Genomic Analysis Research Articles

Distinct molecular responses of mangrove plants to hypoxia and reoxygenation stresses contribute to their resilience in coastal wetland environment

Mangroves adapt to periodical submergence and constitute resilient ecosystems in coastal environments. The question is whether they can sustain long submergence stress when sea level rises as a consequence of climate change. To address this, seedlings of two representative mangrove species that acclimate to low to mid tide (Avicennia marina) and mid to high tide (Kandelia obovata) conditions were treated with continual submergence for 7 days as extended hypoxia, or semi-diurnal cyclic submergence and reoxygenation for 7 days. At specific time points, leaves were collected to construct RNA-Sequencing libraries for gene expression analysis. Through the lens of transcriptome, the initial response of A. marina to submergence was mild but more dramatic after prolong immersion. However, the initial response of K. obovata was drastic and reduced in latitude later, suggesting distinct species-specific responses. After adapting to diurnal cycles, both species minimized transcriptome fluctuations similarly. Metabolically, during initial response, sucrose and starch were converted into glucose for fermentation to increase glycolytic flux, coupled with regeneration of NAD+. The energy amelioration was accompanied by longer term phytohormone regulations where ethylene signal transduction pathway was enhanced, but abscisic acid biosynthesis was reduced. Notably, gibberellic acids biosynthesis increased in A. marina but decreased in K. obovata as a unique feature. Genomic level analysis indicated that only about 30 % of the conserved plant submergence responsive genes were expressed during submergence in these mangroves. The function of an ethylene responsive gene was validated in transgenic Arabidopsis. This research elucidates distinct molecular mechanisms and metabolic pathways that empower A. marina and K. obovata to endure prolonged submergence and hypoxia. By highlighting their unique adaptive strategies in response to rising sea levels, these findings enhance our understanding of mangrove resilience and provide insights for the conservation and management of these essential coastal ecosystems in the face of climate change.

Genomic Insights into Drug Abuse: The Role of DNA and Protein-Coding Regions in Addiction and Genetic Mutation

Abstract This paper explores the genetic and epigenetic impacts of drug abuse, focusing on how chronic drug use can induce mutations in DNA, particularly within protein-coding regions, and alter gene expression through mechanisms such as DNA methylation. The study highlights the significant role of these genetic changes in the brain's reward pathways, which contribute to the development and persistence of addiction. Through a comprehensive literature review, the paper identifies key genetic factors associated with addiction susceptibility and the long-term effects of drug-induced epigenetic modifications. A proposed research framework is presented, emphasizing the need for longitudinal studies to track epigenetic changes over time, targeted genomic analysis to identify critical mutations, and the integration of multi-omics approaches to provide a holistic understanding of drug abuse's impact on the genome. The paper also addresses ethical considerations, including the importance of protecting genetic privacy and preventing stigmatization based on genetic findings. The study concludes that advancing our understanding of the genetic and epigenetic mechanisms underlying addiction can lead to more effective, personalized treatment strategies and inform public health policies aimed at mitigating the effects of drug abuse.

Comparative Genomic Analysis Reveals Distinct Virulence and Resistance Mechanisms in 21 Bacterial Fish Pathogens

The rising bacterial infections threaten world aquaculture and wild fish populations, making it imperative to increase the understanding of the mechanisms of pathogenic virulence and resistance. This study applies comparative genomic analysis to 21 bacterial fish pathogens, using whole-genome sequences from public genomic resources and sophisticated bioinformatics tools for screening of virulence factors, mobile genetic elements, antibiotic resistance genes, anti-phage defense mechanisms and secretory systems. We have seen that the different pathogens depict a wide range of variability regarding virulence and resistance potential, which may be attributed to species-specific adaptation. Notably, Streptococcus agalactiae and Mycobacterium salmoniphilum were found to possess high offensive and defensive virulence potential, but at different regulative controls. We also found diverse secretion systems and intricate mechanisms for antibiotic resistance, which have provided very important insights into how pathogens adapt to their environments. By categorizing functional genes and finding anti-phage systems, our analysis has revealed new insights into the complex interactions among bacterial virulence, resistance, and host defense mechanisms. These findings not only shed new light on the bacterial pathogenesis process in aquaculture but also provide the bases for focused, therapeutically-based strategies and genomic surveillance programs able to improve disease management and sustainability in aquaculture environments.

