Solanum carolinense Linnaeus, belonging to the family Solanaceae, is a perennial herb or subshrub. S. carolinense has become naturalized in Korea as an invasive species, forming a stable population that has grown naturally with native plants for more than 10 years. However, its chloroplast genome structure and complete sequence have not yet been reported. Therefore, we determined the complete chloroplast genome sequence of S. carolinense using genome sequencing, assembly, and annotation. The total length of the chloroplast genome was 155,315 bp with a GC content of 37.6%. It featured a quadripartite structure (a large single-copy region, 86,160 bp; a small single-copy region, 18,459 bp; and two inverted repeat regions, 25,348 bp each). It contains 129 genes, including 84 coding sequences (CDSs), 37 tRNA genes, 8 rRNA genes, and one pseudogene. Phylogenetic analysis of 78 CDSs revealed that S. carolinense is closely related to S. aridum Morong and S. hieronymi Kuntze. These results provide a molecular foundation for phylogenetic and evolutionary studies of the genus Solanum and present a fundamental chloroplast genomic resource for future invasion biology research.

Strophanthus divaricatus (Lour.) Hook. & Arn. (1837) is an important medicinal plant utilized in traditional Chinese and Yao ethnomedicine. Here, we report its complete chloroplast genome based on Illumina sequencing. The circular genome is 155,409 bp in length, with an overall GC content of 38.28%, and displays a typical quadripartite structure comprising a large single-copy region (85,683 bp), a small single-copy region (18,182 bp), and two inverted repeats (25,772 bp each). A total of 130 genes were annotated, including 85 protein-coding genes, 37 tRNAs, and 8 rRNAs. Phylogenetic analysis revealed that S. divaricatus is closely related to S. wallichii.

Genome sequencing (GS) has emerged as the gold standard for diagnosing patients with rare diseases. As with many emerging technologies, equitable access remains a concern. To evaluate the feasibility and diagnostic impact of expanding access to GS, we report our experience implementing CincyKidsSeq, a prospective study offering GS as a "proband-first" test. Participants of all ages with at least one symptom were referred by genetics or non-genetics healthcare providers, or alternatively, were self-referred from February 2024 to February 2025. This diverse referral structure was evaluated for diagnostic yield while maintaining clinical oversight through a hybrid model in which reportable variants are delivered through genetic providers. The overall diagnostic yield of GS on 313 participants was 22% in the unstratified cohort. Self-referred patients had a higher diagnostic yield (11/33; 33%), compared with patients referred by a non-genetics provider (27/98; 27%), or genetics provider (32/182; 18%). Self-referred individuals were older, more likely to be female, frequently test-naïve, and utilized fewer human phenotype ontology (HPO) terms (p value = 0.0016). Self-referral may serve as an effective and complementary pathway for improving access to GS. Empowering families to initiate GS may be a reasonable pathway for an alternative model for genetic service delivery.

Long-term persistence of clonal resistant and multidrug resistant E. coli despite absence of antimicrobial use in weaned dairy heifer rearing systems in Switzerland.

Emergence of ceftriaxone resistant Salmonella Kentucky in India driven by multiple novel variants of Salmonella genomic island carrying blaCTX-M-55.

New insights into host-dermatophyte interactions: pathogenesis, host defense mechanisms, and emerging clinical challenges.

Research note: Identification of SNP-based haplotypes for the A, D, E, I, and L alloantigen systems in the chicken reference genome line UCD-001.

On Tuesday, September 9, 2025, the Cantonal Laboratory of Basel City received reports of cases of vomiting following the consumption of a macaroni dish served at a school canteen. The outbreak involved 27 children, and the emetic symptoms started 40-90min after lunch. Microbiological analyses of food samples obtained from the canteen kitchen revealed the presence of B. cereus at 1100 colony-forming units (cfu)/g in leftovers of a béchamel sauce that was an ingredient of the macaroni dish. Nanopore long-read sequencing methodology and the BTyper3 tool were applied to identify B. mosaicus subsp. cereus biovar Emeticus (B. Emeticus) as the most likely etiological agent of this outbreak. Strain B. Emeticus BH-1 belonged to panC group III, sequence type (ST)164, and contained emetic toxin (cereulide) genes cesA, cesB, cesC, and cesD, but lacked enterotoxins hblD and cytK1 that cause diarrhea. This is one of the few reports of B. Emeticus ST164 implicated in food intoxication. Based on the epidemiological and microbiological investigations, the macaroni dish was identified as the most likely vehicle of transmission in this outbreak, although definitive evidence was limited by the lack of retentionsamples of the full meal. Inadequate temperature control during food holding and serving in the school canteen likely led to B. cereus proliferation and toxin production and was the most probable risk factor that contributed to the outbreak. This outbreak emphasizes the importance of considering the presence of B. cereus for implementing appropriate procedures to ensure the safety of food produced within the catering sector. Our study highlights the added value of a combined approach that used epidemiological, microbiological, and advanced next-generation whole genome sequencing (WGS) methods to identify the likely outbreak source and the etiological B. cereus strain.

