run the pipeline seamlessly, eliminating common obstacles in bioinformatics workflows. MeX_Docker integrates widely-used tools such as FastQC, Fastp, SAMtools, TEfinder, and Ensembl Variant Effect Predictor (VEP) for efficient data preprocessing, alignment, TE calling, and annotation. The pipeline was applied to human paired end whole-genome sequencing cancer datasets (breast, lung, and colorectal cancers), successfully identifying reference and non-reference Alu and L1 elements. In a lung cancer sample, an in-frame insertion in the CATSPERD gene was detected, which was classified as benign polymorphism. These findings highlight the use of MeX_Docker as an efficient tool for studying the impact of transposable elements on genomic instability and their potential role in cancer biology.
{"title":"MeX_Docker: An integrated application for transposon identification and annotation based on the Docker platform","authors":"P. Preeti , Mihir Nakul , Chhavi Dudeja , Abhishek Singh , Arushi Gupta , Yuktika Malhotra , Deepika Yadav , Kamal Rawal","doi":"10.1016/j.genrep.2025.102364","DOIUrl":"10.1016/j.genrep.2025.102364","url":null,"abstract":"<div><div>Transposable elements (TEs) are mobile genetic elements that can disrupt genomic integrity, influencing gene regulation and contributing to various diseases, including cancer. The accurate identification and characterization of TEs in high-throughput sequencing data is essential for understanding their role in genomic instability and tumorigenesis. To streamline this process, we developed MeX_Docker, a pipeline that utilizes Docker containerization to overcome software dependency issues and ensure reproducibility across different computing environments. Docker provides a standardized, portable solution that allows researchers to deploy and run the pipeline seamlessly, eliminating common obstacles in bioinformatics workflows. MeX_Docker integrates widely-used tools such as FastQC, Fastp, SAMtools, TEfinder, and Ensembl Variant Effect Predictor (VEP) for efficient data preprocessing, alignment, TE calling, and annotation. The pipeline was applied to human paired end whole-genome sequencing cancer datasets (breast, lung, and colorectal cancers), successfully identifying reference and non-reference Alu and L1 elements. In a lung cancer sample, an in-frame insertion in the CATSPERD gene was detected, which was classified as benign polymorphism. These findings highlight the use of MeX_Docker as an efficient tool for studying the impact of transposable elements on genomic instability and their potential role in cancer biology.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102364"},"PeriodicalIF":0.9,"publicationDate":"2025-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145412788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-18DOI: 10.1016/j.genrep.2025.102363
Junjie Wang , Xiaoqin Li , Xinghai Li , Yang Xu , Cuihua Xin , Jiangbo Guo
SKP1 (S-phase Kinase-associated Protein 1) functions as an adaptor protein connecting F-box proteins to Cullin1 in the SKP1-Cullin1-F-box (SCF) ubiquitin ligase complex, which performs essential functions in response to abiotic stresses. However, the specific roles of SKP1 in plant responses to tailings dam water stress remain unclear. This study identified 30 SKP1.1 family members in Nicotiana benthamiana through bioinformatics analysis. The expression patterns of NbSKP1.1 were evaluated using quantitative real-time polymerase chain reaction (qRT-PCR) when plants were subjected to tailings dam water stress. Results demonstrated that exposure to tailings dam water pollutants suppressed the expression of NbSKP1.1. Confocal imaging revealed that NbSKP1s (NbSKP1.1, NbSKP1.2, NbSKP1.3, and NbSKP1L1) exhibit dual localization in the nucleus and cytoplasm. This comprehensive analysis of the NbSKP1.1 family in plants establishes a foundation for future investigations into plant-environment interactions.
