Baobab Index

Standardized microhaplotype databases for eight diverse crops enable multiallelic analyses, comparative genetics, and breeding decisions. Microhaplotypes are short genomic segments that contain multiple tightly linked variants, providing multi-allelic data that can enhance genetic resolution compared to traditional biallelic single nucleotide polymorphism (SNP) markers. Here, we present the creation and utilization of separate microhaplotype databases for eight crop species representing diverse genome sizes, ploidy levels, and breeding systems. We developed a standardized, species-agnostic pipeline for processing, filtering, and databasing microhaplotypes generated using the DArTag targeted genotyping platform. To enhance user accessibility, we developed a no-code, user-friendly application, HapApp, that uses an R Shiny front-end interface to allow breeders and researchers to add unique, standardized microhaplotype identities from raw DArTag reports and iteratively update the existing crop-specific database with the newly discovered microhaplotypes. Selected case studies with these databases highlight the operational advantages of microhaplotypes, especially for challenging, highly heterozygous, or polyploid species. They offer an informative alternative to traditional biallelic SNP analyses for resolving population structures and improving linkage map ordering. This integrated framework provides a reproducible and scalable foundation for managing and exploiting microhaplotype data in plant breeding and genetic research, enabling robust cross-project comparisons and facilitating trait discovery in both simple and complex crop genomes, while enabling comparative genomics and cross-species functional transfer that accelerates genetic gains across all crop species.

Fusarium sambucinum species complex (FSAMSC) includes not only major mycotoxin-producing pathogens but also non-pathogenic endophytic species that can promote plant growth and stress tolerance. However, the molecular mechanisms underlying these contrasting lifestyles remain poorly understood, underscoring the need for deeper molecular studies. A non-pathogenic endophytic Fusarium strain, TZ1MST22, isolated from Medicago sativa plants in the Tozeur region of Southern Tunisia, was sequenced using the Illumina NovaSeq 6000 sequencing technology. Here, we report a 39.8 Mb draft genome of TZ1MST22, comprising 160 contigs. Genome completeness was assessed using Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis, which yielded 99.4% completeness. Molecular phylogenetic analysis showed that TZ1MST22 was a Fusarium brachygibbosum belonging to F. sambucinum species complex (FSAMSC). In total, 12396 protein-coding genes were predicted. Of these, 769 genes were annotated as encoding CAZymes, including 46 cellulose-degrading, 62 hemicellulose-degrading, and 38, 25, 8, and 31 chitin/chitosan-, glucan-, lignin-, and pectin-degrading enzymes, respectively, as well as 74 sugar-, poly-, and oligosaccharide-degrading enzymes, and 61 others, including cutinases. In addition, 38 secondary metabolism gene clusters were identified, mainly including terpenes, T1 polyketide synthase genes, and non-ribosomal peptide synthase genes. Comparative genomic analyses revealed that F. brachygibbosum TZ1MST22 harbors more biomass-degrading enzymes than other pathogenic and endophytic Fusarium species. These results expand our genetic knowledge of Fusarium brachygibbosum, as this genome represents the third published genome of this species and the first non-pathogenic one. Our comprehensive whole-genome analysis provides a valuable resource for future studies on gene expression, regulation, function, evolution, and will support efforts to optimize its cultivation for the high-yield production of useful metabolites.

Following the detection of vaccine-derived poliovirus type 2 (cVDPV2) in Algeria in 2022, enhanced surveillance activities along the Tunisian border identified novel Oral Poliovirus type 2 Vaccine (nOPV2) excretion in an apparently healthy nomadic child. Immunological investigations showed no evidence of major humoral, cellular, or phagocytic immune deficiency. To investigate the kinetics of viral shedding and characterize the complete genome of the isolated strain in this case report, longitudinal follow-up stool samples were collected and analyzed using cell culture inoculation, real-time RT-PCRs, and whole-genome sequencing. Virus was detected over a 76 to 126-days observation period. Assuming vaccination occurred in December 2022, the total duration of shedding may have extended up to approximately 138 to 188 days (4 to 7 months) post-vaccination. Despite prolonged replication, the viruses showed limited within-host evolution and retained the major engineered attenuation features of nOPV2, with no evidence of domain V reversion, cre replacement, or recombination, and only limited VP1 divergence which allows its classification as nOPV2 category 8 strains. Our findings underscore the need to further investigate the potential for prolonged excretion and molecular evolution of nOPV2-like strains in immunocompetent individuals. Furthermore, targeted surveillance of high-risk and mobile populations, including migrants and nomadic communities, is essential to strengthen epidemiological security and support global poliovirus eradication initiatives.