Comparative genomic analysis and characterization of novel high-quality draft genomes from the coal metagenome.

Coal, a sedimentary rock harbours a complex microbial community that plays a significant role in its formation and characteristics. However, coal metagenome sequencing and studies were less, limiting our understanding of this complex ecosystem. This study aimed to reconstruct high-quality metagenome-assembled genomes (MAGs) from the coal sample collected in the Neyveli mine to explore the unrevealed diversity of the coal microbiome. Using Illumina sequencing, we obtained high-quality raw reads in FASTQ format. Subsequently, de novo assembly and binning with metaWRAP software facilitated the reconstruction of coal MAGs. Quality assessment using CheckM identified 10 High-Quality MAGs (HQ MAGs), 7 medium-quality MAGs (MQ MAGs), and 6 low-quality MAGs (LQ MAGs). Further analysis using GTDB-Tk revealed four HQ MAGs as known species like Dermacoccus abyssi, Sphingomonas aquatilis, Acinetobacter baumannii, and Burkholderia cenocepacia. The remaining six HQ MAGs were classified as Comamonas, Arthrobacter, Noviherbaspirillum, Acidovorax, Oxalicibacterium, and Bordetella and designated as novel genomes by the validation of digital DNA-DNA hybridization (dDDH). Phylogenetic analysis and further pangenome analysis across the phylogenetic groups revealed a similar pattern with a high proportion of cloud genes. We further analysed the functional potential of these MAGs and closely related genomes using COG. The comparative functional genomics revealed that novel genomes are highly versatile, potentially reflecting adaptations to the coal environment. BlastKOALA was used to conduct a detailed analysis of the metabolic pathways associated with the MAGs. This study highlights the comparative genomic analysis of novel coal genomes with their closely related genomes to understand the evolutionary relationships and functional properties.

Polyphasic identification of Vibrio species from aquatic sources using mass spectrometry, housekeeping gene sequencing and whole genome analysis

Accurate bacterial identification is essential for determining the causative agent of an infection, thus facilitating appropriate treatment and management strategies in both human and animal health contexts. Some species in the Vibrio genus are recognized pathogens, associated with a variety of infections. However, identification of these bacteria is oftentimes controversial. Therefore, we aimed to evaluate different identification approaches in terms of their reliability in distinguishing Vibrio species. To achieve this, we selected a set of 40 Vibrio isolates previously recovered from water and floating plastic samples in a large bay environment and identified them employing MALDI-TOF mass spectrometry, and rrs and pyrH gene sequencing. A subset of isolates was also submitted to whole genome sequencing. Overall, MALDI-TOF was found to be a fast-screening methodology for identification, notably at genus-level. However, for better species discrimination, pyrH gene sequencing stood out as a more reliable tool in contrast to rrs gene sequencing and MALDI-TOF, as corroborated by whole genome sequencing analysis.

Effect of high mobility group box 1 pathway inhibition on gene expression in the prefrontal cortex of mice exposed to alcohol

