Characterization and expression analysis of the MADS-box gene AGL8 in cotton: insights into gene function differentiation in plant growth and stress resistance.

BACKGROUND: AGAMOUS-LIKE 8 (AGL8) belongs to the MADS-box family, which plays important roles in transcriptional regulation, sequence-specific DNA binding and other biological processes and molecular functions. The genome of cotton, a representative polyploid plant, contains multiple AGL8 genes. However, their functional differentiation is still unclear. METHODS AND RESULTS: In this study, a comprehensive genomic analysis of AGL8 genes was conducted. Cotton AGL8s were subdivided into four subgroups (Groups 1, 2, 3, and 4) based on phylogenetic analysis, and different subgroups of AGL8s presented different characteristics, including different structures and conserved motifs. With respect to the promoter regions of the GhAGL8 genes, we successfully predicted cis-elements that respond to phytohormone signal transduction and the stress response of plants. Transcriptome data and real-time quantitative PCR validation indicated that three genes, namely, GH_D07G0744, GH_A03G0856 and GH_A07G0749, were highly induced by methyl jasmonate (MeJA), salicylic acid (SA), and abscisic acid (ABA), which indicated that they function in plant resistance to abiotic and biotic stresses. CONCLUSIONS: The information from the gene structure, number and types of conserved domains, tissue-specific expression levels, and expression patterns under different treatments highlights the differences in sequence and function of the cotton AGL8 genes. Different AGL8s play roles in vegetative growth, reproductive development, and plant stress resistance. These results lay a foundation for further study of GhAGL8s in cotton.

The Evolution of Extreme Genetic Variability in a Parasite-Resistance Complex.

Genomic regions that play a role in parasite defense are often found to be highly variable, with the MHC serving as an iconic example. Single nucleotide polymorphisms may represent only a small portion of this variability, with Indel polymorphisms and copy number variation further contributing. In extreme cases, haplotypes may no longer be recognized as orthologous. Understanding the evolution of such highly divergent regions is challenging because the most extreme variation is not visible using reference-assisted genomic approaches. Here we analyze the case of the Pasteuria Resistance Complex (PRC) in the crustacean Daphnia magna, a defense complex in the host against the common and virulent bacterium Pasteuria ramosa. Two haplotypes of this region have been previously described, with parts of it being non-homologous, and the region has been shown to be under balancing selection. Using pan-genome analysis and tree reconciliation methods to explore the evolution of the PRC and its characteristics within and between species of Daphnia and other Cladoceran species, our analysis revealed a remarkable diversity in this region even among host species, with many non-homologous hyper-divergent-haplotypes. The PRC is characterized by extensive duplication and losses of Fucosyltransferase (FuT) and Galactosyltransferase (GalT) genes that are believed to play a role in parasite defense. The PRC region can be traced back to common ancestors over 250 million years. The unique combination of an ancient resistance complex and a dynamic, hyper-divergent genomic environment presents a fascinating opportunity to investigate the role of such regions in the evolution and long-term maintenance of resistance polymorphisms. Our findings offer valuable insights into the evolutionary forces shaping disease resistance and adaptation, not only in the genus Daphnia, but potentially across the entire Cladocera class.

Complete analysis of G-quadruplex forming sequences in the gapless assembly of human chromosome Y.

Recent advancements have finally delivered a complete human genome assembly, including the elusive Y chromosome. This accomplishment closes a significant knowledge gap. Prior efforts were hampered by challenges in sequencing repetitive DNA structures such as direct and inverted repeats. We used the G4Hunter algorithm to analyze the presence of G-quadruplex forming sequences (G4s) within the current human reference genome (GRCh38) and the new telomere-to-telomere (T2T) Y chromosome assemblies. This analysis served a dual purpose: identifying the location of potential G4s within the genomes and exploring their association with functionally annotated sequences. Compared to GRCh38, the T2T assembly exhibited a significantly higher prevalence of G-quadruplex forming sequences. Notably, these repeats were abundantly located around precursor RNA, exons, genes, and within protein binding sites. This remarkable co-occurrence of G4-forming sequences with these critical regulatory regions suggests their role in fundamental DNA regulation processes. Our findings indicate that the current human reference genome significantly underestimated the number of G4s, potentially overlooking their functional importance.