Inflammatory breast cancer (IBC) is a rare and highly aggressive subtype of breast cancer, associated with poor treatment responses and extremely unfavorable patient outcomes. One of the major challenges in IBC is the absence of objective and standardized diagnostic criteria, as diagnosis currently relies on clinical presentation and requires specialist expertise. This limitation is particularly critical in regions such as North Africa, where IBC prevalence is disproportionately high and diagnostic resources are often limited. Another obstacle to improving patient outcomes lies in the limited understanding of the distinct biological mechanisms underlying IBC. As a result, no IBC-specific therapies have been successfully implemented in clinical practice. In this review, we summarize recent advancements in understanding the biology of IBC, with a special emphasis on the tumor microenvironment and discuss how these insights can inform the development of more effective treatment strategies. Considering the growing relevance of liquid biopsy in oncology, we provide a comprehensive overview of current knowledge on its applications in IBC, highlighting the potential of circulating biomarkers to enhance disease characterization, diagnosis, risk assessment, and personalized treatment. Finally, we explore the promising role of artificial intelligence in improving diagnostic accuracy for IBC, with the potential to facilitate earlier detection and improve clinical management of patients with this aggressive disease.

Prosthetic valve endocarditis (PVE) caused by Corynebacterium diphtheriae is rare and may be associated with severe embolic complications and high mortality. In March 2026, a 61-year-old woman with a mechanical mitral valve receiving chronic acenocoumarol therapy was admitted with fever, malaise, and abdominal pain. Thoracoabdominal computed tomography revealed multiple splenic infarctions suggestive of systemic embolization. Transthoracic echocardiography demonstrated vegetations on the prosthetic mitral valve. Blood cultures yielded C. diphtheriae, identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Whole-genome sequencing confirmed a non-toxigenic C. diphtheriae sequence type 542 lacking the tox gene. Antimicrobial susceptibility testing showed resistance to penicillin G and trimethoprim-sulfamethoxazole, with susceptibility to meropenem, erythromycin, clindamycin, tetracycline, linezolid, vancomycin and rifampicin, and susceptibility with increased exposure to cefotaxime and ciprofloxacin. Cerebral computed tomography angiography demonstrated complete occlusion of the right internal carotid artery without initial parenchymal lesions. Intravenous vancomycin and bisoprolol were initiated. Acenocoumarol was initially continued and subsequently switched to intravenous unfractionated heparin. On hospital day 3, the patient developed sudden neurological deterioration with coma, hemodynamic collapse, and respiratory failure. Brain imaging revealed massive intracerebral hemorrhage with intraventricular extension and cerebral herniation. Despite intensive supportive management, the patient died. This case highlights the severe invasive potential of non-toxigenic C. diphtheriae in PVE and the risk of devastating thromboembolic and hemorrhagic neurological complications. It also emphasizes the necessity of rapid microbiological identification, integration of genomic data, and multidisciplinary management, particularly regarding anticoagulation strategies in patients with mechanical prosthetic valves.

Heat stress is an increasingly important constraint on cattle welfare, fertility, productivity, and developmental resilience. DNA methylation may mediate part of the molecular response to thermal exposure, but current studies differ widely in tissue type, exposure model, assay platform, and endpoint definition. This review systematically synthesizes evidence linking heat stress to DNA methylation changes in cattle and evaluates whether a quantitative meta-analysis of global methylation responses is currently feasible. A PRISMA-informed search was conducted for peer-reviewed bovine studies published between 2015 and early 2026. The PECO framework defined cattle or cattle-derived biological material as the population, heat stress or thermal challenge as the exposure, thermoneutral, cooled, or non-stressed conditions as comparators, and DNA methylation-related measures as outcomes. The predefined primary quantitative endpoint was global DNA methylation or hydroxymethylation reported as a continuous outcome. Locus-specific, promoter-level, DMC, DMR, and multi-omics studies were retained for structured qualitative synthesis. Global methylation studies often reported non-significant bulk changes, whereas sequencing-based and promoter-level studies revealed extensive tissue-specific and locus-specific methylation signatures involving oxidative stress, immune regulation, metabolism, endocrine signaling, and developmental programming. A formal pooled meta-analysis was not statistically defensible because fewer than three independent studies reported complete and comparable group-level data for the predefined global methylation endpoint. Heat stress in cattle appears to induce targeted, tissue-specific methylome remodeling rather than a consistent genome-wide shift in global methylation. Future studies should report extractable group-level methylation statistics, standardized heat-load metrics, tissue and cell-composition information, and phenotypic outcomes to enable robust meta-analysis. Beyond reporting standardization, future trial and cohort designs should prospectively incorporate paired global and locus-specific methylation endpoints to enable meta-analytic pooling within the next research cycle.

