Full-length Sequence Research Articles

16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in Streptomyces.

Streptomyces is among the most extensively studied genera of bacteria but its complex taxonomy remains contested and is suspected to contain significant species-level misclassification. Resolving the classification of Streptomyces would benefit many areas of applied microbiology that rely on an accurate ground truth for grouping of related organisms, including comparative genomics-based searches for novel antimicrobials. We survey taxonomic conflicts between 16S rRNA and whole genome-based Streptomyces classifications using 2276 publicly available Streptomyces genome assemblies and 48 981 publicly available full-length 16S rRNA Streptomyces sequences from silva, Greengenes, Ribosomal Database Project (RDP), and NCBI (National Centre for Biotechnology Information) databases. We construct a full-length 16S gene tree for 14 239 distinct Streptomyces sequences that resolves three major lineages of Streptomyces, but whose topology is not consistent with existing taxonomic assignments. We use these sequence data to delineate 16S and whole genome landscapes for Streptomyces, demonstrating that 16S and whole-genome classifications are frequently in disagreement, and that 16S zero-radius Operational Taxonomic Units (zOTUs) are often inconsistent with Average Nucleotide Identity (ANI)-based taxonomy. Our results strongly imply that 16S rRNA sequence data does not map to taxonomy sufficiently well to delineate Streptomyces species routinely. We propose that alternative marker sequences should be adopted by the community for classification and metabarcoding. Insofar as Streptomyces taxonomy has been determined or supported by 16S sequence data and may in parts be in error, we also propose that reclassification of the genus by alternative approaches may benefit the Streptomyces community.

Integrative analyses of long and short-read RNA sequencing reveal the spliced isoform regulatory network of seedling growth dynamics in upland cotton.

The polyploid genome of cotton has significantly increased the transcript complexity. Recent advances in full-length transcript sequencing are now widely used to characterize the complete landscape of transcriptional events. Such studies in cotton can help us to explore the genetic mechanisms of the cotton seedling growth. Through long-read single-molecule RNA sequencing, this study compared the transcriptomes of three yield contrasting genotypes of upland cotton. Our analysis identified different numbers of spliced isoforms from 31,166, 28,716, and 28,713 genes in SJ48, Z98, and DT8 cotton genotypes, respectively, most of which were novel compared to previous cotton reference transcriptomes, and showed significant differences in the number of exon structures and coding sequence length due to intron retention. Quantification of isoform expression revealed significant differences in expression in the root and leaf of each genotype. An array of key isoform target genes showed protein kinase or phosphorylation functions, and their protein interaction network contained most of the circadian oscillator proteins. Spliced isoforms from the GIGANTEA (GI) protien were differentially regulated in each genotype and might be expected to regulate translational activities, including the sequence and function of target proteins. In addition, these spliced isoforms generate diurnal expression profiles in cotton leaves, which may alter the transcriptional regulatory network of seedling growth. Silencing of the novel spliced GI isoform Gh_A02G0645_N17 significantly affected biomass traits, contributed to variable growth, and increased transcription of the early flowering pathway gene ELF in cotton. Our high-throughput hybrid sequencing results will be useful to dissect functional differences among spliced isoforms in the polyploid cotton genome.

A New Variant of Avian Encephalomyelitis Virus Associated with Neurologic Signs in Turkey Poults.

Avian encephalomyelitis (AE) is a disease caused by the avian encephalomyelitis virus (AEV) of the genus Tremovirus in the family Picornaviridae. Recently, cases of turkey poults showing neurological signs were submitted to the veterinary diagnostic laboratories at South Dakota State University and the University of Minnesota. The affected birds were showing nervous neurological signs such as tremors, inability to stand, torticollis, and wing drop. Clinical signs were observed by 3 weeks of age. Necropsy of birds revealed no significant gross lesions in the internal organs, including the brain. There was no significant bacterial growth in the brains. Microscopic examination of various sections of the brain revealed multifocal lymphocplasmacytic perivascular cuffs in the cerebellum and cerebral cortex. The brain samples were processed for detection and whole genome sequencing by next-generation sequencing. Three full-length polyprotein sequences (6405 nt) of AEV were assembled. All three sequences shared 99.9-100% nucleotide and 100% amino acid identities with each other. Only 77.7-78.5% of nucleotide and 90.3-92.5% of amino acid identities with AEV field strains and vaccine sequences were available in GenBank. This indicates that a new divergent variant of AEV is circulating in the field and causing AE outbreaks in the Midwest region.