Isolation, characterization, and application of a novel Pseudomonas fluorescens phage vB_PF_Y1-MI in contaminated milk.

The food industry has incurred substantial losses from contamination by Pseudomonas fluorescens, emphasizing the critical importance of implementing effective control strategies. Phages are potential sterilizers due to their specific killing abilities and the difficulty bacteria face in developing resistance. However, a significant barrier to their development is the lack of diversity among phage types. In this study, we characterized a novel lytic P. fluorescens phage, named vB_PF_Y1-MI. Phage vB_PF_Y1-MI displayed a latent period of nearly 10 min and a high burst size of 1493 PFU/cell. This phage showed good activity over a wide range of temperature (up to 70 °C) and pH (3-12). The genome of phage vB_PF_Y1-MI spans 93,233 bp with a GC content of 45%. It encompasses 174 open-reading frames and 19 tRNA genes, while no lysogeny or virulence-associated genes were detected. Phylogenetic analysis positions it as a novel unassigned evolutionary lineage within the Caudoviricetes class among related dsDNA phages. Our study provides foundational insights into vB_PF_Y1-MI and emphasizes its potential as an effective biological control agent against P. fluorescens. This research offers crucial theoretical groundwork and technical support for subsequent efforts in preventing and controlling P. fluorescens contamination.

Evaluation of whole genome sequencing utility in identifying driver alterations in cancer genome.

In cancer genome analysis, identifying pathogenic alterations and assessing their effects on oncogenic processes is important. Although whole exome sequencing (WES) can effectively detect such changes, driver alterations could not be identified in 27.8% of the cases, according to a previous study. The objectives of the present study were to evaluate the utility of whole genome sequencing (WGS) and clarify its differences with WES in terms of driver alteration detection. For this purpose, WGS analysis was conducted on 177 driverless WES samples, selected from 5,480 fresh frozen samples derived from 5,140 Japanese patients with cancer. These samples were selected as primary tumor, both WES and transcriptome profiling were performed, estimated tumor content of ≥ 30%, and no driver alterations were identified by WES. WGS identified driver and likely driver alterations in 68.4 and 22.6% of the samples, respectively. The most frequent alteration type was oncogene amplification, followed by tumor suppressor gene deletion and small variants located outside the coding region. In the remaining 9.0% of samples, no such signals were identified; therefore, further investigations are required. The current study clearly demonstrated the role and utility of WGS in identifying genomic alterations that contribute to tumorigenesis.

Isolation and Whole-genome analysis of Desmodesmus sp. SZ-1: Novel acid-tolerant carbon-fixing microalga.

Utilizing microalgae to capture flue gas pollutants is an effective strategy for mitigating greenhouse gas emissions. However, existing carbon-fixing microalgae exhibit poor tolerance towards acidic flue gas. In this study, the Desmodesmus sp. SZ-1, which can thrive in acidic environments and efficiently sequester CO2, was isolated. Desmodesmus sp. SZ-1 exhibited strong acid tolerance ability, with an average carbon fixation rate of 497.6 mg/L/d under 10 % CO2 and pH 3.5. Physiological analysis revealed that SZ-1 responded to high CO2 by increasing chlorophyll levels while coping with acidic stress by activating antioxidant enzymes. Genome analysis revealed a large number of carbon fixation and acid adaptation genes, involved in membrane lipid biosynthesis, H+ pumps, molecular chaperones, peroxidase system, amino acid synthesis, and carbonic anhydrase. This study provides a novel algal resource for mitigating acid gas emissions and a comprehensive genetic database for genetically modifying microalgae.

Annotation-free prediction of microbial dioxygen utilization.

