Genomic Analysis Research Articles

Comparison of Crohn’s disease-associated adherent-invasive Escherichia coli (AIEC) from France and Hong Kong: results from the Pacific study

ABSTRACT Association between ileal colonization by Adherent-Invasive Escherichia coli (AIEC) and Crohn’s disease (CD) has been widely described in high-incidence Western countries but remains unexplored in Asian countries with a fast increase in CD incidence. In the PACIFIC study, we compared the characteristics of AIEC pathobionts retrieved from ileal biopsies of CD patients enrolled in France (FR) and Hong Kong (HK). The prevalence of AIEC was similar in France (24.5%, 25/102) and Hong Kong (30.0%, 18/60) (p = 0.44). No difference was observed between the two populations of AIEC regarding adhesion and invasion levels. When tested for antibiotic resistance, the proportion of AIEC strains resistant to ampicillin, piperacillin, tobramycin, and gentamicin was significantly higher in HK AIEC strains compared to French strains. AIEC strains from FR or HK population were both able to persist in the mice intestine (DSS-treated CEABAC10 mice model). Moreover, genomic analysis of 25 FR and 17 hK AIEC strains using next-generation sequencing revealed the co-existence of several virulence factors associated with enteric E. coli pathotypes, although no single virulence factor was significantly associated with either country of origin or AIEC status. In vitro, all AIEC strains (FR and HK) were sensitive to the EcoActive™ phage cocktail, suggesting that it could be a promising option to target AIEC in CD across the world.

Insight into Antifungal Metabolites from Bacillus stercoris 92p Against Banana Cordana Leaf Spot Caused by Neocordana musae

Banana crop ranks among the most crucial fruit and food crops in tropical and subtropical areas. Despite advancements in production technology, diseases such as cordana leaf spot, caused by Neocordana musae, remain a significant challenge, reducing productivity and quality. Traditional chemical controls are becoming less effective due to the development of resistance in target pathogens, which pose significant environmental and health concerns. Consequently, there is growing attention toward the development of biocontrol strategies. Here, we identified a new bacterial strain, Bacillus stercoris 92p, from the rhizosphere soil of banana. We evaluated its ability to suppress the growth of N. musae and other fungal pathogens that cause leaf spot disease in bananas. The inhibitory effect of B. stercoris 92p were checked using dual culture assays, microscopic observations, and pot experiments. Furthermore, the biocontrol mechanisms were investigated using whole-genome sequencing and biochemical analyses. The results showed that B. stercoris 92p exhibited significant antifungal activity against N. musae and other fungal pathogens, with inhibition rates exceeding 70%. Microscopic examination revealed significant morphological alterations in the hyphae and conidia of the tested pathogens. In pot experiments, B. stercoris 92p effectively reduced the severity of cordana leaf spot, achieving a biocontrol efficacy of 61.55%. Genomic analysis and biochemical tests indicated that B. stercoris 92p produces various antifungal compounds, including lipopeptides (fengycins and surfactins), hydrolytic enzymes (proteases and amylases), and phosphate-solubilizing metabolites. In conclusion, the study highlights that B. stercoris could potentially be used as a potential biological control agent against cordana leaf spot.

Combining Network Pharmacology and Transcriptomic Strategies to Explore the Pharmacological Mechanism of Total Ginsenoside Ginseng Root and Its Impact on Antidepressant Effects

Depression is one of the most common neurological diseases, which imposes a substantial social and economic burden on modern society. The purpose of this study was to explore the mechanism of total ginsenoside ginseng root (TGGR) in the treatment of depression through a comprehensive strategy combining network pharmacology, transcriptomics, and in vivo experimental validation. The Traditional Chinese Medicine Systematic Pharmacology (TCMSP) database and literature were used to collect the main components and targets of TGGR. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were applied to explore the underlying mechanisms. In addition, the chronic unpredictable mild stress (CUMS)-induced C57BL/6 mouse model was used to evaluate the antidepressant activity of TGGR. The results showed that TGGR improved depression-like behavior in mice and increased the decrease in serum 5-hydroxytryptamine (5-HT) and brain-derived neurotrophic factor (BDNF) levels caused by CUMS. Combined network pharmacology and transcriptomic analysis showed that the AMP-activated kinase (AMPK) signaling pathway mainly enriched the core target. Immunohistochemistry, Western blotting, and reverse transcription quantitative polymerase chain reaction (RT-qPCR) were used to confirm whether TGGR exerts antidepressant effects by regulating this pathway. The results showed that TGGR has a regulatory impact on related proteins in the AMPK pathway, and the regulatory effect of TGGR on proteins was inhibited after the administration of related pathway inhibitors. In summary, total ginsenosides may regulate the AMPK signaling pathway and activate the sirtuin 1 (SIRT1) peroxisome proliferator-activated receptor-gamma coactivator 1-alpha (PGC-1α) pathway to have therapeutic effects on depression.