Impact of ovalbumin allergy on oral and gut microbiome dynamics in 6-week-old BALB/c mice.

The gut microbiota is known to have a significant impact on the development of food allergy, and several recent studies have suggested that both oral microbiota, which first come into contact with allergenic foods, may have a profound influence on the development of food allergy. In this study, we have established an ovalbumin-sensitive mice model by utilizing ovalbumin as a sensitizing agent. Subsequently, we performed a comprehensive analysis of the gut and oral microbiota in ovalbumin-sensitive mice and the control mice using full-length 16S rRNA sequencing analysis. Interestingly, both the gut and oral microbiota of ovalbumin-sensitized mice exhibited significant dysbiosis. The relative abundance of s__Lactobacillus_intestinalis in the gut microbiota of ovalbumin-sensitive mice exhibited a significant decrease, whereas the abundance of s__Agrobacterium_radiobacter and s__Acinetobacter_sp__CIP_56_2 displayed a significant increase. Furthermore, the relative abundance of s__unclassified_g__Staphylococcus, s__Streptococcus_hyointestinalis, and s__unclassified_g__Dechloromonas in the oral microbiota of ovalbumin-sensitive mice revealed a significant decrease. In contrast, the abundance of 63 other species, including s__Proteiniclasticum_ruminis, s__Guggenheimella_bovis, and s__Romboutsia_timonensis, demonstrated a significant increase. The random forest classifier achieved the best accuracy in predicting the outcome of food allergy using three gut and three oral biomarkers, with accuracies of 94.12 and 100%, respectively. Based on the predictions of the PICRUSt2 analysis, the only consistent finding observed across multiple samples from both the groups of mice was a significant up-regulation of the nucleotide-binding oligomerization domain (NOD)-like receptor signaling pathway in the ovalbumin-sensitized mice. Our study demonstrates that ovalbumin-sensitized mice experience substantial alterations in both gut and oral microbial composition and structure, and specific strains identified in this study may serve as potential biomarkers for food allergy screening. Moreover, our findings highlight that the oral environment, under the same experimental conditions, exhibited greater precision in detecting a larger number of species. Additionally, it is worth noting that the NOD-like receptor signaling pathway plays a vital role in the pathogenesis of OVA (ovalbumin)-induced allergy. These findings will generate novel concepts and strategies in the realm of food allergy prevention and treatment.

Cloning, identification, and functional analysis of foxl2 gene and its expression after 17β‐estradiol (E2) treatment in Dabry’s sturgeon, Acipenser dabryanus

The study focuses on the critically endangered Dabry’s sturgeon (Acipenser dabryanus), a species on the brink of extinction in the wild. This research investigates the role of the Forkhead box protein L2 (foxl2) in the gonadal development and differentiation of this species. The foxl2 gene, known for its role in various physiological processes, including sexual maturation, is hypothesized to play a significant role in the sex differentiation of Dabry’s sturgeon. This study cloned the full-length cds sequence of the foxl2 gene and analyzed its expression across various tissues, focusing on its response to estradiol treatment. Our findings indicate that foxl2 is predominantly expressed in ovaries and shows a dose-dependent response to estradiol, suggesting its potential role in ovarian differentiation. This research underscores the importance of foxl2 in understanding reproductive biology and offers a foundation for future conservation strategies.

Species-level characterization of the core microbiome in healthy dogs using full-length 16S rRNA gene sequencing.

Despite considerable interest and research in the canine fecal microbiome, our understanding of its species-level composition remains incomplete, as the majority of studies have only provided genus-level resolution. Here, we used full-length 16S rRNA gene sequencing to characterize the fecal microbiomes of 286 presumed healthy dogs living in homes in North America who are devoid of clinical signs, physical conditions, medication use, and behavioral problems. We identified the bacterial species comprising the core microbiome and investigated whether a dog's sex & neuter status, age, body weight, diet, and geographic region predicted microbiome variation. Our analysis revealed that 23 bacterial species comprised the core microbiome, among them Collinsella intestinalis, Megamonas funiformis, Peptacetobacter hiranonis, Prevotella copri, and Turicibacter sanguinis. The 23 taxa comprised 75% of the microbiome on average. Sterilized females, dogs of intermediate body sizes, and those exclusively fed kibble tended to harbor the most core taxa. Host diet category, geographic region, and body weight predicted microbiome beta-diversity, but the effect sizes were modest. Specifically, the fecal microbiomes of dogs fed kibble were enriched in several core taxa, including C. intestinalis, P. copri, and Holdemanella biformis, compared to those fed raw or cooked food. Conversely, dogs on a raw food diet exhibited higher abundances of Bacteroides vulgatus, Caballeronia sordicola, and Enterococcus faecium, among others. In summary, our study provides novel insights into the species-level composition and drivers of the fecal microbiome in healthy dogs living in homes; however, extrapolation of our findings to different dog populations will require further study.