The high mobility group box 1 (HMGB1) pathway plays a pivotal role in the development of alcohol-induced brain injury. Glycyrrhizinic acid (GlyA) is widely regarded as an inhibitor of HMGB1. The objective is to investigate the impact on gene expression in the prefrontal cortex,we sequenced the transcriptome in control, alcohol-exposed, and HMGB1-inhibited groups of mice. We verified our findings by real-time quantitative PCR (qRT-PCR). An alcohol exposure model was established in mice by intraperitoneal injection of alcohol. Transcriptome sequencing and bioinformatics analyses were performed on prefrontal cortex tissue. Kyoto Encyclopedia of Genes and Genomes analysis was performed to identify pivotal pathways of differentially expressed genes. The role of relevant genes was verified by qRT-PCR. Expression of genes involved in the neuroactive ligand-receptor interaction pathway exhibited an increase in mice from the alcohol-exposed group.However, there were no significant differences observed in the expression of these genes between control and those receiving an intraperitoneal injection of alcohol along with a HMGB1 inhibitor. Mice in the alcohol-exposed group showed increased gene expression of Cysltr2, Chrna6, Chrna3, Chrnb4, and Pmch. Expression of these genes was decreased in mice injected with HMGB1 inhibitor. Our study demonstrates that alcohol primarily influences gene expression in the prefrontal cortex of mice through the neuroactive ligand-receptor interaction pathway. HMGB1 inhibitor effectively inhibited the expression of this pathway. This study provides a novel route for drug development in alcohol-induced brain injury.

A series of patients infected with the emerging tick-borne Yezo virus in China: an active surveillance and genomic analysis

A series of patients infected with the emerging tick-borne Yezo virus in China: an active surveillance and genomic analysis

SSR markers based QTL mapping and genetic analysis for yield and yield-attributing traits in bitter gourd (Momordica charantia L.)

The present study was conducted for QTL mapping for yield and other yield attributing traits in bitter gourd using Simple Sequence Repeat (SSR) markers. A total of 630 SSR markers were screened for polymorphism in two contrasting parents (DBGS-2 and Pusa Purvi), out of which only 35 were polymorphic. F1 plants (10 individuals) in which hybridity was ascertained (using these polymorphic markers); were further employed for development of mapping population (F2) consisting of 120 plants. Higher variation was present in the mapping population as evident from the wider range value of the characters. Continuous frequency distribution classes combined with bell-shaped, symmetrical normal distribution curve, revealed the quantitative inheritance nature of the traits studied. Higher PCV than the GCV for all the traits, along with high difference between the PCV and GCV for majority of traits indicated higher influence of environment in expression of these traits in the mapping population. Presence of transgressive segregation was also noted for majority of the traits. Amongst the various linkage groups (LG), LG 4 had the maximum number of markers, covering 171.07 cM map distance. LG4 also possessed the maximum number (nine) of QTLs while LG1 had six. QTL mapping using polymorphic SSRs resulted in detection of a total of 28 QTLs for fourteen traits viz. yield per plant (kg), earliness or flower related traits (node to first female flower, node to first male flower, days to first male flower, male to female flower ratio), fruit traits (fruit number per plant, fruit diameter (cm), fruit length/ diameter ratio, pericarp thickness (mm) and number of seed per fruit) and vegetative traits (internodal length (cm), number of primary branches, leaf width (cm), length and width ratio). The LOD score of these QTLs ranged from 3.01 to 64.47, the total phenotypic variances (PVE) ranged from 1.52 to 34.57 % and additive effects ranged from –3.69 to 17.07. Of the total, nineteen were major QTLs, having PVE >10 %. Three QTLs were detected for yield per plant while a total of seven for the traits imparting earliness viz. days to first male flower, node to first female flower and node to first male flower. Amongst all the QTLs detected, qFrtLDR-4-1 (K) had the maximum LOD (64.47) and PVE (34.57 %) value. Two hotspots were detected with multiple QTLs clustered in the LG 1. The first hotspot possessed four QTLs [qLfW-1-1, qMFR-1-1 (K), qSPF-1-1, qNFmlF-1-1 (K)] while the second had two related to yield per plant [qYldpl-1-1 (K) and qYldpl-1-1]. Many of these QTLs are also being reported for the first time in bitter gourd. The findings of the present study can be used to fasten the bitter gourd improvement by utilizing these in MAS, DNA fingerprinting, genetic mapping, genomics analysis etc.