Therapeutic potential of Lacticaseibacillus rhamnosus grx10 and its derived postbiotic through gut microbiota and MAPK/MLCK/MLC pathway-mediated intestinal barrier repairment in ulcerative colitis.

Lacticaseibacillus rhamnosus grx10 (grx10) has shown promising potential in promoting intestinal health as predicted by genomic and metabolomic analyses. Given the increasing prevalence of ulcerative colitis (UC) and the limitations of existing treatments, exploring alternative therapeutic strategies is essential. This study explored the therapeutic effects and underlying mechanisms of grx10 and its derived postbiotic (P-grx10) in a mouse model of dextran sulfate sodium (DSS)-induced chronic UC. The intervention with grx10 and P-grx10 significantly alleviated clinical symptoms and improved biochemical markers in UC mice. These effects included reducing the disease activity index (DAI), improving colon length and histopathological damage, decreasing the secretion of inflammatory cytokines, and preventing the reduction of antioxidant enzymes. Additionally, grx10 and P-grx10 downregulated key proteins in the Mitogen-Activated Protein Kinase (MAPK)/myosin light chain kinase (MLCK)/myosin light chain (MLC) pathway, prevented the dissociation of tight junction (TJ) proteins and E-cadherin, reduced intestinal permeability, and restored the integrity of the intestinal barrier. Furthermore, both grx10 and P-grx10 modulated the composition and abundance of gut microbiota, helping to maintain intestinal microbiome homeostasis. In conclusion, this study provided evidence regarding the role of grx10 and P-grx10 in alleviating intestinal barrier dysfunction associated with UC and restoring gut microbiota balance. Notably, P-grx10 exhibited higher anti-inflammatory activity and better restoration of intestinal barrier function, whereas the live probiotic grx10 showed a stronger regulatory effect on the gut microbiota. These findings suggest that grx10 and P-grx10 could serve as promising nutritional adjunct therapies for UC, providing novel insights into the distinct roles of probiotic and its derived postbiotic in UC treatment.

The denitrification ability and nitrogen metabolism pathway of aerobic denitrifier Marinobacter alkaliphilus SBY-1 under low C/N ratios

Mariculture tail water is characterized as the low C/N ratios and thus blocks the conventional heterotrophic denitrification process due to insufficient carbon source. Therefore, oligotrophic marine bacteria with heterotrophic nitrification and aerobic denitrification (HN-AD) are urgently required to bioaugment aerobic biological filter. In this study, Marinobacter alkaliphilus SBY-1 was isolated and confirmed optimal nitrate removal capacity at a rate of 716 mg/L·d without ammonia production or nitrite accumulation under initial nitrate concentration of 800 mg/L, pH 7, salinity 20 ‰, sodium acetate as the carbon source, and low C/N ratios of 3.6. SBY-1 also demonstrated heterotrophic nitrification capability with a maximum ammonia removal rate reaching 69.21 % when ammonia was used as the nitrogen source. The enzymes involved in the HN-AD process including ammonia monooxygenase (AMO), nitrate reductase (NR), and nitrite reductase (NIR) were all detected in SBY-1 with superior activity observed for NR and NIR. Additionally, analysis of EPS and auto-aggregation revealed that SBY-1 exhibited excellent auto-aggregation ability under high influent nitrogen concentration conditions, making it more suitable for biofilm formation and further application in biofilm-based denitrification process. Genome analysis identified genes associated with Nar, Nap, Nas, Nir, Nif, Nrt, Nrf, Nor, Nos which confirmed that SBY-1 possessed a complete HN-AD pathway for nitrogen metabolism. The predicted nitrogen metabolism pathway of SBY-1 was NO3−-N → NO2−-N → NO→N2O → N2. These findings provide new insights into the efficient removal of nitrate by SBY-1 under lower C/N conditions.