Aerobes require dioxygen (O2) to grow; anaerobes do not. However, nearly all microbes-aerobes, anaerobes, and facultative organisms alike-express enzymes whose substrates include O2, if only for detoxification. This presents a challenge when trying to assess which organisms are aerobic from genomic data alone. This challenge can be overcome by noting that O2 utilization has wide-ranging effects on microbes: aerobes typically have larger genomes encoding distinctive O2-utilizing enzymes, for example. These effects permit high-quality prediction of O2 utilization from annotated genome sequences, with several models displaying ≈80% accuracy on a ternary classification task for which blind guessing is only 33% accurate. Since genome annotation is compute-intensive and relies on many assumptions, we asked if annotation-free methods also perform well. We discovered that simple and efficient models based entirely on genomic sequence content-e.g., triplets of amino acids-perform as well as intensive annotation-based classifiers, enabling rapid processing of genomes. We further show that amino acid trimers are useful because they encode information about protein composition and phylogeny. To showcase the utility of rapid prediction, we estimated the prevalence of aerobes and anaerobes in diverse natural environments cataloged in the Earth Microbiome Project. Focusing on a well-studied O2 gradient in the Black Sea, we found quantitative correspondence between local chemistry (O2:sulfide concentration ratio) and the composition of microbial communities. We, therefore, suggest that statistical methods like ours might be used to estimate, or "sense," pivotal features of the chemical environment using DNA sequencing data.IMPORTANCEWe now have access to sequence data from a wide variety of natural environments. These data document a bewildering diversity of microbes, many known only from their genomes. Physiology-an organism's capacity to engage metabolically with its environment-may provide a more useful lens than taxonomy for understanding microbial communities. As an example of this broader principle, we developed algorithms that accurately predict microbial dioxygen utilization directly from genome sequences without annotating genes, e.g., by considering only the amino acids in protein sequences. Annotation-free algorithms enable rapid characterization of natural samples, highlighting quantitative correspondence between sequences and local O2 levels in a data set from the Black Sea. This example suggests that DNA sequencing might be repurposed as a multi-pronged chemical sensor, estimating concentrations of O2 and other key facets of complex natural settings.

Aequorivita flava sp. nov., isolated from deep-sea sediments.

Three Gram-stain-negative, aerobic, non-motile, chemoheterotrophic, short-rod-shaped bacteria, designated CDY1-MB1T, CDY2-MB3, and BDY3-MB2, were isolated from three marine sediment samples collected in the eastern Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains were related to the genus Aequorivita and close to the type strain of Aequorivita vitellina F4716T (with similarities of 98.0-98.1%). Strain CDY1-MB1T can grow at 15-37 °C (optimum 30 °C) and in media with pH 6-9 (optimum, pH 7), and tolerate up to 10% (w/v) NaCl. The predominant cellular fatty acids of strain CDY1-MB1T were iso-C15 : 0 (20.7%) and iso-C17 : 0 3-OH (12.8%); the sole respiratory quinone was menaquinone 6; the major polar lipids were phosphatidylethanolamine, two unidentified aminolipids and two unidentified polar lipids. The digital DNA-DNA hybridization/average nucleotide identity values between strains CDY1-MB1T, CDY2-MB3, and BDY3-MB2 and A. vitellina F4716T were 24.7%/81.6-81.7%, thereby indicating that strain CDY1-MB1T should represent a novel species of the genus Aequorivita. The genomic DNA G+C contents were 37.6 % in all three strains. Genomic analysis showed the presence of genes related to nitrogen and sulphur cycling, as well as metal reduction. The genetic traits of these strains indicate their possible roles in nutrient cycling and detoxification processes, potentially shaping the deep-sea ecosystem's health and resilience. Based upon the consensus of phenotypic and genotypic analyses, strain CDY1-MB1T should be classified as a novel species of the genus Aequorivita, for which the name Aequorivita flava sp. nov. is proposed. The type strain is CDY1-MB1T (=MCCC 1A16935T=KCTC 102223T).

A layout framework for genome-wide multiple sequence alignment graphs.