Bokeelamides: Lipopeptides from Bacteria Associated with Marine Egg Masses.

Moon snails (family: Naticidae) lay egg masses that are rich in bacterial species distinct from the surrounding environment. We hypothesized that this microbiome chemically defends the moon snail eggs from predation and pathogens. Herein, we report the discovery of bokeelamides, new lipopeptides from the egg mass-associated bacterium, Ectopseudomonas khazarica, which were discovered using mass spectrometry (MS)-based metabolomics. The structures of the bokeelamides were elucidated using two-dimensional (2D) nuclear magnetic resonance (NMR), tandem MS, Marfey's, and genomic analyses.

Longitudinal analysis of genetic and epigenetic changes in human pluripotent stem cells in the landscape of culture-induced abnormality.

Human embryonic stem cells (hESCs) are naturally equipped to maintain genome integrity to minimize genetic mutations during early embryo development. However, genetic aberration risks and subsequent cellular changes in hESCs during in vitro culture pose a significant threat to stem cell therapy. While a few studies have reported specific somatic mutations and copy number variations (CNVs), the molecular mechanisms underlying the acquisition of 'culture-adapted phenotypes' by hESCs are largely unknown. Therefore, we conducted comprehensive genomic, single-cell transcriptomic, and single-cell ATAC-seq analyses of an isogenic hESC model displaying definitive 'culture-adapted phenotypes'. We found that hESCs lacking TP53, in which loss-of-function mutations were identified in human pluripotent stem cells (hPSCs), presented a surge in somatic mutations. Notably, hPSCs with a copy number gain of 20q11.21 during early passage did not present 'culture-adapted phenotypes' or BCL2L1 induction. Single-cell RNA-seq and ATAC-seq analyses revealed active transcriptional regulation at the 20q11.21 locus. Furthermore, the induction of BCL2L1 and TPX2 to trigger 'culture-adapted phenotypes' was associated with epigenetic changes facilitating TEA domain (TEAD) binding. These results suggest that 20q11.21 copy number gain and additional epigenetic changes are necessary for expressing 'culture-adapted phenotypes' by activating gene transcription at this specific locus.

Molecular characterization of rabies virus from wild and domestic animals in the Sultanate of Oman.

Rabies virus (RV) is endemic in some Arabian countries. However, it is difficult to control RV without understanding the epidemiological evolution of endemic RV isolates. The current study aimed to characterize RV from domestic and wild animal clinical cases in Oman. Twelve brain samples from domestic (Five camels, three goats and one cattle) and wild animals (Two foxes and one honey badger) were investigated from different locations in Oman between 2017 and 2020. All samples were confirmed by RV nucleoprotein (N) gene-specific primers. Seven out of the 12 amplified samples were successfully sequenced and subjected to sequence and phylogenetic analysis. The detected RVs shared an in-between 96.8%-98.7% and 96.9%-99% nucleotide and amino acid identities, respectively. However, the wild animal RVs shared only 92.6%-93.9% and 95.9% nucleotide and amino acid identities with the domestic animal RVs, respectively. Negri bodies were detected histologically in six brain samples from camels (n = 3), goats (n = 1) and foxes (n = 2). The RVs from domestic animals shared 97%-98.7% and 98%-100% nucleotide and amino acid identities with the previously published fox RVs from Oman and Gulf countries. Phylogenetic analysis suggested that all RV sequences belong to a distinct clade confined to the previously reported clade V within the Middle Eastern Cluster. As indicated by the analysis of RVs from different locations between 2017 and 2020, a genetic variant isolated to the Gulf region may exist within the Middle East clade. Moreover, it appears that new RV lineages are emerging rapidly within this region. Therefore, a comprehensive genomic and phylogenetic analysis of the circulating RV is important for the development of future prevention and control strategies.