{"title":"Genome-wide identification, characterization, and expression analysis of the SKP1.1 family in Nicotiana benthamiana exposed to tailings dam wastewater","authors":"Junjie Wang , Xiaoqin Li , Xinghai Li , Yang Xu , Cuihua Xin , Jiangbo Guo","doi":"10.1016/j.genrep.2025.102363","DOIUrl":"10.1016/j.genrep.2025.102363","url":null,"abstract":"<div><div>SKP1 (S-phase Kinase-associated Protein 1) functions as an adaptor protein connecting F-box proteins to Cullin1 in the SKP1-Cullin1-F-box (SCF) ubiquitin ligase complex, which performs essential functions in response to abiotic stresses. However, the specific roles of SKP1 in plant responses to tailings dam water stress remain unclear. This study identified 30 <em>SKP1.1</em> family members in <em>Nicotiana benthamiana</em> through bioinformatics analysis. The expression patterns of NbSKP1.1 were evaluated using quantitative real-time polymerase chain reaction (qRT-PCR) when plants were subjected to tailings dam water stress. Results demonstrated that exposure to tailings dam water pollutants suppressed the expression of <em>NbSKP1.1</em>. Confocal imaging revealed that NbSKP1s (NbSKP1.1, NbSKP1.2, NbSKP1.3, and NbSKP1L1) exhibit dual localization in the nucleus and cytoplasm. This comprehensive analysis of the <em>NbSKP1.1</em> family in plants establishes a foundation for future investigations into plant-environment interactions.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102363"},"PeriodicalIF":0.9,"publicationDate":"2025-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145358390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-18DOI: 10.1016/j.genrep.2025.102360
Yasir Adil Jabbar Alabdali
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and Cas (CRISPR associated proteins) are the acquired immune system in bacteria against foreign DNA pieces. Nevertheless, it is not known how prevalent cas5 (type I-C CRISPR-Cas) is and whether it has a clinical isolate phenotypic implication in Iraq. Pseudomonas aeruginosa is among the most harmful species of opportunistic pathogenic bacteria that lead to illness, particularly in patients with cystic fibrosis, burns, and wounds. Cas5 was found in 10 isolates (15.6 %) of P. aeruginosa in 64 clinical isolates of the bacteria, collected between January and April 2024 All of the total of ten cas5-positive isolates had the virulence genes plcH, plcN, lasB, toxA, exoS, and algD (100 %) present. Most notably, resistance to all the tested antibiotics was lower in cas5-positive isolates. These findings suggest the existence of the potential connection between cas5 carriage, antibiotic resistance and biofilm adherence.
Significance statement
The present study offers a clear understanding regarding the impact of the CRISPR-Cas5 system on the Pseudomonas aeruginosa resistance to antibiotics and presents new information that could be utilised to create an infection control strategy in patients with cystic fibrosis and burn injuries.
{"title":"Detection of cas5 and virulence genes in Pseudomonas aeruginosa from cystic fibrosis, and burn wounds: Impact on biofilm and antibiotic resistance","authors":"Yasir Adil Jabbar Alabdali","doi":"10.1016/j.genrep.2025.102360","DOIUrl":"10.1016/j.genrep.2025.102360","url":null,"abstract":"<div><div>CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and Cas (CRISPR associated proteins) are the acquired immune system in bacteria against foreign DNA pieces. Nevertheless, it is not known how prevalent <em>cas5</em> (type I-C CRISPR-Cas) is and whether it has a clinical isolate phenotypic implication in Iraq. <em>Pseudomonas aeruginosa</em> is among the most harmful species of opportunistic pathogenic bacteria that lead to illness, particularly in patients with cystic fibrosis, burns, and wounds. Cas5 was found in 10 isolates (15.6 %) of <em>P. aeruginosa</em> in 64 clinical isolates of the bacteria, collected between January and April 2024 All of the total of ten cas5-positive isolates had the virulence genes <em>plcH</em>, <em>plcN</em>, <em>lasB</em>, <em>toxA</em>, <em>exoS</em>, and <em>algD</em> (100 %) present. Most notably, resistance to all the tested antibiotics was lower in cas5-positive isolates. These findings suggest the existence of the potential connection between cas5 carriage, antibiotic resistance and biofilm adherence.</div></div><div><h3>Significance statement</h3><div>The present study offers a clear understanding regarding the impact of the CRISPR-Cas5 system on the <em>Pseudomonas aeruginosa</em> resistance to antibiotics and presents new information that could be utilised to create an infection control strategy in patients with cystic fibrosis and burn injuries.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102360"},"PeriodicalIF":0.9,"publicationDate":"2025-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145358386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Antibiotic resistance in Pseudomonas aeruginosa has become a significant public health concern, particularly in burn patients. This study aimed to evaluate the effect of Arnebia euchroma extract on the expression of the lasR and lasI genes, which are crucial for the pathogenicity of this bacterium.