Whole genome sequence (WGS) data provides opportunities for comprehensive evaluation of variants that may influence complex traits. However, prioritizing the large number of variants, particularly those in non-coding regions, is a challenge. Here we present an approach that uses pedigree-based haplotyping to identify the risk haplotype and resulting set of prioritized variants in a region of interest (ROI) defined by identity-by-descent (IBD) sharing among familial cases. The approach is applicable for use in both a full range of pedigree sizes and for the full allele frequency spectrum of variants without the need for a large reference sample. By determining haplotype sharing among individuals with WGS data, we demonstrate the ability to accurately identify a risk haplotype and a strongly reduced list of potential risk alleles for a trait of interest along with the cases who carry the risk haplotype. This is important in the context of complex traits where the disease may be etiologically heterogeneous even within a single pedigree. Application to both simulated and real Alzheimer's disease family data shows that the approach leads to accurate risk-haplotype identification with marked reduction in the number of potential trait-associated variants. Simulation also shows that the approach provides accurate risk haplotypes in ROIs.

We present a draft genome dataset for Xylaria sp. (KR-3U) isolated as an endophyte from Catharanthus roseus leaves in India. Whole genome sequencing was performed using Illumina NovaSeq 6000 platform, generating 35.2 million paired-end raw reads (150 bp), providing ∼120× coverage (∼5.32 Gb of raw data) for a 44.24 Mb assembly (960 contigs >1 kb, GC content of 47.76%, and an N50 of 101,126 bp). Read remapping showed 96.07% alignment to the assembly. BUSCO (fungi_odb10) analysis indicated 97.0% completeness. Gene prediction using AUGUSTUS identified 11,916protein coding genes. BLASTp searches against the Swiss-Prot database yielded significant hits for 7299 proteins, of which 7204 were mapped to Gene Ontology (GO) terms and 5869 sequences received functional annotations . Integration of InterProScan-supported annotations resulted in 5645 proteins assigned at least one GO term. KEGG KAAS assigned 4,144genes (3,391KO numbers) to diverse pathways. Carbohydrate active enzyme (CAZyme) analysis revealed 556 CAZyme encoding genes, with 39.74% (221 genes) predicted to be secreted. antiSMASH detected 111 biosynthetic gene clusters (BGCs), including polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), terpenes and hybrid clusters. The complete genome sequence and raw reads have been deposited in National Center for Biotechnology Information (NCBI) under the GenBank accession number JBSEFG000000000, BioProject number PRJNA1335662, BioSample ID SAMN52018968, and SRA (raw reads) accession number SRR35731853 The genome assembly (FASTA), gene annotation (GFF3), and secondary genome analysis files are deposited in Mendeley Data (Version 3; DOI: 10.17632/b8jn5rtwkg.3) under a CC BY 4.0 license to ensure transparency, reproducibility, and reuse of the analyses.

Genomic diversity of human adenoviruses in Tanzanian children under five: Insights into F40, F41, B, and rare A18 genotypes.

A novel Queuovirinae subfamily phage targeting Acinetobacter baumannii: Isolation, characterization, and synergistic lysis system.

Construction of Kongyu 131 mutant library provides genetic resources for rice functional genomics and germplasm improvement.

Genomic epidemiology of a 2023-2024 Oropouche virus disease outbreak in Iquitos, Peru: descriptive analysis of a case control study for acute febrile illness.

Plant genome biology is entering a new era defined by fully phased, chromosome-scale, telomere-to-telomere assemblies, enabled by the convergence of long-read sequencing technologies, improved assembly algorithms, and powerful scaffolding strategies. Gapless, haplotype-resolved genomes are now feasible even for polyploid species, shifting the bottleneck from assembly to annotation and interpretation. Genome annotation remains one of the greatest opportunities and challenges in plant biology. While ab initio methods still form the backbone of structural prediction, evidence-based frameworks that integrate RNA sequencing, chromatin accessibility, methylation, and 3D genome data are rapidly advancing the field. At the same time, artificial intelligence-driven protein-coding gene predictors are redefining ab initio gene finding, and large-scale orthology networks continue to improve functional inference. The next frontier is extending annotation beyond protein-coding genes into regulatory and structural dimensions, a goal increasingly enabled by single-cell and multi-omic technologies. Looking forward, the integration of AI, multi-omics, and large language models promises to standardize and automate workflows from DNA isolation to functional annotation. These innovations will accelerate fundamental plant biology discovery, enable next-generation biodiversity conservation, and transform strategies for crop improvement and biotechnology.