Genomic characterization and probiotic potency of Bacillus velezensis CPA1-1 reveals its potential for aquaculture applications

Biological prevention and control are increasingly applied in sustainable aquaculture, and Bacillus spp. has been revealed to good alternatives to antibiotics. This research examined the probiotic capabilities of Bacillus velezensis CPA1-1 by genomic and phenotypic analysis. The genome sequence showed that B. velezensis CPA1-1 has a 3,925,520 bp chromosome with 46.49 % GC content and 3762 CDSs. And eight clusters of secondary metabolite biosynthesis genes related to antibacterial compounds were predicted in CPA1-1 genome, including surfactin, difficidin, bacillibactin, fengycin, bacilysin, bacillaene, macrolactin H, butirosin A. Besides, the antimicrobial assay indicated that strain CPA1-1 exhibited strong antagonistic capacity against non-O1/O139 Vibrio cholerae GXFL1-4 isolated from diseased Macrobrachium rosenbergii, and MIC of CPA1-1 fermentation broth against GXFL1-4 was 1.0 × 105 CFU/mL. Furthermore, administering CPA1-1 markedly elevated the activities of ACP, AKP, and SOD in M. rosenbergii, and the immune-related genes, including ALF, Crustin, Hemocyanin, Prophenoloxidase, C-type lectin and HSP70, also exhibited higher expression in the CPA1-1 treated groups. Additionally, M. rosenbergii in the test group treated with CPA1-1 could resist non-O1/O139 V. cholerae GXFL1-4 infection by the challenge test. Our study contributed to reveal biocontrol mechanisms of B. velezensis CPA1-1, and demonstrated that CPA1-1 has promise as a probiotic agent for aquaculture.

Predictive genomic and transcriptomic analysis on endoscopic ultrasound-guided fine needle aspiration materials from primary pancreatic adenocarcinoma: a prospective multicentre study

We apply endoscopic ultrasound-guided fine needle aspiration biopsy to cytopathologically diagnose and sample nucleic acids from primary tumours regardless of the disease stage. 397 patients with proven pancreatic adenocarcinoma were included and followed up in a multicentre prospective study. DNA and mRNA were extracted from materials of primary tumours obtained by endoscopic ultrasound-guided fine needle aspiration biopsy and analysed using targeted deep sequencing and RNAseq respectively. The variant allele frequency of the KRAS mutation was used to evaluate the tumour cellularity, ranging from 15 to 20% in all cells, regardless of the tumour stage. The molecular profile of metastatic primary tumours significantly differed from other types of tumours, more frequently having TP53 mutations (p=0.0002), less frequently having RNF43 mutations, and possessing more basal-like mRNA component (p=0.001). Molecular markers associated with improved overall survival were: mutations in homologous recombination deficiency genes in patients who received first-line platinum-based chemotherapy (p=0.025) and wild-type TP53 gene in patients with locally advanced tumours who received radio-chemotherapy (p=0.01). The GemPred transcriptomic profile was associated with a significantly better overall survival in patients with locally advanced or metastatic pancreatic cancer who received a gemcitabine-based first-line treatment (p=0.019). The combination of genomic and transcriptomic analyses of primary pancreatic tumours enables us to distinguish metastatic tumours from other tumour types. Our molecular strategy may assist in predicting overall survival outcomes for platinum or gemcitabine-based chemotherapies, as well as radio-chemotherapy. Institut National Du Cancer (BCB INCa_7294), CHU of Toulouse, Inserm and Ligue Nationale Contre le Cancer (CIT program).

Non-coding RNA alterations in occlusal disharmony-induced anxiety-like behaviour.