Full-length nanopore sequencing of circular RNA landscape in peripheral blood cells following sequential BNT162b2 mRNA vaccination

Circular RNAs (circRNA) lack 5′ or 3′ ends; their unique covalently closed structures prevent RNA degradation by exonucleases. These characteristics provide circRNAs with high pharmaceutical stability and biostability relative to current standard-of-care linear mRNAs. CircRNA levels are reportedly associated with certain human diseases, making them novel disease biomarkers and a noncanonical class of therapeutic targets. In this study, the endogenous circRNAs underlying the response to BNT162b2 mRNA vaccination were evaluated. To this end, peripheral blood samples were subjected to full-length sequencing of circRNAs via nanopore sequencing and transcriptome sequencing. Fifteen samples, comprising pre-, first, and second vaccination cohorts, were obtained from five healthcare workers with no history of SARS-CoV-2 infection or previous vaccination. A total of 4706 circRNAs were detected; following full-length sequencing, 4217 novel circRNAs were identified as being specifically expressed during vaccination. These circRNAs were enriched in the binding motifs of stress granule assemblies and SARS-CoV-2 RNA binding proteins, namely poly(A) binding protein cytoplasmic 1 (PABPC1), pumilio RNA binding family member 1 (PUM1), and Y box binding protein 1 (YBX1). Moreover, 489 circRNAs were identified as previously reported miRNA sponges. The differentially expressed circRNAs putatively originated from plasma B cells compared to circRNAs reported in human blood single-cell RNA sequencing datasets. The pre- and post-vaccination differences observed in the circRNA expression landscape in response to the SARS-CoV-2 BNT162b2 mRNA vaccine.

Molecular characterization of avian metapneumovirus subtype C associated with hydrosalpinx fluid and egg drop syndrome in Jinding ducks.

A disease called "hydrosalpinx fluid and egg drop syndrome" (HFEDS) was observed in four flocks of Jinding ducks (Anas platyrhynchos domesticus) in Northeast China during the years 2022 to 2023. Here, we investigated the possible involvement of avian metapneumovirus (AMPV) infection. Full-length genome sequencing and sequence analysis of two AMPV strains showed that they belong to Eurasian lineage of AMPV subtype C. Based on surface glycoprotein (G) sequence comparisons, the Eurasian lineage can be divided into two sublineages (E1 and E2), and sublineage E2 is circulating in Jinding duck populations in Northeast China.

Identification and antibacterial activity of a novel phage-type lysozyme from the freshwater mussel Hyriopsis cumingii

A cDNA encoding a phage-type lysozyme, designated as HcPLYZ, was successfully cloned from Hyriopsis cumingii. The full-length cDNA sequence of HcPLYZ was determined to be 896 base pairs in length. Analysis revealed the absence of a signal peptide at its N-terminus, and identified two highly conserved phage-type lysozyme activity sites, Glu20 and Asp29, within the deduced amino acid sequence of HcPLYZ. The results of the cloning and sequencing symbiotic bacteria in tissues were consistent with those obtained using tissue cDNA as the template, suggesting that HcPLYZ may originate a symbiotic bacterium. The expression levels of HcPLYZ mRNA exhibited significant variations across different tissues. Successful expression was induced using IPTG, and the native recombinant protein was subsequently purified through affinity chromatography employing Ni2+, and the optimal pH and temperature of which were determined to be 5.5 and 50°C, respectively. Following exposure to Aeromonas hydrophila, there was a significant increase in the levels of HcPLYZ mRNA in the hemocytes, hepatopancreas, and gills. HcPLYZ was demonstrated the inhibition activity of 55% and 83% against Micrococcus lysodeikticus under pH 5.5 and 50 °C conditions, respectively. These results suggested that HcPLYZ possessed antibacterial activity against both A. hydrophila and M. lysodeikticus.