Hydin as the Candidate Master Sex Determination Gene in Channel Catfish (Ictalurus punctatus) and Its Epigenetic Regulation.

Sex determination is a fascinating area of research. To date, more than 20 master sex determination (SD) genes have been reported from vertebrate animals. With channel catfish (Ictalurus punctatus), much work has been conducted to determine its master SD gene, ranging from genetic linkage mapping, genome-wide association (GWA) analysis, genome sequencing, comparative genome analysis, epigenomic analysis, transcriptome analysis, and functional studies. Here in this mini review, we provide positional, expression, regulatory, and functional evidence supporting hydin (hydrocephalus-inducing protein or HYDIN axonemal central pair apparatus protein-like) as a master SD gene in channel catfish. Hydin is located within the sex determination region (SDR) within a mapped 8.9-Mb non-recombinational segment on chromosome 4 of channel catfish. It is highly expressed in genetic males, but not in genetic females. The alleles of X and Y are highly differentially methylated with the X chromosome being hypermethylated and the Y chromosome hypomethylated. The hypomethylated Y allele of hydin is expressed while the hypermethylated X allele is not expressed. Such allelic expression fits well with the XY sex determination system of channel catfish. Functional analysis using a methylation blocker, 5-aza-dC, demonstrated that demethylation, especially within the SDR, is accompanied with increased expression of hydin, which led to sex reversal of genetic females into phenotypic males. These evidences support the candidacy of hydin as a master SD gene in channel catfish. Future knockout and analysis of affected genes after hydin knockout should provide insights into how hydin functions as a master SD gene.

Genome assembly of an endemic butterfly (Minois Aurata) shed light on the genetic mechanisms underlying ecological adaptation to arid valley habitat

BackgroundThe Hengduan Mountains, one of the global biodiversity hotspots with exceptional species richness and high endemism, contains numerous arid valleys that create a distinctive geographical and ecological landscape. However, the adaptive evolutionary mechanisms of organism in the arid valley remain poorly understood. Minois aurata, an endemic butterfly species found exclusively in the arid valley of the upper Minjiang River, represents an attractive model system for studying adaptive evolutionary mechanisms to arid valley environments.ResultsHere, we present the first chromosome-level genome assembly for Minois aurata, with a total size of approximately 609.17 Mb, and a scaffold N50 size of 23.88 Mb. These scaffolds were further clustered and anchored onto 29 chromosomes based on Hi-C data. A total of 16,163 protein-coding genes were predicted, of which 91.83% were functionally annotated. The expansion of transposable elements (TEs) accounts for the relatively large genome size of M. aurata, potentially aiding its adaptation to environmental conditions. Phylogenomic analyses based on 3,785 single-copy genes revealed that M. aurata is most closely related to Hipparchia semele. Further mitochondrial genome analysis of four Minois species placed M. aurata in a basal position within the genus, supporting it as an independent species. A total of 185 rapidly evolving and 232 specific gene families were identified in M. aurata. Functional enrichment analysis indicated that these gene families were mainly associated with ultraviolet radiation, heat and hypoxia responses. We also identified 234 positive selected genes in M. aurata, some of which are related to compound eye photoreceptor development, osmotic stress, and light stimulus response. Demographic analysis indicated that the effective population size of M. aurata decreased around 0.4 and 0.04 million years ago, respectively, coinciding with the localized sub-glaciation.ConclusionThe chromosome-level genome offers a comprehensive genomic basis for understanding the evolutionary and adaptive strategies of Minois aurata in the unique arid valley environment of the Hengduan Mountains, while also providing valuable insights into the broader mechanisms of organism adaptation to such habitats.