Methods
Five P. aeruginosa strains were isolated from burn wounds, identified with selective media and differential tests. The methanolic extract of A. euchroma was prepared by maceration and tested for antimicrobial activity. Antibiotic susceptibility was assessed using the disc diffusion method. The presence of lasI and lasR genes in clinical strains was confirmed by PCR, and their expression levels were quantified by Real-Time PCR. Active compounds in the extract were identified using gas chromatography–mass spectrometry.
Results
The A. euchroma root extract exhibited significant antibacterial effects, forming clear inhibition zones on agar plates. Its minimum inhibitory concentration ranged from 62.5 to 250 μg/mL, while the minimum bactericidal concentration was between 125 and 250 μg/mL. All tested P. aeruginosa isolates were positive for the lasI and lasR genes, with gene expression significantly reduced in the presence of the extract. The extract inhibited over 75 % of lasI and lasR expression, comparable to tobramycin. Diacetone alcohol, alpha-terpinenyl acetate, and xanthosine were identified as the most abundant compounds in the root.
Conclusion
The findings suggest that A. euchroma extract has potential as an antimicrobial and quorum sensing inhibitor. However, further studies with larger strain collections and in vivo validation are needed to confirm its therapeutic relevance.
{"title":"Evaluation of the antimicrobial activity of Arnebia euchroma extract and its influence on quorum sensing gene expression in Pseudomonas aeruginosa","authors":"Leila Yadegari , Maryam Mohammadi-Sichani , Soodabeh Rostami","doi":"10.1016/j.genrep.2025.102362","DOIUrl":"10.1016/j.genrep.2025.102362","url":null,"abstract":"<div><h3>Background</h3><div>Antibiotic resistance in <em>Pseudomonas aeruginosa</em> has become a significant public health concern, particularly in burn patients. This study aimed to evaluate the effect of <em>Arnebia euchroma</em> extract on the expression of the <em>lasR</em> and <em>lasI</em> genes, which are crucial for the pathogenicity of this bacterium.</div></div><div><h3>Methods</h3><div>Five <em>P. aeruginosa</em> strains were isolated from burn wounds, identified with selective media and differential tests. The methanolic extract of <em>A. euchroma</em> was prepared by maceration and tested for antimicrobial activity. Antibiotic susceptibility was assessed using the disc diffusion method. The presence of <em>lasI</em> and <em>lasR</em> genes in clinical strains was confirmed by PCR, and their expression levels were quantified by Real-Time PCR. Active compounds in the extract were identified using gas chromatography–mass spectrometry.</div></div><div><h3>Results</h3><div>The <em>A. euchroma</em> root extract exhibited significant antibacterial effects, forming clear inhibition zones on agar plates. Its minimum inhibitory concentration ranged from 62.5 to 250 μg/mL, while the minimum bactericidal concentration was between 125 and 250 μg/mL. All tested <em>P. aeruginosa</em> isolates were positive for the <em>lasI</em> and <em>lasR</em> genes, with gene expression significantly reduced in the presence of the extract. The extract inhibited over 75 % of <em>lasI</em> and <em>lasR</em> expression, comparable to tobramycin. Diacetone alcohol, alpha-terpinenyl acetate, and xanthosine were identified as the most abundant compounds in the root.</div></div><div><h3>Conclusion</h3><div>The findings suggest that <em>A. euchroma</em> extract has potential as an antimicrobial and quorum sensing inhibitor. However, further studies with larger strain collections and in vivo validation are needed to confirm its therapeutic relevance.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102362"},"PeriodicalIF":0.9,"publicationDate":"2025-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145358391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Advanced general-purpose compressors like gzip and zstd have difficulties when compressing genome sequences. The lack of sequence-specific traits and limited-scale features leads to inferior performance. However, molecular sequence databases have preferred these compressors for years. To get around these limitations, this article proposes a compressor called NGC (Normalized Genome Compressor) to make general-purpose compressors work better to compress genome sequences. NGC is a reference-free compression tool consisting of two phases. Initially, it takes the primary domain of the genome, i.e., A, C, G, and T, and then proceeds with normalization. In the subsequent phase, based on user specifications, it utilizes one of the eight general-purpose compressors, including 7-zip, paq8px, bsc, gzip, zstd, bzip2, zpaq, or cmix. We compare the standard version (S) of each compressor, known as the S-compressor, the sequence normalized file (nf), and the S-compressor applied to the nf format, referred to as the proposed compressor (P-compressor). Subsequently, we evaluate the performance of NGC in two genome datasets, including seventeen and eleven primary genome sequences, respectively. The result is the weighted average compression ratio (WACR) for the initial dataset of 4.13 for P-gzip vs. 3.63 for S-gzip and 4.8 for P-zstd vs. 4.3 for S-zstd. P-gzip is 91.101 times and P-zstd is 22.734 times faster than the S-compressor. The outcomes for the remaining six compressors are likewise beneficial. The findings indicate that the use of a general-purpose compressor in the nf significantly enhances the results.
