Necrotic enteritis (NE) is one of the most economically important diseases affecting the poultry industry worldwide. Understanding the regulatory mechanisms that control host resistance to NE is essential for identifying molecular markers associated with disease resilience. Promoter regions and microRNAs (miRNAs) play critical roles in regulating gene expression and coordinating immune responses; therefore, their characterization may provide valuable insights into the molecular basis of disease resistance. The present study aimed to identify key regulatory elements, including promoter motifs, transcription factors, and miRNAs, associated with upregulated genes in resistant White Leghorn chicken line co-infected with Eimeria maxima and Clostridium perfringens. In this study, gene networks, gene ontologies, biological pathways, identification of hub genes, promoter interactions and interactions between miRNAs and hub genes in the spleens of Marek’s disease-resistant Leghorn chickens infected with C. perfringens and E. maxima were investigated. Bioinformatics tools were used to conduct this study. For the gene interaction analysis, 216 genes with a p-value of less than 0.01 and a fold change of greater than two relative to the control group were used. miRNA targets of hub genes were predicted using miRDB, and only high-confidence interactions (score > 80) were considered. The results revealed that a substantial proportion of the analyzed upregulated genes were involved in immune-related processes, and several hub genes, including CD molecules and cytokines, were identified. In addition, network analysis revealed hub genes and their interactions led to the identification of three functional clusters. The KEGG pathways of cell adhesion molecules, the intestinal immune network for IgA production, and cytokine-cytokine receptor interactions were commonly identified across all three clusters, indicating their importance in the network. Promoter motif analysis revealed notable binding sites for the upregulated hub genes. Six effective motif binding sites were identified for the upregulated genes. The transcription factors MIX-A, PHOX2B, ZNF384, KLF15, ZNF610, and PATZ1 were found at all six of these loci. The top five gene ontology terms predicted for these motifs were protein transport, translation, regulation of transcription, and DNA dependent, which are common biological processes. The integrated analysis of upregulated genes in resistant chickens revealed that immune-related pathways, key hub genes, transcription factor binding motifs, and miRNA-gene interactions collectively contribute to the host response against necrotic enteritis. The identified regulatory network suggests that both transcriptional and post-transcriptional mechanisms are involved in disease resistance. In particular, hub genes such as TNFSF13B and PTPRC emerged as central regulatory components and may represent promising candidates for future functional validation and biomarker development. These findings provide insights into the molecular mechanisms underlying the immune response to necrotic enteritis in poultry, which could contribute to the development of new strategies for disease control.
Acinetobacter pittii, a member of the Acinetobacter calcoaceticus-baumannii complex, is increasingly recognized as an opportunistic pathogen with substantial genomic and ecological diversity. Although its genomic representation has expanded considerably, human-associated genomes from sub-Saharan Africa remain comparatively underrepresented. We characterized A. pittii AP66, a high-quality metagenome-assembled genome (MAG) recovered from a stool-derived mixed bacterial culture during diagnostic investigation for enteric pathogens in Nigeria. The AP66 genome comprised 3.79 Mb across 67 contigs and was estimated to be 100
Populus euphratica and Populus pruinosa represent core germplasm resources of desert riparian forests in northwest China. Accurate discrimination of putative interspecific hybrids between the two species is fundamental to population genetic research of desert poplars. Currently, publicly available and standardized genome-wide InDel marker resources specifically for desert poplars remain scarce. Traditional morphological identification exhibits low accuracy and reliability, and conventional markers (RAPD, AFLP, SSR) have limited repeatability and species specificity, failing to support standardized genotyping. Based on large-scale whole-genome resequencing data, this study developed and validated a set of highly specific and stable InDel markers to provide valuable genomic resources for subsequent genetic research on desert poplars. A total of 56,864 interspecific InDel loci with fragment length differences over 5 bp were screened from 439 P. euphratica and 146 P. pruinosa resequencing accessions, among which 3,417 loci had interspecific allele frequency differences > 0.9. After primer design and native polyacrylamide gel electrophoresis (native-PAGE) validation, 11 universal InDel primer pairs were obtained, and two robust diagnostic markers (P1599-3, P1599-4) were finally verified. Population validation involving 50 P. euphratica, 41 P. pruinosa and 93 morphologically selected putative-hybrid individuals revealed that this dual-marker set could reliably detect biparental banding patterns among tested candidates. The two verified co-dominant InDel markers provide reusable molecular resources for preliminary germplasm authentication and screening of putative hybrids within Populus sect. Turanga. The standardized screening and PAGE genotyping pipeline provided in this study can be transferred to other woody hybrid species, supporting marker-assisted breeding and germplasm conservation of arid poplars.
