Baobab Index

The burden of triple-negative breast cancer (TNBC) may be shaped by genetic factors, particularly inherited and somatic mutation profiles. However, data on this topic remain limited, especially for the African continent, where a higher TNBC incidence is observed. In the age of precision medicine, cataloguing TNBC diversity in African patients becomes imperative. We performed whole exome sequencing, including untranslated regions, on 30 samples from Angola and Cape Verde, which allowed to ascertain on potential regulatory mutations in TNBC for the first time. A high somatic burden was observed for the African cohort, with 86% of variants being so far unreported. Recurring to predictive functional algorithms, 17% of the somatic single nucleotide variants were predicted to be deleterious at the protein level, and 20% overlapped with candidate cis-regulatory elements controlling gene expression. Several of these somatic functionally-impactful mutations and copy number variation (mainly in 1q, 8q, 6 and 10p) occur in known BC- and all cancer-driver genes, enriched for several cancer mechanisms, including response to radiation and related DNA repair mechanisms. TP53 is the top of these known BC-driver genes, but our results identified possible novel TNBC driver genes that may play a main role in the African context, as TTN, CEACAM7, DEFB132, COPZ2 and GAS1. These findings emphasize the need to expand cancer omics screenings across the African continent, the region of the globe with highest genomic diversity, accelerating the discovery of new somatic mutations and cancer-related pathways.

Characterizing genetic and epigenetic diversity is crucial for assessing the adaptive potential of threatened populations and species in the face of climate change. Sea turtles are particularly vulnerable due to their temperature-dependent sex determination (TSD) system, which heightens the risk of extreme sex ratio bias and extinction under future climate scenarios. High-quality genomic and epigenomic resources will therefore support conservation efforts for these endangered flagship species with such plastic traits. We generated a chromosome-level genome assembly for the loggerhead sea turtle (Caretta caretta) from the globally important Cabo Verde rookery. Using Oxford Nanopore Technology (ONT) and Illumina reads followed by homology-guided scaffolding to the same species, we achieved a contiguous (N50: 129.7 Mbp) and complete (BUSCO: 97.1%) assembly, with 98.9% of the genome scaffolded into 28 chromosomes and 33,887 annotated genes. We also extracted the blood methylome profile from our ONT reads, which was confirmed to be representative of the reference population via whole-genome bisulfite sequencing of 10 additional loggerheads from the same population. Applying our novel resources, we revealed high conservation of synteny between sea turtle species, reconstructed population size fluctuations in line with major climatic events, and identified microchromosomes as key regions for monitoring genetic diversity and epigenetic flexibility. Isolating 199 TSD-linked genes, we further built a large network of functional protein associations and blood-based methylation patterns. We present a high-quality loggerhead sea turtle genome and methylome from the globally significant East Atlantic population. By leveraging ONT sequencing, we generate genomic and epigenomic resources simultaneously and showcase the potential of this approach for driving molecular insights for conservation of endangered sea turtles.

Organic farming can help mitigate the negative impacts of agriculture on biodiversity, but its effects remain controversial and poorly understood for many taxa, especially from a genetic perspective, where major knowledge gaps persist. This study investigates how the organic and conventional management of banana groves influences population dynamics (i.e., total abundance and abundance by sex and developmental stage) and mitochondrial genetic diversity (cytochrome b gene) of the earwig

Drought alters the soil microbiota by selecting for functional traits that preserve fitness in dry conditions. Legacy effects or ecological memory refers to how past stress exposure influences microbiota responses to future environmental challenges. How precipitation legacy effects impact soil microorganisms and plants is unclear, especially in the context of subsequent drought. Here we characterized the metagenomes of six prairie soils spanning a precipitation gradient in Kansas, United States. A microbial precipitation legacy, which persisted over a 5-month-long experimental drought, mitigated the negative physiological effects of acute drought for a native wild grass species, but not for the domesticated crop species maize. RNA sequencing of roots revealed that soil microbiota with a low precipitation legacy altered expression of plant genes that mediate transpiration and intrinsic water-use efficiency during drought. Our results show how historical exposure to water stress alters soil microbiota, with consequences for future drought responses of some plant species.

Boron (B) is a crucial micronutrient, particularly in volcanic soils where its deficiency hampers agriculture. Here, we investigate the genetic basis of leaf B accumulation in natural populations of

Drought response in plants is complex, involving integration across a range of physiological processes. However, our knowledge of how different mechanisms of drought response are linked at the genetic level is limited. We investigated multi-trait adaptation in Arabidopsis thaliana from the Cape Verde Islands (CVI). Using a high-throughput phenotyping platform that minimizes spatial heterogeneity, we measured variation in rosette area, growth rate, leaf color, water use efficiency (WUE), and stomatal patterning under precisely controlled water conditions. Relative to the Moroccan outgroup, CVI populations evolved earlier flowering, a smaller rosette size with faster growth, and reduced WUE, consistent with drought escape adaptation. Genome-wide association mapping revealed evidence for pleiotropy involving MPK12 (WUE, rosette area, growth rate, and leaf color), NHL26 (WUE and leaf color), SUVH4 (stomatal patterning, rosette area, and leaf color), and FRI (flowering time, WUE, and leaf color), along with an enrichment of signals in ABA response. This study advances our knowledge of the genetic mechanisms driving plant adaptation to a novel precipitation environment. By identifying key genetic components and their contributions to multi-trait adaptation, our findings offer insights into how plants respond to environmental challenges and contribute to predicting plant responses to future climate change.

