BMC Genomics

Abstract Background Aquatic hypoxia frequently occurs as a recurring environmental stressor, exerting detrimental effects on the growth and survival of fish. As a typical endemic fish species inhabiting the Qinghai-Tibetan Plateau, Gymnocypris eckloni displays outstanding resilience to hypoxia, however, limited knowledge exists regarding the dynamic changes of immune system in G. eckloni to hypox…

Abstract Background In response to the threat of antimicrobial resistance, the Chicken Farmers of Canada banned the prophylactic use of Category II antimicrobials in 2018, thereby increasing the reliance on bacitracin to prevent necrotic enteritis in broiler chickens. This study hypothesised that the significant increase in bacitracin use, a Category III antibiotic, following the ban may have inc…

Abstract Background Quantifying protein–protein binding affinity is essential for understanding molecular recognition and guiding antibody and inhibitor design. However, binding affinity is governed by tightly coupled sequence, structural, and chemical determinants. Existing models often encode these factors in isolation, limiting their ability to capture the multi-level dependencies underlying b…

Mitogen-activated protein kinase kinases (Mapkks) are pivotal signaling hubs within the evolutionarily conserved Mapk cascade, governing essential processes such as development and stress adaptation in insects. Fireflies, serving as critical ecological indicators, are experiencing global population declines, primarily due to escalating anthropogenic pressures including widespread pesticide and an…

Accurate analysis of long, structured, and repetitive integrated DNA elements is frequently confounded by PCR amplification bias and the intrinsically high error rates of long-read sequencing technologies. Lentiviral vectors (LVs), which are fundamental tools in clinical cell engineering, typically span 3–10 kb and contain GC-rich regulatory modules and terminal repeats. These features challenge …

Reads that remain after host subtraction are usually discarded from host-centered plant sequencing projects, but they may contain residual host sequence, organellar fragments, microbial candidate signal, laboratory or reagent contamination, and unresolved genomic content. These components are especially difficult to interpret when public datasets combine reduced-representation and whole-genome se…

Diaporthe is a taxonomically complex genus that includes pathogens, endophytes, and saprobes associated with diverse plant hosts. Diaporthe sojae is historically linked to soybean diseases, but individual isolates may occur in other host contexts; strain J-7 was obtained from citrus. Publicly reusable, high-contiguity assemblies with detailed isolate-level annotations remain limited. Here, we ass…

Somatic mutations are unevenly distributed across the genome, with certain loci recurrently mutated across independent tumors. Both local DNA sequence context and chromatin organization have been associated with mutation rate variation, yet their combined effects at single-nucleotide resolution remain incompletely characterized. We developed MutFormer, a multimodal framework that integrates seque…

Environmental exposures co-occurring during early life have a profound influence on neurodevelopment. Our previous work in rats suggests that postnatal maternal care modulates the effects of prenatal exposure to bisphenols, an estrogenic endocrine disrupting chemical, on offspring neurodevelopment. Elevated maternal licking/grooming and prenatal bisphenol exposure have opposing effects on estroge…

The brown rat ( Rattus norvegicus ) serves as a cornerstone model organism in biomedical research, particularly for understanding physiological homeostasis and stress responses. The basic leucine zipper (bZIP) transcription factor family is a pivotal regulatory network involved in growth, organogenesis, and neurodevelopment. Despite its importance, a systematic characterization of the bZIP gene f…

The number of vertebrae is an economically significant trait in livestock, with variations in this trait directly influencing meat and hide production performance. Within the Dezhou donkey population, five distinct thoracolumbar vertebrae combinations have been identified (T17L5, T17L6, T18L5, T18L6, and T19L5). This study employed whole-genome resequencing and selective sweep analysis to identif…

Single-nucleotide polymorphism markers (SNPs) have important applications in gene conservation, breeding, and fundamental genetics research. Our long-term goal is to develop routine approaches for SNP genotyping in forest trees. Ideally, these approaches would be inexpensive, able to accommodate a wide range of samples and SNPs, available through commercial providers, and produce high-quality SNP…

Abstract Background Accurate species-level identification of bacteria in complex environmental samples is essential for applications in biotechnology, ecological monitoring, and clinical diagnostics. Short-read platforms such as Illumina frequently truncate the 16S rRNA gene, limiting taxonomic resolution. In this work, we applied Oxford Nanopore Technology (ONT) long-read sequencing to full-leng…