Sequence alignments are often used to analyze genomic data. However, such alignments are often only calculated and compared on small sequence intervals for analysis purposes. When comparing longer sequences, these are usually divided into shorter sequence intervals for better alignment results. This usually means that the order context of the original sequence is lost. To prevent this, it is possible to use a graph structure to represent the order of the original sequence on the alignment blocks. The visualization of these graph structures can provide insights into the structural variations of genomes in a semi-global context. In this paper, we propose a new graph drawing framework for representing gMSA data. We produce a hierarchical graph layout that supports the comparative analysis of genomes. Based on a reference, the differences and similarities of the different genome orders are visualized. In this work, we present a complete graph drawing framework for gMSA graphs together with the respective algorithms for each of the steps. Additionally, we provide a prototype and an example data set for analyzing gMSA graphs. Based on this data set, we demonstrate the functionalities of the framework using two examples.

Reclassification of Butyrivibrio crossotus Moore et al. 1976 (Approved Lists 1980) into a novel genus as Eshraghiella crossota gen. nov., comb. nov.

The reclassification of Butyrivibrio crossotus Moore et al. 1976 (Approved Lists 1980) as Eshraghiella crossota gen. nov., comb. nov. is proposed within the family Lachnospiraceae. This reclassification is based on differences revealed through the analysis of 16S rRNA, groEL, recA, and rpoB genes, as well as genome sequences, distinguishing it from other Butyrivibrio species. Comparative analysis showed that B. crossotus exhibited digital DNA-DNA hybridization (dDDH) values of 19.40-27.20% and average nucleotide identities based on blast (ANIb) values of 67.06-67.64% with other Butyrivibrio species. These values are significantly below the species delineation thresholds (dDDH, 70%; ANIb, 95-96%), justifying the proposed reclassification. Additionally, the results of the average amino acid identity (AAI) analysis indicated that this species shares 59.22-60.17% AAI with the other species of the genus Butyrivibrio, which is below the AAI threshold (65%) for a genus boundary. In addition, biochemical and morphological characteristics also support the proposal that this species is different from other species of the genus Butyrivibrio. The type strain is ATCC 29175T (DSM 2876T=T9-40AT).

Isolation and identification, genome-wide analysis and pathogenicity study of a novel PRRSV-1 in southern China.

Porcine reproductive and respiratory syndrome virus (PRRSV) has caused severe economic losses to the global swine industry. In recent years, the incidence of PRRSV-1 has been gradually increasing in China, but there are still few studies on it. In this study, clinical samples for PRRS virus isolation were collected from a pig farm in South China in 2022. We effectively isolated a strain of PRRSV utilizing PAM cells and demonstrated its consistent transmission capability on Marc-145 cells. The isolated strain was confirmed as PRRSV-1 by RT-qPCR, IFA, electron microscopy, etiolated spot purification and whole genome sequencing, the strain was named GD2022. The length of GD2022 genome is 15058nt; Based on the genome-wide genetic evolutionary analysis of GD2022, the strain was classified as PRRSV-1. Further genetic evolutionary analysis of its ORF5 gene showed that GD2022 belonged to PRRSV-1 subtype 1 and formed an independent branch in the evolutionary tree. Compared with the sequence of the classical PRRSV-1 strain (LV strain), GD2022 has several amino acid site mutations in the antigenic region from GP3 to GP5, these mutations are different from those of other PRRSV-1 strains in China. Recombination analysis showed no recombination events with GD2022. In addition, piglets infected with GD2022 displayed clinical respiratory symptoms and typical pathological changes. In this study, a strain of the PRRSV-1 virus was isolated using both PAM cells and Marc-145 and proved to be pathogenic to piglets, providing an important reference for the identification, prevention, and control of PRRSV-1.

[Biological and genome characteristics of a novel broad host-range phage ΦEP1 infecting enteroinvasive Escherichia coli].