{"title":"A study of the cutting-edge general-purpose compressors’ performance on the normalized genome sequence","authors":"Subhankar Roy , Arnab Charit , Mriganka Patra , Ananya Sadhukhan , Diya Chakraborty , Partha Ghosh , Kingshuk Chatterjee , Anirban Mukhopadhyay","doi":"10.1016/j.genrep.2025.102358","DOIUrl":"10.1016/j.genrep.2025.102358","url":null,"abstract":"<div><div>Advanced general-purpose compressors like gzip and zstd have difficulties when compressing genome sequences. The lack of sequence-specific traits and limited-scale features leads to inferior performance. However, molecular sequence databases have preferred these compressors for years. To get around these limitations, this article proposes a compressor called NGC (<u>N</u>ormalized <u>G</u>enome <u>C</u>ompressor) to make general-purpose compressors work better to compress genome sequences. NGC is a reference-free compression tool consisting of two phases. Initially, it takes the primary domain of the genome, i.e., A, C, G, and T, and then proceeds with normalization. In the subsequent phase, based on user specifications, it utilizes one of the eight general-purpose compressors, including 7-zip, paq8px, bsc, gzip, zstd, bzip2, zpaq, or cmix. We compare the standard version (S) of each compressor, known as the S-compressor, the sequence normalized file (nf), and the S-compressor applied to the nf format, referred to as the proposed compressor (P-compressor). Subsequently, we evaluate the performance of NGC in two genome datasets, including seventeen and eleven primary genome sequences, respectively. The result is the weighted average compression ratio (WACR) for the initial dataset of 4.13 for P-gzip vs. 3.63 for S-gzip and 4.8 for P-zstd vs. 4.3 for S-zstd. P-gzip is <span><math><mo>∼</mo></math></span>91.101 times and P-zstd is <span><math><mo>∼</mo></math></span>22.734 times faster than the S-compressor. The outcomes for the remaining six compressors are likewise beneficial. The findings indicate that the use of a general-purpose compressor in the nf significantly enhances the results.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102358"},"PeriodicalIF":0.9,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145358388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-17DOI: 10.1016/j.genrep.2025.102361
Stephanni Figueiredo da Silva , Klaucia Rodrigues Vasconcelos , Julia Deffune Profeta Cidin Almeida , Natália Rocha Guimarães , Luiz Marcelo Ribeiro Tomé , Vagner Fonseca , Diniz Pereira Leite Júnior , Marta Giovanetti , Elaine Cristina de Oliveira , Luiz Carlos Júnior Alcântara
The emergence of SARS-CoV-2 in December 2019 impacted global public health as the most severe modern pandemic ever recorded. Remarkably, it was possible to monitor its evolution in real-time, including viral evolution and the emergence of new lineages, thanks to technology and the speed of communication via the internet. Understanding the circulating viral variants and their characteristics within the population was crucial for effectively guiding public health actions in combating the disease. In this study, we conducted detailed phylogenetic analyses as a result of a recently established genomic surveillance hub at LACEN-MT. The samples were sequenced and subsequently deposited on the GISAID platform between October 21, 2021 and March 31, 2023. The findings of this study suggest that the SARS-CoV-2 epidemic in Mato Grosso State was characterized by the successive introduction of new strains from different countries, leading to the generation of waves of infection. Overall, this study underscores the importance of investigating the spatiotemporal evolution of the SARS-CoV-2 epidemic and how its variants spread across the state, contributing to pandemic peaks in the region. It also highlights the significance of disseminating this information to the management team in Mato Grosso to help implement monitoring strategies that could reduce cases and deaths in the state.