Transcriptome and Metabolomic Analyses Reveal Tissue-Specific Glycosylation of Phenylpropanoids and Flavonoids in Toxicodendron vernicifluum.

Toxicodendron vernicifluum (Stokes) F. A. Barkley is a tree species used primarily for lacquer production. Our study utilized transcriptome and metabolomic analysis to investigate the biosynthesis of phenylpropanoids and flavonoids, specifically the glycosylated forms, in T. vernicifluum roots, stems, and leaves. HPLC-QTOF-MS/MS identified 186 compounds, with tissue-specific distributions revealed by PCA. Flavonoids and phenylpropanoids glycosides were significantly more abundant in leaves compared with roots and stems. Full-length sequencing uncovered 17,266 transcripts in T. vernicifluum. Gene expression analysis showed higher activity of phenylpropanoid and flavonoid biosynthesis pathways in leaves. Certain genes, such as CYP73A, 4CL, CRR, CYP84A/F5H, and CYP93C, displayed associations with compound content distributions. Root tissue exhibited a higher concentration of isoflavones. Notably, glycosyltransferase expression demonstrated significant correlations with glycosylated compounds' content. Biochemical validation confirmed the involvement of TvPB_c0_g2904, encoding a UDP-glucosyltransferase, in genistin biosynthesis in T. vernicifluum.

The Prevalence and Molecular Characterization of Bovine Leukemia Virus among Dairy Cattle in Henan Province, China.

Enzootic bovine leukosis, a neoplastic disease caused by the bovine leukemia virus (BLV), was the primary cancer affecting cattle in China before 1985. Although its prevalence decreased significantly between 1986 and 2000, enzootic bovine leukosis has been re-emerging since 2000. This re-emergence has been largely overlooked, possibly due to the latent nature of BLV infection or the perceived lack of sufficient evidence. This study investigated the molecular epidemiology of BLV infections in dairy cattle in Henan province, Central China. Blood samples from 668 dairy cattle across nine farms were tested using nested polymerase chain reaction assays targeting the partial envelope (env) gene (gp51 fragment). Twenty-three samples tested positive (animal-level prevalence of 3.4%; 95% confidence interval: 2.2, 5.1). The full-length env gene sequences from these positive samples were obtained and phylogenetically analyzed, along with previously reported sequences from the GenBank database. The sequences from positive samples were clustered into four genotypes (1, 4, 6, and 7). The geographical annotation of the maximum clade credibility trees suggested that the two genotype 1 strains in Henan might have originated from Japan, while the genotype 7 strain is likely to have originated from Moldova. Subsequent Bayesian stochastic search variable selection analysis further indicated a strong geographical association between the Henan strains and Japan, as well as Moldova. The estimated substitution rate for the env gene ranged from 4.39 × 10-4 to 2.38 × 10-3 substitutions per site per year. Additionally, codons 291, 326, 385, and 480 were identified as positively selected sites, potentially associated with membrane fusion, epitope peptide vaccine design, and transmembrane signal transduction. These findings contribute to the broader understanding of BLV epidemiology in Chinese dairy cattle and highlight the need for measures to mitigate further BLV transmission within and between cattle herds in China.

Large-scale HEV genotype 3 outbreak on New Caledonia Island.

Several symptomatic cases of HEV infections were reported to the New Caledonia Island Public Health Service between August and December 2023. This prompted epidemiological and virological investigations to identify the source of infection. HEV RNA was assessed in symptomatic patients, various food items, and pig farms on the Island. HEV strains were characterized by sequencing. A seroprevalence study was also conducted on asymptomatic blood donors before and after the outbreak. One hundred twenty-seven symptomatic cases were reported. Hospitalization was required for 29/127 patients (22.8%). Hospitalized patients presented more frequently with comorbidities, including liver and cardiovascular diseases (80.7% vs. 27%, p < 0.01), and 3 persons died (2.3%). Among the 100 HEV RNA-positive samples received at the French National Reference Centre for HEV, viral sequencing was possible for 76 samples. All strains were identified as HEV genotype 3, and 74/76 strains were grouped together (nucleotide identity: 98%-100%). Full-length sequencing indicated a new HEV-3 subtype within HEV-3 subclade abk. Only genotype 3f strains were detected on the Island's pig farms. No food items tested positive for HEV RNA. The seroprevalence of HEV IgG and IgM in blood donors was 9.2% (9/98) and 0%, respectively, in 2020, rising to 17.3% (17/98) and 2% (2/98) in 2024. Although all previous large-scale epidemics in Asia and Africa were associated with HEV-1 or 2, the New Caledonia outbreak was linked to HEV-3. A high number of symptomatic cases were admitted to the hospital, with a case-fatality rate of 2.3%.