The mobile tmexCD-toprJ gene clusters encode resistance-nodulation-division (RND)-type multidrug efflux pumps which confer resistance to multiple antimicrobials, including tigecycline. Here we report the first identification of tmexCD-toprJ-harbouring Pseudomonas aeruginosa strain KAM950, isolated from hospital sewage in Japan in 2022. The isolate exhibited reduced susceptibility to tigecycline and carbapenems. Complete genome sequence analysis showed that KAM950 belongs to sequence type 244 (ST244) according to multilocus sequence typing, an internationally recognised epidemic clone, and harbours multiple antimicrobial resistance genes, including the tmexCD-toprJ variant, tmexC6D6-toprJ1b. Notably, the tmexC6D6-toprJ1b gene cluster was located on the chromosome, adjacent to the transcriptional regulator gene tnfxB6 and an IS5/IS1182 family transposase gene. Furthermore, an IS4-mediated disruption of the porin gene oprD was observed, potentially contributing to carbapenem resistance. BLASTn analysis revealed that the IS5/IS1182-tnfxB6-tmexC6D6-toprJ1b gene cluster present in both chromosomal and plasmid sequences among the order Pseudomonadaceae, indicating potential horizontal gene transfer of tnfxB6-tmexC6D6-toprJ1b mediated by IS5/IS1182. Our findings highlight the ongoing expansion of variant diversity and geographic spread of tmexCD-toprJ-like gene clusters, and underscore the importance of genomic surveillance for emerging antimicrobial resistance determinants in both clinical and environmental settings.

The evolving landscape of Mpox: Clinical and genomic insights into Clade Ib emergence in India.

Significant advances have been made in elucidating the pathophysiological mechanisms of Parkinson's disease (PD). Levodopa remains the main therapeutic option - although it presents heterogeneous clinical benefits among patients. Mutations related to levodopa metabolic pathways have been investigated, but not for mtDNA. Since levodopa metabolism is highly dependent on ionic gradients, endocytosis, and vesicular transport - all ATP-dependent processes - the normal function of OXPHOS is essential not only for adequate levodopa metabolism but also for its therapeutic efficacy. This study aimed to analyze levodopa short duration responsiveness profiles considering the mitochondrial genomic component in Brazilian admixed populations. A total of 49 patients with PD underwent a levodopa challenge test (LCT), followed by whole mitochondrial genome sequencing, pathogenicity prediction of identified variants, and in silico structural analyses. Variants most frequently affected ND4, ND5, and ND6 subunits in both groups (responsive and non-responsive). Among them, the responsive group presented variants in MT-ND4 (m.12018C>G - T420S) and ND5 (m.13130C>A - P265H) as those with the most significant structural impact, suggesting a loss of the native conformation and alterations in protein efficiency. Additionally, five unique variants were detected only among non-responsive patients, two of which were absent from the dbSNP and ClinVar databases, which indicates the possibility that they are novel variants and potentially population-specific. We provide molecular evidence suggesting that variants in mitochondrial ND4, ND5, and ND6 subunits, in addition to mitochondrial ancestry, may contribute to distinct levodopa short duration response in PD patients.

A microreactor system for point-of-care viral genome sequencing.

This study reports the whole-genome sequence data and functional annotations of a novel Stutzerimonas marianensis strain LB-0542 isolated from the decomposing pelagic Sargassum biomass stranded on Long Beach, Barbados. The genomic DNA was sequenced with the Illumina NextSeq2000 platform. The genome assembly was performed with the SPAdes Genome Assembler (ver 3.15.5). The assembled genome has a size of 4520,813 bp, a coverage of 110X, a GC content of 63.2 %, a L50 of 2 and a N50 of 1079,143 bp. The genome consists of 12 contigs, 0 CRISPR, 3 rRNA, 56 tRNA and 4166 CDSs (coding sequences) with a coding ratio of 89.4 %. The genome annotation results for the COG (cluster of orthologous genes) and subsystem features indicate that the metabolism and the amino acids and derivatives are the most dominant categories, respectively. The analysis of the genome for the existence of Carbohydrate-Active Enzymes (CAZymes) identified 230 genes encoding four functional classes of CAZymes [glycoside hydrolases (75 genes), glycosyltransferases (95 genes), carbohydrate esterases (9 genes) and carbohydrate-binding modules (51 genes)]. The functional annotation of the genome for plastic degradation revealed the presence of 34 genes, which could catalyse the degradation process of 14 types of plastics, polyethylene glycol [PEG (29 %)], polylactic acid [PLA (11 %)], poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [PHBV (9 %)], polyhydroxyalkanoates [PHA (9 %)], polyethylene [PE (6 %)], polycaprolactone [PCL (6 %)], polyethersulfone [PES (6 %)], polyethylene terephthalate [PET (6 %)], poly(butylene adipate-co-terephthalate [PBAT (3 %)], (polystyrene [PS (3 %)], polybutylene succinate [PBSA (3 %)], poly(3-hydroxyvalerate) [P3HV (3 %)], polyvinyl alcohol [PVA (3 %)] and natural rubber [NR (3 %)]. The genome mining for plant growth-promoting traits identified 3175 genes that are associated with the colonizing plant system (26 %), competitive exclusion (21 %), stress control (21 %), biofertilization (14 %), phytohormone and plant signal production (10 %), bioremediation (7 %) and plant immune response stimulation (1 %). These genome mining results are an indication of the biotechnological and ecological significance of the novel strain LB-0542 for sustainable biocatalytic processing of Sargassum and plastic-containing waste. The genome sequence data is available in DDBJ/EMBL/GenBank with the accession number BAAIAE000000000.