We analyzed the biological and genome characteristics of a phage infecting enteroinvasive Escherichia coli (EIEC), aiming to provide resources and a reference for the prevention and treatment of EIEC. With the EIEC preserved in our laboratory as the host bacterium, one strain of phage was isolated from the effluent sample from a chicken farm in Huzhou, Zhejiang and named ΦEP1. The titer, optimal multiplicity of infection, one-step growth curve, temperature, pH value, chloroform and bile salt sensitivity of ΦEP1 were determined by the double-layer agar plate method. The morphology of the phage was observed by transmission electron microscopy. The biocontrol effects of ΦEP1 in different food matrixes and the protective effect of this phage on Caco-2 cells were tested. The phage ΦEP1 showed the optimal multiplicity of infection of 0.1, the titer of 1.3×1010 PFU/mL, strong tolerance to temperature, pH, chloroform, and bile salt, and a broad host spectrum. Furthermore, it expressed lysis activity against multiple strains of multiple antibiotic-resistant pathogenic E. coli and Shigella with different serotypes. Phage ΦEP1 had an incubation period of 10 min, an outbreak period of 80 min, and an outbreak volume of 48 PFU/cell. According to the morphology observed by transmission electron microscopy, phage ΦEP1 belonged to the order of Caudovirales, and it had a good protective effect on Caco-2 cells. Phage ΦEP1 had a genome of 87 182 bp with the GC content of 39.80%, 128 putative open reading frames, and no antibiotic resistance genes or virulence genes. ΦEP1 inhibited the growth of EIEC in artificially contaminated milk and beef and eliminated EIEC in cell protection experiments. It significantly increased the survival rate of Caco-2 cells and down-regulated the expression of interleukin (IL)-6 and IL-1ß to reduce inflammation. We obtained an EIEC-targeting phage ΦEP1 with a high titer and strong tolerance to the environment, which provided a basis for the application of phages in food preservation and other fields.

Full genome sequence analysis of the predominant and uncommon G9P[4] rotavirus strains circulating in Tehran, Iran, 2021-2022: Evidence for inter and intra-genotype recombination.

Group A rotaviruses (RVAs) are a major cause of acute gastroenteritis in children under 5 years of age worldwide. Herein, the genetic sequences of 11 RNA segments from three uncommon G9P[4] RVA strains found in the stool samples of children under 5 years of age in Iran were analyzed using next-generation sequencing (NGS) technology. The genomic constellations of these three uncommon G9P[4] strains indicated the presence of the double and quadruple reassortants of two G9P[4] strains, containing the VP7/NSP2 and VP7/VP2/NSP2/NSP4 genes on a DS-1-like genetic background, respectively. The genome of one strain indicated a Wa-like genetic backbone in a single-reassortant with the VP4 of the DS1-like human strains. With the exception of VP1, VP2, VP7, NSP2, NSP3, and NSP4 genes, which clustered with RVA of human origins belonging to cognate gene sequences of genogroup 1/2 genotypes/lineages, the remaining five genes (VP8/VP4, VP3, VP6, NSP1, NSP5) displayed direct evidence of recombination. It is presumed that the presence of uncommon G9P[4] strains in Iran is not linked to vaccination pressure, but rather to the high prevalence of RVA co-infection or the direct import of these uncommon RVA reassortants strains from other countries (especially those that have implemented RV vaccination).

Draft genome sequence of Listeria aquatica strain SG_BD1, isolated from a cow dung sample in Bangladesh.

Here, we present the genome of Listeria aquatica strain SG_BD1, isolated from cow dung in Dhaka, Bangladesh, and assembled after Oxford Nanopore sequencing. The genome is 2,690,148 bp with 2,855 predicted coding DNA sequences, G + C content of 39.6%, and displays a putative virulence gene clpP and 9 CRISPRs.

The identification of Finegoldia dalianensis sp. nov., isolated from the pus of the patient with skin abscess and genomic analysis of the strains belonging to Finegoldia genus.