Molecular characterization and expression profiling of 3 beta-hydroxysteroid dehydrogenase and hydroxysteroid 17-beta dehydrogenase in response to HCG stimulation in striped murrel, Channa striata (Bloch, 1793)

Striped murrel (Channa striata) is highly valued in the Indian subcontinent and Southeast Asia for its nutritional and medicinal benefits. However, the limited availability of high-quality seeds of murrel and the asynchronous maturation of brooders, particularly during peak spawning seasons creates problems in aquaculture. Beta-hydroxysteroid dehydrogenases (β-HSDs) are steroidogenic enzymes involved in the biosynthesis of active steroids in gametogenesis and steroidogenesis. This study aimed to clone and characterize the full-length cDNA sequences of two crucial enzymes, 3-beta hydroxysteroid dehydrogenase (Hsd3β) and 17-beta hydroxysteroid dehydrogenase (Hsd17β). It resulted in full-length cDNA sequences for Hsd3β and Hsd17β with 1101bp and 771bp length, respectively, encoding 366 and 256 amino acids. Signal peptide analysis indicated that both proteins are secretory, and hydropathy profiles suggested their hydrophilic nature. Notably, Rossmann-fold NAD(P)(+)-binding domains characteristic of Short-chain dehydrogenases/reductases (SDR) family genes were identified in Hsd3β (between 9-355 aa) and in Hsd17β (between 10-254 aa). Gene expression analyses were performed in testes and ovaries using qPCR at three key stages: preparatory, mature, and 16 h post human chorionic gonadotropin (hCG) injection (16 hpi). Results demonstrated a significant 2-fold upregulation of Hsd17β in mature and 16 hpi testes, while Hsd3β showed a significant 10-fold upregulation in mature testes compared to premature and 16 hpi stages. Ovarian expression of Hsd3β and Hsd17β showed minimal expression upon hCG injection (P < 0.05). These findings contribute to our understanding of Beta-hydroxysteroid dehydrogenases (β-HSDs), providing insights into regulating sex steroid hormone synthesis during the gonadal development of striped murrel.

New lineages of RNA viruses from clinical isolates of Rhizopus microsporus revealed by fragmented and primer-ligated dsRNA sequencing (FLDS) analysis.

Rhizopus microsporus is a species in the order Mucorales that is known to cause mucormycosis, but it is poorly understood as a host of viruses. Here, we examined 25 clinical strains of R. microsporus for viral infection with a conventional double-stranded RNA (dsRNA) assay using agarose gel electrophoresis (AGE) and the recently established fragmented and primer-ligated dsRNA sequencing (FLDS) protocol. By AGE, five virus-infected strains were detected. Then, full-length genomic sequences of 12 novel RNA viruses were revealed by FLDS, which were related to the families Mitoviridae, Narnaviridae, and Endornaviridae, ill-defined groups of single-stranded RNA (ssRNA) viruses with similarity to the established families Virgaviridae and Phasmaviridae, and the proposed family "Ambiguiviridae." All the characterized viruses, except a potential phasmavirid with a negative-sense RNA genome, had positive-sense RNA genomes. One virus belonged to a previously established species within the family Mitoviridae, whereas the other 11 viruses represented new species or even new genera. These results show that the fungal pathogen R. microsporus harbors diverse RNA viruses and extend our understanding of the diversity of RNA viruses in the fungal order Mucorales, division Mucoromycota. Identifying RNA viruses from clinical isolates of R. microsporus may expand the repertoire of natural therapeutic agents for mucormycosis in the future.IMPORTANCEThe diversity of mycoviruses in fungal hosts in the division Mucoromycota has been underestimated, mainly within the species Rhizopus microsporus. Only five positive-sense RNA genomes had previously been discovered in this species. Because current sequencing methods poorly complete the termini of genomes, we used fragmented and primer-ligated double-stranded RNA sequencing to acquire the full-length genomes. Eleven novel mycoviruses were detected in this study, including the first negative-sense RNA genome reported in R. microsporus. Our findings extend the understanding of the viral diversity in clinical strains of Mucoromycota, may provide insights into the pathogenesis and ecology of this fungus, and may offer therapeutic options.