Genomic Insights into Stutzerimonas kunmingensis TFRC-KFRI-1 Isolated from Manila Clam (Ruditapes philippinarum): Functional and Phylogenetic Analysis

Stutzerimonas kunmingensis TFRC-KFRI-1, isolated from the gut of Manila Clam in the sediment of the West Sea of Korea, was investigated for its potential as a probiotic bacterium. This strain, belonging to the family Pseudomonadaceae, was previously classified as Pseudomonas kunmingensis but later reclassified to the genus Stutzerimonas, known for species with bioremediation and probiotic properties. To evaluate its genomic features and potential applications, we performed draft-genome sequencing and analysis. The genome of S. kunmingensis TFRC-KFRI-1 was assembled into a 4,756,396 bp sequence with a 62.8% GC content. Genomic analysis suggested potential genes for carbohydrate degradation and lactic acid production. The strain exhibited high average nucleotide identity (ANI) and 16S rRNA similarity with S. kunmingensis HL22-2T, further supporting its potential as a probiotic. This genome sequence provides valuable insights into the functional capabilities of S. kunmingensis TFRC-KFRI-1 and its potential applications in various industries, including aquaculture and food biotechnology. The genome sequence is available under GenBank accession number JBGJJB000000000.1, with related project information under BioProject PRJNA1147901 and Bio-Sample SAMN43173893.

Metatranscriptomic Analysis Reveals Actively Expressed Antimicrobial-Resistant Genes and Their Hosts in Hospital Wastewater

Antimicrobial resistance is a major global concern and economic threat, necessitating a reliable monitoring approach to understand its frequency and spread via the environment. Hospital wastewater serves as a critical reservoir for antimicrobial-resistant organisms; however, its role in resistance gene distribution and dissemination remains poorly understood. This study integrates metagenomic and metatranscriptomic analyses, elucidating the dynamics of antimicrobial resistance in hospital wastewater. Integrated metagenomic and metatranscriptomic sequencing were used to identify actively expressed antimicrobial-resistant genes and antimicrobial-resistant bacteria, offering comprehensive insights into antimicrobial resistance dynamics in hospital wastewater. Liquid chromatography–tandem mass spectrometry analysis revealed the presence of ampicillin, sulbactam, levofloxacin, sulfamethoxazole, and trimethoprim in the sample, which could apply selective pressure on antimicrobial resistance gene expression. While multidrug resistance genes were the most prevalent sequences in both metagenome-assembled genomes and plasmids, plasmid-derived sequences showed a high mRNA/DNA ratio, emphasizing the presence of functionally expressed antimicrobial resistance genes on plasmids rather than on chromosomes. The metagenomic and metatranscriptomic analyses revealed Serratia nevei MAG14 with high mRNA levels of antimicrobial resistance genes; moreover, multidrug-resistant Serratia sp., genetically related to MAG14, was isolated from the wastewater, supporting the phenotypic characterization of crucial antimicrobial-resistant bacteria and validating the genome analysis results. The findings underscore key genes and bacteria as targets for antimicrobial resistance surveillance in hospital wastewater to protect public and environmental health.

Phage cocktail amikacin combination as a potential therapy for bacteremia associated with carbapenemase producing colistin resistant Klebsiella pneumoniae

The increasing occurrence of hospital-associated infections, particularly bacteremia, caused by extensively drug-resistant (XDR) carbapenemase-producing colistin-resistant Klebsiella pneumoniae highlights a critical requirement to discover new therapeutic alternatives. Bacteriophages having host-specific bacteriolytic effects are promising alternatives for combating these pathogens. Among 12 phages isolated from public wastewater in Thailand, two phages-vB_kpnM_05 (myovirus) and vB_kpnP_08 (podovirus) showed broad-host range, producing bacteriolytic activities against 81.3% (n = 26) and 78.1% (n = 25) of 32 XDR carbapenemase-producing colistin-resistant K. pneumoniae, with capsular types—K15, K17, K50, K51, K52/wzi-50 and K2/wzi-2. Both phages showed short replication times, large burst sizes with rapid adsorptions. They exhibited significant stability under various environmental conditions. Genomic analysis revealed that both phages are genetically distinct phages from Myoviridae and Podoviridae family, with the lack of toxin, virulence, lysogeny and antibiotic resistance genes. These characteristics highlighted their promising potential for utilizing in phage therapy for combating XDR K. pneumoniae. Although phage cocktail combining vB_kpnM_05 and vB_kpnP_08 provided significant bacteriolysis for longer duration (8 h) than its monophage (6 h), bacterial regrowth was observed which suggested an evitable development of phage resistance under phages’ selection pressures. Future study will be undertaken to elucidate the precise mechanisms by which these XDR K. pneumoniae developed phage resistance and their associated fitness cost. Remarkably, combining phage cocktail with amikacin at their sub-inhibitory concentrations produced potent synergy by completely suppressing bacterial regrowth in vitro. Our study demonstrated the significant therapeutic and prophylactic effectiveness of a phage cocktail-amikacin combination as a promising alternative strategy for overcoming bacteremia associated with XDR K. pneumoniae having carbapenemase and colistin resistance in vivo.