Arid and semi-arid ecosystems constitute important carbon reservoirs, yet their contribution to climate regulation remains insufficiently documented, particularly in Small Island Developing States (SIDS). In this context, invasive or introduced woody species may contribute substantially to biomass accumulation in degraded drylands, although quantitative evidence for Neltuma juliflora remains limited. This study provides the first block-scale assessment of carbon stocks in N. juliflora stands on Santiago Island, Cabo Verde, using validated allometric equations and topsoil analyses across 11 sampling blocks. A total of 463 individuals were measured. Aboveground carbon stocks varied markedly among blocks, ranging from 27.4 to 85.3 Mg C ha⁻

Persistent SARS-CoV-2 transmission, ongoing mpox outbreaks, and the continued spread of endemic diseases such as typhoid fever and cholera underscore the urgent need for global, multiomics surveillance. In this Personal View, we present Project ODIN, a consortium of European and African partners launched in 2023 that aims to meet this challenge by deploying innovative systems for near real-time pathogen detection and actionable public health insights. The project is a collaboration between high-income and low-income countries in northern Europe and sub-Saharan Africa. Focusing on low-income and middle-income countries, ODIN integrates metagenomics with mobile laboratory systems for comprehensive pathogen monitoring across diverse environments. ODIN emphasises standardised sampling, bioinformatics pipelines, and data-sharing protocols to ensure reliable, interoperable results while addressing infrastructure and resource limitations. By bridging gaps in genomic surveillance, these initiatives seek to strengthen outbreak preparedness, improve pathogen detection, monitor antimicrobial resistance, and provide a holistic approach to One Health challenges. Together, these innovations could advance global surveillance capacity-particularly in under-resourced regions-paving the way for effective disease control and evidence-based policy making.

Over the past four decades, the HIV epidemic in sub-Saharan Africa has shifted from an acute, high-mortality phase to an era of widespread antiretroviral therapy (ART), driven by global scale up and the introduction of potent regimens such as dolutegravir-based combinations. While viral suppression is now increasingly achievable, the central challenge has evolved toward maintaining durable virological control across the life course. We argue that program success can no longer be defined by the mere attainment of suppression, but by the sustained maintenance of undetectable viral load and preservation of drug effectiveness at the population level. From a virological perspective, incomplete suppression, including persistent low-level viremia, creates predictable conditions for resistance selection over time, even with high-genetic barrier agents. In settings where CD4 monitoring is infrequent, gradual immune deterioration may go unnoticed despite apparently acceptable viral load thresholds. Emerging integrase inhibitor resistance should therefore be interpreted as a systems-level warning signal rather than an isolated clinical event. We discuss dolutegravir as an extraordinary yet finite therapeutic resource, the risks of functional monotherapy when nucleoside backbones are compromised, and the role of postfailure strategies, including protease inhibitor-anchored regimens, within optimized care pathways. Central to this approach is recognizing diagnostics-viral load monitoring, CD4 assessment, and targeted genotypic resistance testing-as essential clinical infrastructure. Sustaining ART gains in Africa requires moving from "minimum for all" toward differentiated, high-quality lifelong care integrated within broader public health platforms.

Cervical cancer (CC) is one of the most common cancer types affecting women globally. Cervical cancer is largely associated with human papillomavirus infections; however, approximately 5% to 11% of CC cases are non-human papillomavirus virus-related. Malawi has the second highest CC prevalence and mortality rate worldwide. This study investigated the burden of rare genetic variants in genes associated with CC among Malawian women. Ethical approval was obtained from the National Health Science Research committee on 28 August 2023. Whole-genome sequencing was performed on 20 Malawian CC patients, followed by variant discovery and annotation using the Genome Analysis Toolkit and Ensembl's Variant Effector Predictor. Test for Rare Variants Against Public Database was performed on qualifying variants using 76 156 genomes from the Genome Aggregation database as controls. Bonferroni correction was applied to account for multiple testing. We identified 372 genes with a significant burden of rare variants ( A significant burden of rare variants associated with CC was observed in known genes associated with lung, ovarian and osteosarcoma cancers, suggesting an increased population risk of developing CC and other cancers among Malawian women that needs further investigation. The high burden of rare variants in the