Transcriptome Analysis of Multiple Plant Parts in the Woody Oil Tree Camellia drupifera Loureiro

Camellia drupifera is mainly used in forestry for its high-value industrial products; however, limited information is available on its transcriptome. This study aimed to construct a full-length transcriptome sequence based on the PacBio sequencing platform for various plant parts of C. drupifera, including flower buds, leaves, leaf buds, branches, the pericarp, and seed kernels. The transcriptomes were annotated with 23,207 genes, with 58 subgroups in the GO classification. The KEGG database revealed 10,407 genes involved in the metabolic pathway analysis, with 68,192 coding sequences, 3352 TF families, 48,541 SSRs, 1421 IncRNAs, and 2625 variable shears predicted. The transcriptomes of different parts were analyzed and compared. The majority of differentially expressed genes (DEGs) were found between the pericarp and seed kernels, followed by leaves and the pericarp with 5662 DEGs, and flower buds and leaf buds with 1616 DEGs. GO and KEGG enrichment analyses showed that KEGG differential genes were significant in microbial metabolism, carbon metabolism, and other functions. The data annotation and analysis of the full-length transcriptome and the comparative analysis between different plant parts provided a theoretical basis for studying gene function, metabolic pathway regulation, and gene expression analysis in KEGG.

Full-length direct RNA sequencing uncovers stress-granule dependent RNA decay upon cellular stress.

Cells react to stress by triggering response pathways, leading to extensive alterations in the transcriptome to restore cellular homeostasis. The role of RNA metabolism in shaping the cellular response to stress is vital, yet the global changes in RNA stability under these conditions remain unclear. In this work, we employ direct RNA sequencing with nanopores, enhanced by 5' end adaptor ligation, to comprehensively interrogate the human transcriptome at single-molecule and nucleotide resolution. By developing a statistical framework to identify robust RNA length variations in nanopore data, we find that cellular stress induces prevalent 5' end RNA decay that is coupled to translation and ribosome occupancy. Unlike typical RNA decay models in normal conditions, we show that stress-induced RNA decay is dependent on XRN1 but does not depend on deadenylation or decapping. We observed that RNAs undergoing decay are predominantly enriched in the stress granule transcriptome while inhibition of stress granule formation via genetic ablation of G3BP1 and G3BP2 rescues RNA length. Our findings reveal RNA decay as a key determinant of RNA metabolism upon cellular stress and dependent on stress-granule formation.

Unveiling microbial dynamics in lung adenocarcinoma and adjacent nontumor tissues: insights from nicotine exposure and diverse clinical stages via nanopore sequencing technology.

Lung is the largest mucosal area of the human body and directly connected to the external environment, facing microbial exposure and environmental stimuli. Therefore, studying the internal microorganisms of the lung is crucial for a deeper understanding of the relationship between microorganisms and the occurrence and progression of lung cancer. Tumor and adjacent nontumor tissues were collected from 38 lung adenocarcinoma patients and used nanopore sequencing technology to sequence the 16s full-length sequence of bacteria, and combining bioinformatics methods to identify and quantitatively analyze microorganisms in tissues, as well as to enrich the metabolic pathways of microorganisms. the microbial composition in lung adenocarcinoma tissues is highly similar to that in adjacent tissues, but the alpha diversity is significantly lower than that in adjacent tissues. The difference analysis results show that the bacterial communities of Streptococcaceae, Lactobacillaceae, and Neisseriales were significantly enriched in cancer tissues. The results of metabolic pathway analysis indicate that pathways related to cellular communication, transcription, and protein synthesis were significantly enriched in cancer tissue. In addition, clinical staging analysis of nicotine exposure and lung cancer found that Haemophilus, paralinfluenzae, Streptococcus gordonii were significantly enriched in the nicotine exposure group, while the microbiota of Cardiobactereae and Cardiobacterales were significantly enriched in stage II tumors. The microbiota significantly enriched in IA-II stages were Neisseriaeae, Enterobacteriales, and Cardiobacterales, respectively. Nanopore sequencing technology was performed on the full length 16s sequence, which preliminarily depicted the microbial changes and enrichment of microbial metabolic pathways in tumor and adjacent nontumor tissues. The relationship between nicotine exposure, tumor progression, and microorganisms was explored, providing a theoretical basis for the treatment of lung cancer through microbial targets.