Population Genetics and Invasion History of the European Starling Across Aotearoa New Zealand.

The expansion of human settlements over the past few centuries is responsible for an unprecedented number of invasive species introductions globally. An important component of biological invasion management is understanding how introduction history and postintroduction processes have jointly shaped present-day distributions and patterns of population structure, diversity and adaptation. One example of a successful invader is the European starling (Sturnus vulgaris), which was intentionally introduced to numerous countries in the 19th century, including Aotearoa New Zealand, where it has become firmly established. We used reduced representation sequencing to characterise the genetic population structure of the European starling in New Zealand, comparing it to that present in sampling locations in the native range and invasive Australian range. The population structure and genetic diversity patterns we found suggested restricted gene flow from the majority of New Zealand to the northmost sampling location (Auckland). We also profiled genetic bottlenecks and shared outlier genomic regions, which supported historical accounts of translocations between both Australian subpopulations and New Zealand, and provided evidence of which documented translocation events were more likely to have been successful. Using these results as well as historic demographic patterns, we demonstrate how genomic analysis complements even well-documented invasion histories to better understand invasion processes, with direct implications for understanding contemporary gene flow and informing invasion management.

Genomic and taxonomic characterization of the Comamonas sp. nov., a bacterium isolated from Brazilian Cerrado soil.

A novel strain identified as Comamonas sp. was isolated from the soil of the Brazilian savanna-like Cerrado biome, a global hotspot for biodiversity. Phylogenetic analysis based on 16S rRNA gene sequences showed that this strain is classified as Betaproteobacteria from the family Comamonadaceae. The digital DNA-DNA hybridization (dDDH) and Average Nucleotide Identity (ANI) results, of respectively 48.6% and < 93%, indicated that Comamonas sp. consists in a new species with Comamonas testosteroni as its closest strain. Comamonas sp. is a Gram-negative, rod-shaped, and non-spore-forming bacterium. Its colonies typically exhibit a round, convex, and irregular shape with a clear color and spotted edges. It is characterized as non-fermenting, aerobic, and motile, presenting both oxidase and catalase activities. The optimal growth parameters for this bacterial strain are 30°C, a pH range of 5-8, and 0% NaCl. In addition, its fatty acid profile included palmitic acid (C16:0) at 26.94%, 13-Methyltetradecanoic Acid (iso-C15:0) at 10.94%, myristic acid (C14:0) at 8.94%, and a summed feature comprising 16:1 ω7c, 16:1 ω6c, or 16:1 at 15.8%. Genomic analysis of Comamonas sp. revealed a GC content of 62.1% across its 5.6Mb genome. Phylogenomic and pangenome analyses, along with in silico phenotypic characterization indicate that this strain represents a novel species within the Comamonas genus, which we propose to name Comamonas brasiliensis nov.

Clinical and Genomic Phenotype of Brain Metastasis in Nasopharyngeal Carcinoma.