Occlusal disharmony (OD) may induce anxiety-like behaviours; however, the underlying mechanism remains unclear. Herein, we explored the expression profiles of non-coding RNAs (ncRNAs), along with their biological function and regulatory network, in anxiety-like behaviour induced by OD. Occlusal disharmony was produced by anterior crossbite of C57BL/6 mice. Behavioural tests, corticosterone (CORT) and serotonin (5-HT) levels were used to measure anxiety. In addition, RNA sequencing was used to screen all differentially expressed (DE) ncRNAs. Moreover, the RNA-binding proteins interacting with ncRNAs were predicted by the ENCORI database and confirmed using western blots. The significant differences in behavioural tests and CORT suggested the successful induction of anxiety-like behaviour by OD. In OD mice, ncRNAs were significantly dysregulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested that the DE ncRNAs were enriched in anxiety-related pathways. CircRNA10039 was upregulated, and PTBP1 was predicted to interact with circRNA10039. In addition, KEGG pathway analysis showed that PTBP1 may be associated with messenger RNA biogenesis and spliceosomes. OD induced by anterior crossbite can lead to the anxiety-like behaviours. During this process, ncRNA also changes. CircRNA10039 and PTBP1 may play a role in OD-induced anxiety-like behaviours.

Genomic epidemiology and immune escape of SARS-CoV-2 recombinant strains circulating in Botswana

Background: SARS-CoV-2 continues to evolve and evade host immunity. We characterized the molecular and mutational landscape of SARS-CoV-2 recombinant strains in Botswana.Methods: We performed genomic, phylogenetic, and immunoinformatic analyses of 5,254 near-complete genomes from 2020 to 2023. We assessed the presence of mutations of interested (MutOI) that may be associated with immune escape in silico.Results: We observed a few recombinant strains in Botswana, with the majority being descendants of Omicron (XBB*), except for XV and XM. Most recombinant sequences corresponded to transmission clusters. Most recombination events occurred within the Receptor Binding Domain (RBD) of the Spike (S) protein. We identified 17 MutOI among different proteins, with the majority occurring at a very low (<4.8 × 10⁻⁵) global prevalence. We also observed S:Q474K, a MutOI in the RBD, that was predicted to escape HLA class I-mediated immune responses. Molecular surveillance is vital to inform early detection and response to potential variants with heightened immune and vaccine breakthrough properties.Conclusions: These results underscore the need for continued molecular surveillance to map the evolutionary landscape of SARS-CoV-2.

Somatic reversion in Wiskott-Aldrich syndrome: Case reports and mechanistic insights.

This report describes two brothers from India and a Chinese patient with somatic reversion of an inherited deleterious mutation in the WAS gene. Both the Indian siblings had inherited a single nucleotide deletion causing a frameshift mutation (c.1190del, p.Pro397Argfs*48) (variant 1: marked in blue) from the mother. Another variant (variant 2: marked in red), a 12-nucleotide deletion at position 1188-1199 (c.1188_1199del, p.P401_P404del) was also found, which resulted in restoration of the frame and subsequent rescue of the protein sequence. DNA sequencing from buccal mucosal cells revealed only the inherited variant (variant 1), while no reversion mutation was identified in the mucosal cells. Similarly, the Chinese patient was found to have a novel germline 14-base duplication (ACGAAAATGCTTGG) c.120_132 + 1dup (variant 1). This resulted in abolishment of the original splice junction coupled with the creation of a new junction 14 bases 3' and a frameshift mutation with predicted protein truncation p. Thr45Aspfs*. DNA from the patient's PBMC showed co-existence of wild-type and mutated sequences, but only the mutant was present in the buccal cells. Genomic and mRNA analysis of the isolated CD3+ T lymphocytes, CD3- mononuclear cells, and EBV-transformed B lymphocytes indicated that the reverant variant (germline variant was restored to wild-type sequence) were selectively found in CD3+ T lymphocytes.

Exploration and identification of diabetes targets in nursing: CDH1 and DVL1.