The gharial (Gavialis gangeticus) is a freshwater crocodylian endemic to the Indian subcontinent that has experienced ancient and recent catastrophic declines in population size. Conservation interventions initiated in the mid-1970s have enabled partial recovery of the species. Yet, how ancient and recent demographic declines have shaped contemporary genomic diversity in gharial remains unknown. Here, we present the first genome-wide analysis of the gharial using a single high-coverage whole-genome sequence and ddRAD data from 21 individuals sampled across five nesting sites along the Chambal River. Our results reveal extremely low genomic diversity in the largest gharial population, with Watterson’s θ = 0.0008 ± 0.0001 (mean ± SD) and Nucleotide diversity = 0.00036 ± 0.00005, both substantially lower than those reported for other extant crocodylians. Analyses of population genomic structure indicated weak, partially resolved structuring, with individuals from Radi forming a distinct group, whereas individuals from other sites showed limited spatial structuring. Demographic reconstructions revealed declines in effective population size across multiple timescales, including an ancient decline occurring 10,000 years ago and a more recent severe decline within the last 250 years. Consistent with this recent decline, long ROH suggest that recent close inbreeding ( 4 generations), rather than ancient demographic history alone, is the primary contributor to contemporary genome-wide homozygosity. Overall, these findings reflect both deep-time demographic constraints and ongoing genetic erosion in gharial, providing a critical foundation for genomics-informed conservation planning.
Staphylococcus aureus is an important cause of healthcare- and community-associated infections and can acquire antimicrobial resistance (AMR), virulence determinants, and mobile genetic elements that influence colonization, persistence, and disease potential. Whole-genome sequencing (WGS) enables integrated isolate-level characterization of these features, including in resource-constrained hospital settings where genomic surveillance data remain limited. We performed a descriptive WGS-based characterization of two S. aureus isolates collected from the orthopaedics ward at Bugando Medical Centre, Mwanza, Tanzania, in 2020. A55934 was recovered from a wheelchair handle on 16 January 2020 and is described as a fomite-associated isolate. A55935 was recovered from a rectal swab collected from a 43-year-old male patient 24 h after admission for a patella fracture on 6 April 2020 and is described as a patient-associated rectal-swab isolate. The two isolates were collected approximately 11 weeks apart and were not used to infer transmission or contemporaneous circulation. Genomes were analysed using the rMAP 2.0 bioinformatics pipeline for lineage assignment, AMR determinants, virulence-associated genes, and mobile genetic elements. The isolates were also placed within a contextual core-genome phylogeny of publicly available Tanzanian S. aureus genomes. The two isolates belonged to distinct lineages: A55934 was assigned to ST152, while A55935 was assigned to ST8. The patient-associated rectal-swab ST8 isolate carried mecA, consistent with an MRSA genotype, together with additional predicted AMR determinants including erm(C), tet(K), and dfrG, and multiple plasmid replicons. A blaOXA−60-like hit was also detected but is interpreted cautiously because OXA-type beta-lactamases are atypical in S. aureus and require further validation. In contrast, the fomite-associated ST152 isolate had no acquired AMR genes detected at the reporting thresholds and was consistent with an MSSA genotype. Both isolates carried genes associated with adhesion, biofilm formation, immune evasion, and other virulence-related functions, while leukocidin-associated genes were detected only in the ST8 isolate at the applied thresholds. In the contextual phylogeny, the two study isolates occupied distinct positions within broader Tanzanian S. aureus diversity. This two-isolate analysis provides a descriptive, proof-of-concept genomic characterization of source-distinct S. aureus isolates from a Tanzanian orthopaedics ward. The findings show that WGS can resolve lineage, AMR genotype, virulence-gene content, and mobile-element profiles from both fomite-associated and patient-associated isolates. However, because the isolates were few, non-contemporaneous, and not epidemiologically linked, these data cannot establish transmission, ward-level circulation, environmental reservoirs, or representativeness of the broader S. aureus population. Larger longitudinal studies integrating patient and environmental sampling, phenotypic antimicrobial susceptibility testing, and detailed epidemiological metadata are needed to define transmission dynamics and the contribution of high-touch surfaces to S. aureus persistence and AMR dissemination in this setting. Not applicable.