Brain metastasis in nasopharyngeal carcinoma is a rare but poor prognosis clinical problem. This study aims to investigate the clinical characteristics and identify the genomic profiling of nasopharyngeal carcinoma brain metastasis. Patients with a diagnosis of nasopharyngeal carcinoma who visited at the Fifth Affiliated Hospital of Sun Yat-sen University since January 2013 to December 2023 were retrospectively collected. Clinical data of patients diagnosed with nasopharyngeal carcinoma brain metastasis were extracted. Paraffin blocks of NPC brain metastases were acquired for immunohistochemistry and genetic testing. High-throughput second generation sequencing was performed for genomic analysis. The mutation landscape was further analyzed. Of the 2378 NPC patients from our database, only six were clinically diagnosed with nasopharyngeal carcinoma brain metastasis. Three were pathologically diagnosed with nasopharyngeal carcinoma brain metastasis. The time interval from the first diagnosis of nasopharyngeal carcinoma to brain metastasis was 15-56 months. The common sites of brain metastasis were frontal lobe and cerebellum, and could be single or multiple, cystic or solid lesions. The OS ranged from 7 to 48 months. Single nucleotide variants were found in 32 genes, such as PTEN, TP53, NFKBIA, KMT2C, and NOTCH1. Copy number variation occurred in five genes, including PTEN, CCDN1, FGF19, FGF3 and FGF4. PTEN and fibroblast growth factors might be involved in the molecular regulation of brain metastasis in nasopharyngeal carcinoma.

Re-sensitization of imipenem-resistant Pseudomonas aeruginosa and restoration of cephalosporins susceptibility in Enterobacteriaceae by recombinant Esterase B.

Sphingobium sp. SM42 Esterase B (EstB) is an enzyme with a dual function in degrading dibutyl phthalate (DBP) and catalyzing the cleavage of the C-S bond in C3-sidechains of the dihydrothiazine ring of cephalosporins, generating more active β-lactam derivatives. Global prokaryotic genome analysis revealed the existence of a gene identical to estB in Pseudomonas aeruginosa strain PS1 suggesting a horizontal gene transfer event involving estB. To investigate the effect of ectopic expression of EstB in the periplasm of Pseudomonas aeruginosa and several Enterobacteriaceae on antibiotic susceptibility levels, plasmid, pEstB, carrying a recombinant EstB fused with the signal peptide from Escherichia coli outer membrane protein A (OmpA) for periplasmic localization was constructed. The expression of EstB in the periplasm of P. aeruginosa and the Enterobacteriaceae: E. coli, Klebsiella pneumoniae, and Salmonella enterica serovar Typhi, increased susceptibility to carbapenems and cephalosporins. EstB reversed the imipenem resistance of P. aeruginosa ΔmexS and restored the changes in susceptibility to cephalosporins conferred by the downregulation of the outer membrane proteins, OmpK35 and OmpK36, in K. pneumoniae ΔramR-ompK36 to wild-type level. The introduction of EstB to the periplasmic space of Gram-negative bacteria can increase carbapenem and cephalosporin susceptibility.

Genome sequencing and comparative genomic analysis of bovine mastitis-associated non-aureus staphylococci and mammaliicocci (NASM) strains from India

We describe the whole-genome sequencing and comparative genomic analysis of 22 mastitis-associated NASM strains isolated from India. The mean genome size of the strains was 2.55 Mbp, with an average GC content of 32.2%. We identified 14 different sequence types (STs) among the 22 NASM strains. Of these, ST1 and ST6 of S. chromogenes were exclusively associated with bovine mastitis. Genome-wide SNP-based minimum spanning tree revealed the intricate phylogenetic relationships among NASM strains from India, categorizing them into five major clades. Interestingly, mastitis-associated strains formed separate subclades in all the NASM species studied, indicating distinct host-specific co-evolution. The study identified 32 antimicrobial resistance (AMR) genes and 53 virulence-associated genes, providing insights into the genetic factors that could contribute to the pathogenicity of NASM species. Some virulence and AMR genes were found in the predicted genomic islands, suggesting possible horizontal transfer events.

Chloroplast genome of four Amorphophallus species: genomic features,comparative analysis, and phylogenetic relationships among Amorphophallus species