OBJECTIVES: To comprehensively characterize a new species, named Finegoldia dalianensis sp. nov., isolated from the pus of a skin abscess from a patient and genomic analysis of the strains belonging to Finegoldia genus. METHODS: Strain LY240594T was definitively characterized through phylogenetic, genomic, and biochemical approach. Extensive genomic comparisons, involving the genome of LY240594T and those of 82 Finegoldia strains from GenBank, were instrumental in revealing genetic relationships within the Finegoldia genus. RESULTS: Strain LY240594 was initially identified as F. magna based on MALDI-TOF MS analysis, showing 99.7% 16S rRNA gene sequence similarity with the type strain of F. magna CCUG 17636T. However, there were 68.5% similarity with dDDH method and 90.9% similarity by ANI analysis respectively, between LY240594T and the selected type strain, F. magna DSM 20470T.Biochemical differences were also found between two strains. The ANI and genomic analysis of 82 Finegoldia sp. strains and Strain LY240594 revealed that those strains could be categorized into at least three groups using a 95% ANI threshold. CONCLUSION: Comprehensive characterization supported the proposal of a new species within the genus Finegoldia, named Finegoldia dalianensis sp. nov. The type strain, LY240594T (=GDMCC 1.4375T =KCTC 25838T), features 1,938 genes and a G+C content of 31.8 mol%. Genomic comparisons and ANI studies elucidated substantial heterogeneity within the Finegoldia genus.

Comparative genome analysis of cluster EF bacteriophages Ajin and OverHedge isolated from soil in Tennessee.

Bacteriophages Ajin and OverHedge were isolated from soil in Tennessee using the bacterium Microbacterium foliorum. Ajin and OverHedge (cluster EF) have a genome of 56,993 bp and 56,559 bp, containing 86 and 81 predicted genes, respectively. The Ajin genome has unique genes, phosphatase and glycosyltransferase, compared to the OverHedge.

Isolation and characterization of lytic bacteriophage vB_KpnP_23: A promising antimicrobial candidate against carbapenem-resistant Klebsiella pneumoniae.

The global health threat posed by carbapenem-resistant Klebsiella pneumoniae (CRKP) is exacerbated by the limited availability of effective treatments. Bacteriophages are promising alternatives to conventional antimicrobial agents. However, current phage databases are limited. Thus, identifying and characterizing new phages could provide biological options for the treatment of multi-drug resistant bacterial infections. Here, we report the characterization of a novel lytic phage, vB_KpnP_23, isolated from hospital sewage. This phage exhibited potent activity against carbapenemase-producing CRKP strains and was characterised by an icosahedral head, a retractable tail, and a genome comprising 40,987 base pairs, with a G + C content of 51 %. Capable of targeting and lysing nine different capsule types (K-types) of CRKP, including the clinically relevant ST11-K64, it demonstrated both high bacteriolytic efficiency and stability in various environmental contexts. Crucially, vB_KpnP_23 lacks virulence factors, antimicrobial resistance genes, or tRNA, aligning with the key criteria for therapeutic application. In vitro evaluation of phage-antibiotic combinations revealed a significant synergistic effect between vB_KpnP_23 and meropenem, levofloxacin, or amikacin. This synergy could lead to an 8-fold reduction in the minimum inhibitory concentration (MIC), suggesting that integrated treatments combining this phage with the aforementioned antibiotics may substantially enhance drug effectiveness. This approach not only extends the clinical utility of these antibiotics but also presents a strategic advance in combating antibiotic resistance. Specifically, it underscores the potential of phage-antibiotic combinations as a powerful tool in the treatment of infections caused by CRKP, offering a promising avenue to mitigate the public health challenges of antibiotic-resistant pathogens.

Characterization and Genomic Analyses of dsDNA Vibriophage vB_VpaM_XM1, Representing a New Viral Family.