Achromobacter xylosoxidans is an emerging opportunistic pathogen related to cystic fibrosis (CF). Its clinical impact is variable among patients depending on strain-specific genomic diversity and interaction with co-infecting pathogens. Hence, genomic analysis plays a key role in understanding its pathogenic potential and adaptation in the CF disease. This study included a clinical strain isolated from sputum of a patient with CF. The strain was evaluated for its antimicrobial susceptibility using VITEK 2 and biofilm formation / inhibition using crystal violet assay in the presence and absence of PAβN. Whole-genome sequencing was conducted using Illumina technology, followed by genome assembly and annotation. The resistome and virulence profiling of MICB25 was achieved using BV-BRC and PGAP pipelines. The clinically strain (MICB25) was identified as Achromobacter xylosoxidans. Our study shows that secretion systems, multidrug efflux systems are functionally linked to biofilm formation in a CF-associated A. xylosoxidans MICB25, as evidenced by PAβN-mediated biofilm inhibition. The whole-genome sequencing revealed a multifaceted resistome including β-lactamases, aminoglycoside-modifying enzymes, and other resistance determinants in addition to an exceptionally broad and varied efflux repertoire covering ABC, MFS, RND, and SMR families. The application of whole-genome sequencing in this study provides crucial insights into the persistence-oriented pathogenic strategy of this emerging CF pathogen A. xylosoxidans. The coexistence of multidrug efflux determinants and PAβN-sensitive biofilm formation suggests that efflux activity could be involved in persistence and warrants addditional mechanistic investigation.

Tyrosine kinase inhibitors (TKIs) targeting the BCR::ABL1 fusion protein have revolutionized the treatment of chronic myeloid leukemia (CML), transforming it into a chronic and manageable disease with markedly improved survival. However, prolonged TKI exposure has been associated with rare hematological complications, including secondary lymphoid malignancies. We describe a 39-year-old woman with CML who developed diffuse large B-cell lymphoma (DLBCL) after long-term nilotinib therapy. She had previously received imatinib and dasatinib, both discontinued due to intolerance and cytogenetic failure. Five years after initiating nilotinib, she presented with gastric pain and right cervical lymphadenopathy. Histopathological examination confirmed a nongerminal center B-cell (non-GCB) subtype DLBCL (CD20+, MUM1+, BCL6+, Ki-67: 80%). The patient received eight cycles of R-CHOP, achieving complete remission. At the most recent follow-up, she maintained a major molecular response for CML and complete remission for lymphoma. This case highlights a rare occurrence of DLBCL following long-term TKI therapy for CML. Although a direct causal relationship remains unproven, cumulative drug exposure, immune dysregulation, and genomic instability may contribute to lymphomagenesis. Continuous long-term surveillance is essential for early detection and management of secondary malignancies in patients receiving chronic TKI therapy.

A large fraction of agricultural pesticides, including insecticides, fails to reach target organisms and instead persists in soil, where residues may accumulate and generate transformation products with unpredictable or enhanced toxicity. Therefore, sustainable mitigation strategies require not only efficient pesticide removal but also effective detoxification. Soil-dwelling bacteria, particularly actinobacteria, possess diverse enzymatic capabilities that can contribute to the transformation of these chemical compounds, thereby influencing their environmental fate. In this study, we evaluated the insecticide-removal potential of 70 actinobacterial strains isolated from oligotrophic environments (dust and stone surfaces) in Tunisia using deltamethrin (a pyrethroid) and malathion (an organophosphate) as model insecticides. Thirty-two strains grew in minimal medium containing 3.2 mg/L of at least one insecticide, with 14 strains growing on both compounds. Among them, the actinobacterium