BackgroundThe genus Amorphophallus (Araceae) contains approximately 250 species, most of which have high ecological and economic significance. The chloroplast genome data and the comprehensive analysis of the chloroplast genome structure of Amorphophallus is limited. In this study, four chloroplast genomes of Amorphophallus were sequenced and assembled. For the first time, comparative analyses of chloroplast genomes were conducted on the 13 Amorphophallus species in conjunction with nine published sequences.ResultsThe Amorphophallus chloroplast genomes exhibited typical quadripartite structures with lengths ranging from 164,417 to 177,076 bp. These structures consisted of a large single copy (LSC, 90,705 − 98,561 bp), a small single copy (SSC, 14,172 − 21,575 bp), and a pair of inverted repeats (IRs, 26,225 − 35,204 bp). The genomes contain 108 − 113 unique genes, including 76 − 79 protein-coding genes, 28 − 29 tRNA genes, and 4 rRNA genes. The molecular structure, gene order, content, codon usage, long repeats, and simple sequence repeats (SSRs) within Amorphophallus were generally conserved. However, several variations in intron loss and gene expansion on the IR-SSC boundary regions were found among these 13 genomes. Four mutational hotspot regions, including trnM-atpE, atpB, atpB-rbcL and ycf1 were identified. They could identify and phylogeny future species in the genus Amorphophallus. Positive selection was found for rpl36, ccsA, rpl16, rps4, rps8, rps11, rps12, rps14, clpP, rps3, ycf1, rpl20, rps2, rps18, rps19, atpA, atpF, rpl14, rpoA, rpoC1, rpoC2 and rps15 based on the analyses of Ka/Ks ratios. Phylogenetic inferences based on the complete chloroplast genomes revealed a sister relationship between Amorphophallus and Caladieae. All Amorphophallus species formed a monophyletic evolutionary clade and were divided into three groups, including CA-II, SEA, and CA-I. Amorphophallus albus, A. krausei, A. kachinensis and A. konjac were clustered into the CA-II clade, A. paeoniifolius and A. titanum were clustered into the SEA clade, A. muelleri ‘zhuyajin1’, Amorphophallus sp, A. coaetaneus, A. tonkinensis and A. yunnanensis were clustered into CA- I clade.ConclusionsThe genome structure and gene content of Amorphophallus chloroplast genomes are consistent across various species. In this study, the structural variation and comparative genome of chloroplast genomes of Amorphophallus were comprehensively analyzed for the first time. The results provide important genetic information for species classification, identification, molecular breeding, and evolutionary exploration of the genus Amorphophallus.

The unique and enigmatic spirochete symbiont of latrunculid sponges.

Bacterial symbionts are critical members of many marine sponge holobionts. Some sponge-associated bacterial lineages, such as Poribacteria, sponge-associated unclassified lineage (SAUL), and Tethybacterales, appear to have broad-host ranges and associate with a diversity of sponge species, while others are more species-specific, having adapted to the niche environment of their host. Host-associated spirochete symbionts that are numerically dominant have been documented in several invertebrates including termites, starfish, and corals. However, dominant spirochete populations are rare in marine sponges, having thus far been observed only in Clathrina clathrus and various species within the Latrunculiidae family, where they are co-dominant alongside Tethybacterales symbionts. This study aimed to characterize these spirochetes and their potential role in the host sponge. Analysis of metagenome-assembled genomes from eight latrunculid sponges revealed that these unusual spirochetes are relatively recent symbionts and are phylogenetically distinct from other sponge-associated spirochetes. Functional comparative analysis suggests that the host sponge may have selected for these spirochetes due to their ability to produce terpenoids and/or possible structural contributions.IMPORTANCESouth African latrunculid sponges are host to co-dominant Tethybacterales and Spirochete symbionts. While the Tethybacterales are broad-host range symbionts, the spirochetes have not been reported as abundant in any other marine sponge except Clathrina clathrus. However, spirochetes are regularly the most dominant populations in marine corals and terrestrial invertebrates where they are predicted to serve as beneficial symbionts. Here, we interrogated eight metagenome-assembled genomes of the latrunculid-associated spirochetes and found that these symbionts are phylogenetically distinct from all invertebrate-associated spirochetes. The symbiosis between the spirochetes and their sponge host appears to have been established relatively recently.

Exosomal LncRNA and CircRNA Regulate Peripheral Blood Mononuclear Cell Function through a Competitive Endogenous RNA Mechanism in Allergic Rhinitis.