Transcriptome data for an ancient ‘living-fossil’ mollusc, Entemnotrochus rumphii

The Pleurotomarioidea, commonly referred to as slit shells, constitute one of the most ancient and enduring lineages within the phylum Mollusca, with its fossil record tracing back to the Upper Cambrian epoch. Its rareness and evolutionary antiquity surpass even that of the nautilus. In this study, we conducted the first transcriptome sequencing and analyses of Entemnotrochus rumphii (Schepman, 1879), a representative species of Pleurotomarioidea. Full-length transcriptome sequencing of E. rumphii was performed using the PacBio Sequel II platform with SMRT technology. A total of 64.38 gigabytes of data and 964,550 polymerase reads were generated, resulting in 28,068,998 subreads after data filtering. After de-duplication, correction, and clustering, we identified 19,273 genes. Additionally, next-generation sequencing was performed on 11 tissues of E. rumphii. This investigation provides a detailed portrayal and analytical scrutiny of its transcriptomic landscape.

De Novo Deep Intron ELANE Mutation Resulting in Severe Congenital Neutropenia.

Severe congenital neutropenia (SCN) comprises a diverse range of rare hematological disorders characterized by recurrent, often life-threatening infections that manifest within the first months of life. Mutations in the ELANE gene are the most prevalent cause of SCN. While over 230 mutations in ELANE have been documented, including substitutions, frameshifts, nonsense mutations, and splice site alterations, the occurrence of deep intronic mutations has not been previously reported. Herein, we present the case of a young girl who exhibited recurrent fever, respiratory infections, skin abscesses, and gingivitis shortly after birth. Laboratory analysis revealed markedly diminished neutrophil levels alongside elevated monocyte and eosinophil counts. Bone marrow examination disclosed a halt in myelopoiesis maturation. ELANE gene full-length sequencing identified a novel de novo deep intron mutation in ELANE (c.598 + 79G > T), subsequently confirmed by Sanger sequencing. cDNA sequencing of the patient demonstrated aberrant gene splicing. Utilizing a mini-gene splicing assay for ELANE intronic variants, we identified a mutant ELANE allele (c.597 + 1_597 + 83ins) leading to the creation of a premature termination codon (p.Gly200ValfsTer40). Confocal microscopy revealed heightened expression of myeloperoxidase and neutrophil elastase in the patient, suggesting a potential role for the unfolded protein response in the pathogenesis of the deep intron ELANE mutation. In summary, our findings illustrate the first reported instance of de novo deep intron ELANE mutations associated with SCN, underscoring the importance of exploring deep intronic regions in SCN patients lacking identifiable disease-causing gene mutations.

Characterization of bean common mosaic virus isolates infecting three leguminous bean crops from South and Southeast Asia.

Bean common mosaic virus (BCMV) is causing economically important diseases in leguminous crops worldwide. In this study, BCMV isolates from country bean (CB, Lablab purpureus), yard-long bean (YLB, Vigna unguiculata) and rajma bean (RB, Phaseolus vulgaris) collected from Bangladesh, Nepal and Cambodia were characterized. Samples tested positive for BCMV in serological assays were subjected to high-throughput sequencing to generate near full-length genome sequences. In pair-wise comparisons of the polyprotein open reading frame, thirteen BCMV isolates from Bangladesh, Cambodia, and Nepal showed sequence identity of 92.1 to 98.8% at the nucleotide and 94.2 to 99% at the amino acid level among themselves and with corresponding sequences of BCMV reported previously. In phylogenetic analyses using the global BCMV sequences, they segregated into five distinct lineages, with RB isolates from Nepal clustering with US1/NL1-clade of common bean isolates from different countries, YLB isolates aligning with blackeye cowpea strain sequences reported from China, and CB isolates from Nepal and Bangladesh clustering with soybean isolates from China. One YLB isolate from Nepal was identified as a putative recombinant. None of the BCMV sequences aligned with isolates representing the RU1 or PStV clades. In grow-out tests, seed samples from local markets showed 14.3 to 38.1% transmission efficiency rate of BCMV with CB seed lots and from 9.5% to 33.3% with YLB seed lots.