{"title":"Genomic surveillance of SARS-CoV-2 in the State of Mato Grosso, Midwest Brazil","authors":"Stephanni Figueiredo da Silva , Klaucia Rodrigues Vasconcelos , Julia Deffune Profeta Cidin Almeida , Natália Rocha Guimarães , Luiz Marcelo Ribeiro Tomé , Vagner Fonseca , Diniz Pereira Leite Júnior , Marta Giovanetti , Elaine Cristina de Oliveira , Luiz Carlos Júnior Alcântara","doi":"10.1016/j.genrep.2025.102361","DOIUrl":"10.1016/j.genrep.2025.102361","url":null,"abstract":"<div><div>The emergence of SARS-CoV-2 in December 2019 impacted global public health as the most severe modern pandemic ever recorded. Remarkably, it was possible to monitor its evolution in real-time, including viral evolution and the emergence of new lineages, thanks to technology and the speed of communication via the internet. Understanding the circulating viral variants and their characteristics within the population was crucial for effectively guiding public health actions in combating the disease. In this study, we conducted detailed phylogenetic analyses as a result of a recently established genomic surveillance hub at LACEN-MT. The samples were sequenced and subsequently deposited on the GISAID platform between October 21, 2021 and March 31, 2023. The findings of this study suggest that the SARS-CoV-2 epidemic in Mato Grosso State was characterized by the successive introduction of new strains from different countries, leading to the generation of waves of infection. Overall, this study underscores the importance of investigating the spatiotemporal evolution of the SARS-CoV-2 epidemic and how its variants spread across the state, contributing to pandemic peaks in the region. It also highlights the significance of disseminating this information to the management team in Mato Grosso to help implement monitoring strategies that could reduce cases and deaths in the state.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102361"},"PeriodicalIF":0.9,"publicationDate":"2025-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145412787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-14DOI: 10.1016/j.genrep.2025.102356
José Germán Serrano-Gamboa , José Tomás Tavarez-Arriaga , Mario L. Iza-Arteaga , Martín Romualdo Ide-Pérez , Irán Tapia-Vázquez , Jorge L. Folch-Mallol
A novel strain of the genus Pseudomonas was isolated from a high-altitude volcano in Toluca, Mexico. This isolate, designed as Pseudomonas marginalis BMH-2007, could grow at 4 °C, whereas other microbes usually stop growth at this temperature. The fact of its isolation from snow implies that the population was big enough to thrive at low temperature, making it a psychrotolerant bacterium.
Previous characterization of BMH-2007 revealed interesting characteristics related to plant growth promotion, including auxin production, siderophore production, and phosphate solubilization capacity. In this work, the ability of BMH-2007 to stimulate the early development of Capsicum annuum plants without signs of phytopathogenicity was proven. A thorough whole-genome analysis revealed that isolate BMH-2007 belongs to the Pseudomonas fluorescens species complex, specifically to the species P. marginalis, with a Mash distance of 0.0118927 from the closest reference genome (RefSeq: GCF_007858175.1).
The phylogenomic evidence allowed us to confirm the new strain designation. Notably, its genomic features were consistent with those of plant growth-promoting traits, and we observed coding sequences for IAA biosynthesis and iron and phosphate transport, among others. As it is a species associated with phytopathogenicity, the virulence factors encoded by the genome were analyzed, which revealed the presence of a type VI secretion system associated with both biological control and plant growth promotion.