Peripheral blood mononuclear cells (PBMCs) dysfunction is involved in the pathogenesis and progression of allergic rhinitis (AR). This study aims to investigate the competing endogenous RNA (ceRNA) networks in PBMCs influenced by differentially expressed long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) found in plasma exosomes induced by AR. All subjects were from the Affiliated Taizhou People's Hospital of Nanjing Medical University. Differential expression of mRNAs in PBMCs and lncRNAs/circRNAs in plasma exosomes was analyzed using high-throughput sequencing. Differentially expressed lncRNAs and circRNAs that target mRNAs were identified using bioinformatics methods. The predicted target mRNAs were intersected with the differentially expressed mRNAs in PBMCs to construct ceRNA networks. The subcellular localizations of lncRNAs and circRNAs within the ceRNA networks were determined using RNA fluorescence in situ hybridization or bioinformatics methods. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of differentially expressed mRNAs in PBMCs were conducted using the clusterProfiler R package. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to validate the expression levels of each molecule within the constructed ceRNA networks in clinical samples, along with receiver operating characteristic (ROC) curve analysis to assess diagnostic value. Further validation was performed using in vitro cultured PBMCs and dual-luciferase reporter assays. Five differentially expressed circRNAs and 31 differentially expressed lncRNAs were identified in exosomes. In PBMCs, 130 differentially expressed mRNAs were identified. Six ceRNA networks were constructed, affecting PBMCs chemorepellent activity, JAK-STAT signaling pathway, and other functions or pathways. The expression level of ENST00000650850 in plasma exosomes was significantly lower in AR patients, suggesting its potential diagnostic value. The expression level of ENST00000650850 in plasma exosomes was positively correlated with the expression levels of ENST00000650850 and IL6 mRNA in PBMCs. PBMCs from healthy individuals were stimulated with plasma exosomes isolated from AR patients, leading to a reduction in IL6R mRNA expression levels in the PBMCs. Differentially expressed lncRNA (ENST00000650850) in plasma-derived exosomes of AR patients may regulate IL6R mRNA expression in PBMCs via miR-6747-3p, thereby influencing PBMC function and contributing to the pathogenesis and progression of AR.

Ultra-weak photon emission from DNA

It is conventionally believed that macromolecules found in living cells, including DNA, RNA, and proteins, do not exhibit inherent light emission. However, recent studies have challenged this concept by demonstrating spontaneous light emission from nucleic acids under certain conditions and physiological temperatures. By noninvasive monitoring of barley genomic DNA and advanced statistical physics analyses, temperature-induced dynamic entropy fluctuations and fractal dimension oscillations were identified at a key organizational threshold. The study revealed evidence for non-equilibrium phase transitions, a noticeable photovoltaic current jump at zero bias voltage, and a proportional increase (scaling) of the photoinduced current corresponding to increasing amounts of DNA. In addition, we estimated DNA’s energy production rate at criticality and introduced an interferometer using coherent light emissions from the DNA-water interface. These findings suggest that DNA is a major source of ultraweak photon emission in biological systems.

Assessment of genomic diversity within and between two cryptic shiners, the West Texas shiner (Notropis megalops) and the Texas shiner (Notropis amabilis).

The presence of cryptic species can hinder effective conservation planning and implementation, as has been the case for speciose groups of freshwater fishes that are difficult to differentiate due to conserved morphologies. The West Texas shiner Notropis megalops and the Texas shiner Notropis amabilis are a cryptic pair of leuciscids (minnows) that co-occur in spring-fed tributaries of the Rio Grande in Texas and Mexico. Both N. megalops and N. amabilis are listed as Species of Greatest Conservation Need by the Texas Parks and Wildlife Department. Notropis amabilis is widespread and listed as apparently secure by Texas Parks and Wildlife Department whereas N. megalops has a very limited distribution and has not been ranked by Texas Parks and Wildlife Department because of data deficiency. Morphological differences between these species have been described; however, proper identification in situ remains problematic. Furthermore, given their range of overlap there is potential for hybridization, and limited genetic data have been collected comparing the species. Therefore, reduced representation genomic and mitochondrial sequencing data were used to reassess the distinctness of the species, screen for hybridization, and characterize their relative frequencies throughout their range of overlap. Genomic analyses recovered two distinct genetic groups corresponding to the species (F'CT = 0.89) with no evidence of admixture or introgression. The species were found to co-occur at three sampling locations, two in the Devils River and one in the Pecos, but not in equal frequencies. Overall, these results provide data and tools for further research on N. megalops needed for accurate conservation policies and management practices.