Diabetes is a chronic disease caused by absolute or relative insufficiency of insulin secretion and impaired insulin utilization. CDH1 and DVL1 role in diabetes and its nursing care is unclear. The diabetes dataset GSE21321 and GSE19790 profiles were downloaded from the gene expression omnibus (GEO) database. Perform differentially expressed genes (DEGs) screening, weighted gene co-expression network analysis (WGCNA), protein-protein interaction (PPI) network construction and analysis, functional enrichment analysis, gene set enrichment analysis (GSEA), immune infiltration analysis, and Comparative Toxicogenomics Database (CTD) analysis. Gene expression heat map was drawn. TargetScan was used to screen the miRNA that regulates central DEGs. 1983 DEGs were obtained. According to Gene Ontology (GO) analysis, they were mainly enriched in signal regulation, catenin complexes, and signal receptor binding. In Kyoto Encyclopedia of Gene and Genome (KEGG) analysis, they were mainly concentrated in the Rap1 signaling pathway, cAMP signaling pathway, and Hippo signaling pathway. The DEGs are mainly enriched in cell signaling, Wnt signaling vesicles, growth factor activity, and the interaction between neural active ligands and receptors. In the enrichment project of Metascape, BMP signaling pathways and cell population proliferation can be seen in the GO enrichment project. The soft threshold power in WGCNA is set to 5. A total of 15 modules were generated. Core gene expression heatmap showed that core genes (CTNNB1, CDH1, DVL1) were highly expressed in diabetes samples. CTD analysis showed thatCTNNB1, CDH1, DVL1were associated with weight gain, inflammation, and necrosis. CDH1 and DVL1 are highly expressed in diabetes and may become molecular targets for diabetes and its care.

Characterization and genome analysis of two Aeromonas phages isolated from various sources related to chilled chicken

Characterization and genome analysis of two Aeromonas phages isolated from various sources related to chilled chicken

Chromosomal Type II Toxin–Antitoxin Systems May Enhance Bacterial Fitness of a Hybrid Pathogenic Escherichia coli Strain Under Stress Conditions

The functions of bacterial plasmid-encoded toxin–antitoxin (TA) systems are unambiguous in the sense of controlling cells that fail to inherit a plasmid copy. However, its role in chromosomal copies is contradictory, including stress-response-promoting fitness and antibiotic treatment survival. A hybrid pathogenic Escherichia coli strain may have the ability to colonize distinct host niches, facing contrasting stress environments. Herein, we determined the influence of multiple environmental stress factors on the bacterial growth dynamic and expression profile of previously described TA systems present in the chromosome of a hybrid atypical enteropathogenic and extraintestinal E. coli strain. Genomic analysis revealed 26 TA loci and the presence of five type II TA systems in the chromosome. Among the tested stress conditions, osmotic and acid stress significantly altered the growth dynamics of the hybrid strain, enhancing the necessary time to reach the stationary phase. Using qPCR analyses, 80% of the studied TA systems were differentially expressed in at least one of the tested conditions, either in the log or in the stationary phase. These data indicate that type II TA systems may contribute to the physiology of pathogenic hybrid strains, enabling their adaptation to different milieus.

Genome sequencing and transcriptome analysis provide an insight into the hypoxia resistance of Channa asiatica

Channa asiatica is an economically valuable fish species and excellent model for studying hypoxic tolerance. However, the underlying genetic and molecular mechanisms are poorly understood. In this study, we assembled a high-quality C. asiatica genome (23 chromosomes, totaling 722 Mb) using a combination of Illumina short-read, PacBio long-read, and Hi-C sequencing. Repetitive elements accounted for 28.39%of the C. asiatica genome, and 23,949 protein-coding genes were predicted, with 96.63 % of these functionally annotated. Moreover, a comparative genomic analysis of 12 fish genomes showed that gene families associated with oxygen binding and transport were expanded in C. asiatica. In addition, transcriptome analysis revealed that multiple oxidative stress pathways were activated when C. asiatica was exposed to air. In conclusion, this study provided high-quality genome assembly and transcriptome data, both serving as critical resources for researching the genetic basis of hypoxic tolerance in C. asiatica.