Baobab Index

Although the green revolution adapted a handful of crops to homogeneous and high-input industrialized agriculture, much of the global population still relies on the local production of variable crop cultivars by low-input smallholder farms. This diversity of unhomogenized crops

Benign adult familial myoclonic epilepsy (BAFME) is a rare autosomal dominant disorder characterized by tremor and myoclonic seizures. To date, seven genetic subtypes have been identified, all caused by noncoding pentanucleotide repeat expansions-typically TTTTA expansions with additional TTTCA insertions-across distinct loci. Although aberrant repeat expansions are a shared hallmark, it remains unclear whether different BAFME subtypes exhibit similar patterns of repeat length variability and inheritance. We aimed to characterize pentanucleotide repeat structure, repeat length variability across reads, and intergenerational transmission patterns across multiple BAFME subtypes, and to determine whether these mutational dynamics differ among BAFME1, BAFME4, and BAFME8. We performed whole-genome long-read sequencing and targeted adaptive sampling long-read sequencing on 18 affected individuals from three multigenerational families with BAFME1 (SAMD12), BAFME4 (YEATS2), and BAFME8 (RAI1). Repeat structure, repeat length variability across reads, and intergenerational transmission dynamics were analyzed. Across patients, 7-33 long reads containing expanded repeats were identified. Several differences in repeat length distributions across reads were observed among the families studied. The BAFME1 family showed comparatively narrower distributions, whereas broader variability was observed in the BAFME4 and BAFME8 families. In BAFME1 and BAFME8, TTTCA repeat length showed a positive correlation with age, consistent with age-associated increases in repeat length variability across reads. Parent-to-offspring transmissions were often associated with increases in repeat length, most prominently in BAFME8. Sibling comparisons further indicated higher variability in TTTCA than in TTTTA repeats. Our study demonstrates distinct patterns of repeat length variability and inheritance across the families analyzed. These findings suggest that the genomic context of pentanucleotide expansions may influence repeat behavior and could contribute to phenotypic variability in BAFME.

Mpox is a zoonosis caused by the monkeypox virus. Here, we report Mali's index Mpox case, which was clinically identified at the Mali-Guinea border by the national telemedicine center and confirmed by PCR. The library prepared with NextGenPCR™ MPXV Sequencing Library Prep and sequenced on Minion MK1C revealed a genome length of 197,122 bp with an average depth of 1284.4×. The strain belonged to Clade IIb G1 lineage and exhibited 85 mutations relative to NC_063383.1. To decipher genomic epidemiology, genomes ≥ 195 kb were retrieved from NCBI and aligned with MAFFT. Time-resolved phylogenetic reconstruction and ancestral trait inference were performed with TreeTime v0.11.4. A median joining network was built with Popart v1.7. Phylogeographic analysis revealed clustering with Clade IIb (G.1 lineage) linked to the May 2025 outbreak in Sierra Leone.

Cis-regulatory elements (CREs) drive tissue- and cell-specific gene expression and are essential for safe, sustainable genetic control strategies in pest and vector insects, including the engineering of gene drives in the primary human-malaria vector Anopheles gambiae. Yet CREs remain poorly defined in mosquitoes due to limited computational tools and practical methods for identification and validation. We present a systematic in silico approach for CRE discovery, correlating targeted DNA-motif searches with gene expression, followed by frequency and distribution analysis within putative promoter regions. Applied to the A. gambiae germline, this approach identified hundreds of putative CREs significantly correlated with germline expression in one or both sexes, often linked to distinct sperm developmental stages and chromosomal locations, suggesting roles in broader regulatory mechanisms such as dosage compensation and meiotic silencing. When mapped onto pre-characterised germline promoters, CRE distribution aligned with regions associated with experimental expression patterns. Finally, we validated a top-ranked testis-enriched CRE using an in vivo dual-reporter assay, showing that mutation of conserved nucleotides drastically altered male germline expression. To the best of our knowledge this work provides the first nucleotide-resolution regulatory genome annotation of the A. gambiae germline, offering a transferable framework to aid promoter design for genetic control strategies against malaria mosquitoes and other insect pests.

In sub-Saharan Africa, continental-scale genomic surveillance of Plasmodium falciparum malaria is needed to track the spread of drug and diagnostic resistance, as well as monitor parasite evolutionary responses to vaccine rollout. Yet continental-scale implementation is hindered by a lack of genomic approaches suitable for local laboratories, and the vastness of the continent. Here, we initiate a decentralised scale-up of P. falciparum genomic surveillance by locally sequencing and analysing 1065 samples across six African countries in one year. We achieve this with a novel nanopore sequencing protocol that is rapid (~5 hr) and cost-effective (<$25 USD/sample), providing surveillance of antimalarial drug resistance genes, hrp2/3 deletions, the vaccine target csp, and the polymorphic gene ama1. We couple this to a laptop-based bioinformatics dashboard that runs offline and displays mapping and variant calling results in real-time. We demonstrate robust sequencing coverage across parasitemia levels and laboratories, accurate identification of antimalarial resistance markers and hrp2/3 deletions; and, with a novel variant caller, sensitive detection of mutations carried by minor clones. Our approach will accelerate genomic surveillance of P. falciparum malaria across sub-Saharan Africa at a time of urgent need.

Maize lethal necrosis (MLN) poses a severe threat to maize production in eastern and southern Africa, causing significant yield losses. In this study, marker-assisted backcross introgression (MABI) was used to introgress major-effect MLN resistance Quantitative Trait Loci (QTL). These QTLs located on chromosomes 3 and 6, were introgressed into 14 MLN-susceptible CIMMYT maize lines. Ten Kompetitive Alelle Specific PCR (KASP) SNP markers closely linked to three validated QTL-hotspot regions were applied for foreground selection, with at least two hotspots polymorphic across all donor-recipient combinations. Foreground and background selection enabled fast tracking of MLN resistance alleles and recovery of near-recurrent parent genomes. The resulting BC₄F

Effective control of falciparum malaria depends on the sustained efficacy of frontline antimalarial drugs, particularly artemether-lumefantrine (AL), the most widely used therapy in Africa. However, the emergence of artemisinin partial resistance and reduced lumefantrine susceptibility in eastern Africa threaten malaria control and elimination. Robust genetic markers of decreased susceptibility to lumefantrine remain elusive, and our understanding of artemisinin resistance is incomplete. We report results of a

The practice of malaria parasite genomics has evolved due to changing technology, expanded capacity, shifting funding, and broader applications. What began as a descriptive, discovery-focused field has grown into a global system for routine surveillance that informs public health decisions. This shift is supported by wider access to sequencing and new, cost-effective targeted sequencing methods. These changes, however, introduce new needs for standardizing data formats, analysis pipelines, sharing practices, and approaches for translating genomic insights into action. This review examines the progressive decentralization and diversification of malaria genomic data generation, highlights emerging applications enabled by these trends, and outlines key development needs and growth opportunities for this maturing field.

A fused dihydropyrrolidino-pyrimidine hit with low lipophilicity and excellent ligand efficiency was identified in a biochemical screen of the Global Health Chemical Diversity Library (GHCDL) against