{"title":"Phylogenomic insights into a psychrotolerant, plant growth-promoting strain of Pseudomonas marginalis isolated from Xinantécatl volcano","authors":"José Germán Serrano-Gamboa , José Tomás Tavarez-Arriaga , Mario L. Iza-Arteaga , Martín Romualdo Ide-Pérez , Irán Tapia-Vázquez , Jorge L. Folch-Mallol","doi":"10.1016/j.genrep.2025.102356","DOIUrl":"10.1016/j.genrep.2025.102356","url":null,"abstract":"<div><div>A novel strain of the genus <em>Pseudomonas</em> was isolated from a high-altitude volcano in Toluca, Mexico. This isolate, designed as <em>Pseudomonas marginalis</em> BMH-2007, could grow at 4 °C, whereas other microbes usually stop growth at this temperature. The fact of its isolation from snow implies that the population was big enough to thrive at low temperature, making it a psychrotolerant bacterium.</div><div>Previous characterization of BMH-2007 revealed interesting characteristics related to plant growth promotion, including auxin production, siderophore production, and phosphate solubilization capacity. In this work, the ability of BMH-2007 to stimulate the early development of <em>Capsicum annuum</em> plants without signs of phytopathogenicity was proven. A thorough whole-genome analysis revealed that isolate BMH-2007 belongs to the <em>Pseudomonas fluorescens</em> species complex, specifically to the species <em>P. marginalis</em>, with a Mash distance of 0.0118927 from the closest reference genome (RefSeq: GCF_007858175.1).</div><div>The phylogenomic evidence allowed us to confirm the new strain designation. Notably, its genomic features were consistent with those of plant growth-promoting traits, and we observed coding sequences for IAA biosynthesis and iron and phosphate transport, among others. As it is a species associated with phytopathogenicity, the virulence factors encoded by the genome were analyzed, which revealed the presence of a type VI secretion system associated with both biological control and plant growth promotion.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102356"},"PeriodicalIF":0.9,"publicationDate":"2025-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145358385","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-10-13DOI: 10.1016/j.genrep.2025.102355
Hassan Ghayas , Uroosa Ejaz , Ayaz Taj , Sabiha Yousuf , Muhammad Sohail
Thermophilic microorganisms produce heat-stable metabolites with significant importance in industrial applications. In this study, we present the whole genome sequence of a thermophilic bacterium, Brevibacillus borstelensis UE10, isolated from a crocodile pond in Manghopir, Pakistan. In silico functional annotation and comparative genomic analyses provided valuable insights into the biosynthetic capabilities and metabolic potential of this strain. The draft genome of UE10 was assembled into 132 contigs with a total size of 5,322,029 bp and a GC content of 52 %. The genome contained 5080 coding sequences (CDSs), 116 tRNAs, and 4 rRNAs. Whole genome and 16S rRNA gene sequence comparisons confirmed the identification of the strain as B. borstelensis. Furthermore, seven putative biosynthetic gene clusters (BGCs) involved in the production of potentially antimicrobial and metal-chelating agents were identified. In addition to other metabolic pathways, the presence of a 13-gene xenobiotic degradation pathway, including benzoate degradation, demonstrates the strain's strong potential for bioremediation. Overall, in silico genomic evidence highlights the potential of B. borstelensis UE10 in biotechnological applications and environmental remediation.
{"title":"In silico exploration of the metabolic and biosynthetic potential of Brevibacillus borstelensis UE10 through whole genome analysis","authors":"Hassan Ghayas , Uroosa Ejaz , Ayaz Taj , Sabiha Yousuf , Muhammad Sohail","doi":"10.1016/j.genrep.2025.102355","DOIUrl":"10.1016/j.genrep.2025.102355","url":null,"abstract":"<div><div>Thermophilic microorganisms produce heat-stable metabolites with significant importance in industrial applications. In this study, we present the whole genome sequence of a thermophilic bacterium, <em>Brevibacillus borstelensis</em> UE10, isolated from a crocodile pond in Manghopir, Pakistan. In silico functional annotation and comparative genomic analyses provided valuable insights into the biosynthetic capabilities and metabolic potential of this strain. The draft genome of UE10 was assembled into 132 contigs with a total size of 5,322,029 bp and a GC content of 52 %. The genome contained 5080 coding sequences (CDSs), 116 tRNAs, and 4 rRNAs. Whole genome and 16S rRNA gene sequence comparisons confirmed the identification of the strain as <em>B. borstelensis</em>. Furthermore, seven putative biosynthetic gene clusters (BGCs) involved in the production of potentially antimicrobial and metal-chelating agents were identified. In addition to other metabolic pathways, the presence of a 13-gene xenobiotic degradation pathway, including benzoate degradation, demonstrates the strain's strong potential for bioremediation. Overall, in silico genomic evidence highlights the potential of <em>B. borstelensis</em> UE10 in biotechnological applications and environmental remediation.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102355"},"PeriodicalIF":0.9,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145324273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Multidrug-resistant (MDR) Pseudomonas aeruginosa in drinking water poses a significant public health risk in low-resource settings, resulting in increased morbidity and mortality. This study investigated the prevalence of MDR P. aeruginosa and the occurrence of carbapenem- and quinolone-resistance genes in isolates from drinking water within Katsina Metropolis, Nigeria.