A novel vibriophage vB_VpaM_XM1 (XM1) was described in the present study. Morphological analysis revealed that phage XM1 had Myovirus morphology, with an oblate icosahedral head and a long contractile tail. The genome size of XM1 is 46,056 bp, with a G + C content of 42.51%, encoding 69 open reading frames (ORFs). Moreover, XM1 showed a narrow host range, only lysing Vibrio xuii LMG 21346 (T) JL2919, Vibrio parahaemolyticus 1.1997, and V. parahaemolyticus MCCC 1H00029 among the tested bacteria. One-step growth curves showed that XM1 has a 20-min latent period and a burst size of 398 plaque-forming units (PFU)/cell. In addition, XM1 exhibited broad pH, thermal, and salinity stability, as well as strong lytic activity, even at a multiplicity of infection (MOI) of 0.001. Multiple genome comparisons and phylogenetic analyses showed that phage XM1 is grouped in a clade with three other phages, including Vibrio phages Rostov 7, X29, and phi 2, and is distinct from all known viral families that have ratified by the standard genomic analysis of the International Committee on Taxonomy of Viruses (ICTV). Therefore, the above four phages might represent a new viral family, tentatively named Weiviridae. The broad physiological adaptability of phage XM1 and its high lytic activity and host specificity indicated that this novel phage is a good candidate for being used as a therapeutic bioagent against infections caused by certain V. parahaemolyticus strains.

Hybrid-genome sequence analysis of Enterobacter cloacae FACU and morphological characterization: insights into a highly arsenic-resistant strain.

Many organisms have adapted to survive in environments with high levels of arsenic (As), a naturally occurring metalloid with various oxidation states and a common element in human activities. These organisms employ diverse mechanisms to resist the harmful effects of arsenic compounds. Ten arsenic-resistant bacteria were isolated from contaminated wastewater in this study. The most efficient bacterial isolate able to resist 15,000 ppm Na2HAsO4·7H2O was identified using the 16S rRNA gene and whole genome analysis as Enterobacter cloacae FACU. The arsenic E. cloacae FACU biosorption capability was analyzed. To further unravel the genetic determinants of As stress resistance, the whole genome sequence of E. cloacae FACU was performed. The FACU complete genome sequence consists of one chromosome (5.7 Mb) and two plasmids, pENCL 1 and pENCL 2 (755,058 and 1155666 bp, respectively). 7152 CDSs were identified in the E. cloacae FACU genome. The genome consists of 130 genes for tRNA and 21 for rRNAs. The average G + C content was found to be 54%. Sequencing analysis annotated 58 genes related to resistance to many heavy metals, including 16 genes involved in arsenic efflux transporter and arsenic reduction (five arsRDABC genes) and 42 genes related to lead, zinc, mercury, nickel, silver, copper, cadmium and chromium in FACU. Scanning electron microscopy (SEM) confirmed the difference between the morphological responses of the As-treated FACU compared to the control strain. The study highlights the genes involved in the mechanism of As stress resistance, metabolic pathways, and potential activity of E. cloacae FACU at the genetic level.

An innovative approach to decoding genetic variability in Pseudomonas aeruginosa via amino acid repeats and gene structure profiles.

Pseudomonas aeruginosa, a common pathogen in nosocomial infections, presents significant global health challenges due to its high prevalence and mortality rates. However, the origins and distribution of this bacterium remain unclear, partly due to the lack of effective gene typing methods. This situation necessitates the establishment of trustworthy and high-resolution protocol for differentiating closely related P. aeruginosa strains. In this context, the present study attempted to undertake a comparative genomic analysis of multiple P. aeruginosa strains available in the public database NCBI, with the goal of identifying potential genetic markers for measuring the genetic diversity. The preliminary comparative analysis of 816 P. aeruginosa strains revealed notable variations in two genes-specifically, the CDF family iron/cobalt efflux transporter AitP and the protease modulator HflC-across 44 strains. These variations were associated with single amino acid repeats (SHRs) that responsible for encoding histidine residue. Additionally, comparative gene map analysis revealed differential clustering patterns in the Rsx and TAXI genes among 16 strains. Interestingly, the gene structure pattern observed in TAXI groups displayed a strong correlation with the SHRs pattern in the CDF and HflC groups. In addition, the SHRs pattern of CDF and HflC were strongly correlated with MLST sequence type number. Overall, the study present a novel genetic markers based on SHRs and gene cluster patterns, offering a reliable method for genotyping of P. aeruginosa.