Methods
Forty-five water samples were collected from wells (n = 15), boreholes (n = 15), and sachet-packaged water (n = 15) across five locations. Bacterial isolation and identification were performed using cetrimide agar and standard microbiological methods. Antibiotic susceptibility testing was performed by the disk diffusion method, with isolates resistant to ≥3 antibiotic classes classified as MDR. Carbapenemase production was assessed using the modified Carba NP test, and selected MDR isolates were screened for carbapenem and quinolone resistance genes by PCR.
Results
P. aeruginosa was detected in 71.1 % (32/45) of samples, with the highest prevalence in wells (93.3 %) and the lowest in sachet water (33.3 %). High resistance was observed to ampicillin (100 %), tetracycline (80–100 %), ceftriaxone (20–100 %), and ertapenem (100 %), with lower resistance to ciprofloxacin (20–60 %), chloramphenicol (10–70 %), and imipenem (10–70 %). Carbapenemase production was confirmed in 28.1 % (9/32) of isolates, and 84.3 % (27/32) were MDR. Selected MDR isolates from boreholes carried blaVIM and qnrA, while blaNDM and ParC were detected among well-water isolates.
Conclusion
This study provides baseline data of the prevalence of MDR and carbapenemase-producing P. aeruginosa in drinking water in Katsina Metropolis and underscores the need for enhanced surveillance of water sources for WHO-priority pathogens.
{"title":"Carbapenem and quinolone resistance genes in multidrug-resistant Pseudomonas aeruginosa from drinking water sources within katsina metropolis, Nigeria","authors":"Anas Abdullahi , Emmanuel Dayo Alabi , Adetunji Misbau Kilani , Ayodele Timilehin Adesoji","doi":"10.1016/j.genrep.2025.102359","DOIUrl":"10.1016/j.genrep.2025.102359","url":null,"abstract":"<div><h3>Introduction</h3><div>Multidrug-resistant (MDR) <em>Pseudomonas aeruginosa</em> in drinking water poses a significant public health risk in low-resource settings, resulting in increased morbidity and mortality. This study investigated the prevalence of MDR <em>P. aeruginosa</em> and the occurrence of carbapenem- and quinolone-resistance genes in isolates from drinking water within Katsina Metropolis, Nigeria.</div></div><div><h3>Methods</h3><div>Forty-five water samples were collected from wells (<em>n</em> = 15), boreholes (n = 15), and sachet-packaged water (n = 15) across five locations. Bacterial isolation and identification were performed using cetrimide agar and standard microbiological methods. Antibiotic susceptibility testing was performed by the disk diffusion method, with isolates resistant to ≥3 antibiotic classes classified as MDR. Carbapenemase production was assessed using the modified Carba NP test, and selected MDR isolates were screened for carbapenem and quinolone resistance genes by PCR.</div></div><div><h3>Results</h3><div><em>P. aeruginosa</em> was detected in 71.1 % (32/45) of samples, with the highest prevalence in wells (93.3 %) and the lowest in sachet water (33.3 %). High resistance was observed to ampicillin (100 %), tetracycline (80–100 %), ceftriaxone (20–100 %), and ertapenem (100 %), with lower resistance to ciprofloxacin (20–60 %), chloramphenicol (10–70 %), and imipenem (10–70 %). Carbapenemase production was confirmed in 28.1 % (9/32) of isolates, and 84.3 % (27/32) were MDR. Selected MDR isolates from boreholes carried <em>bla</em><sub><em>VIM</em></sub> and <em>qnrA,</em> while <em>bla</em><sub><em>NDM</em></sub> and <em>ParC</em> were detected among well-water isolates.</div></div><div><h3>Conclusion</h3><div>This study provides baseline data of the prevalence of MDR and carbapenemase-producing <em>P. aeruginosa</em> in drinking water in Katsina Metropolis and underscores the need for enhanced surveillance of water sources for WHO-priority pathogens.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"41 ","pages":"Article 102359"},"PeriodicalIF":0.9,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145324275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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