Chromosome-scale haplotype-resolved pangenomics.

Complete pangenomics is crucial for understanding genetic diversity and evolution across the tree of life. Chromosome-scale, haplotype-resolved pangenomics allows complex structural variations, long-range interactions, and associated functions to be discerned in species populations. We explore the need for high-resolution pangenomes, discuss computational strategies for their development, and describe applications in biodiversity and human health.

Genomic surveillance of SARS-COV-2 reveals diverse circulating variant lineages in Nairobi and Kiambu Counties, Kenya.

Genomic surveillance and identification of COVID-19 outbreaks are important in understanding the genetic diversity, phylogeny, and lineages of SARS-CoV-2. Genomic surveillance provides insights into circulating infections, and the robustness and design of vaccines and other infection control approaches. We sequenced 57 SARS-CoV-2 isolates from a Kenyan clinical population, of which 55 passed quality checks using the Ultrafast Sample placement on the Existing tRee (UShER) workflow. Phylo-genome-temporal analyses across two regions in Kenya (Nairobi and Kiambu County) revealed that B.1.1.7 (Alpha; n = 32, 56.1%) and B.1 (n = 9, 15.8%) were the predominant lineages, exhibiting low Ct values (5-31) suggesting high infectivity, and variant mutations across the two regions. Lineages B.1.617.2, B.1.1, A.23.1, A.2.5.1, B.1.596, A, and B.1.405 were also detected across sampling sites within target populations. The lineages and genetic isolates were traced back to China (A), Costa Rica (A.2.5.1), Europe (B.1, B.1.1, A.23.1), the USA (B.1.405, B.1.596), South Africa (B.1.617.2), and the United Kingdom (B.1.1.7), indicating multiple introduction events. This study represents one of the genomic SARS-CoV-2 epidemiology studies in the Nairobi metropolitan area, and describes the importance of continued surveillance for pandemic control.

Plastome structure of 8 Calanthe s.l. species (Orchidaceae): comparative genomics, phylogenetic analysis.

BACKGROUND: Calanthe (Epidendroideae, Orchidaceae) is a pantropical genus distributed in Asia and Africa. Its species are of great importance in terms of economic, ornamental and medicinal values. However, due to limited and confusing delimitation characters, the taxonomy of the Calanthe alliance (Calanthe, Cephalantheropsis, and Phaius) has not been sufficiently resolved. Additionally, the limited genomic information has shown incongruences in its systematics and phylogeny. In this study, we used illumina platform sequencing, performed a de novo assembly, and did a comparative analysis of 8 Calanthe group species' plastomes: 6 Calanthe and 2 Phaius species. Phylogenetic analyses were used to reconstruct the relationships of the species as well as with other species of the family Orchidaceae. RESULTS: The complete plastomes of the Calanthe group species have a quadripartite structure with varied sizes ranging between 150,105bp-158,714bp, including a large single-copy region (LSC; 83,364bp- 87,450bp), a small single-copy region (SSC; 16,297bp -18,586bp), and a pair of inverted repeat regions (IRs; 25,222bp - 26,430bp). The overall GC content of these plastomes ranged between 36.6-36.9%. These plastomes encoded 131-134 differential genes, which included 85-88 protein-coding genes, 37-38 tRNA genes, and 8 rRNA genes. Comparative analysis showed no significant variations in terms of their sequences, gene content, gene order, sequence repeats and the GC content hence highly conserved. However, some genes were lost in C. delavayi (P. delavayi), including ndhC, ndhF, and ndhK genes. Compared to the coding regions, the non-coding regions had more sequence repeats hence important for species DNA barcoding. Phylogenetic analysis revealed a paraphyletic relationship in the Calanthe group, and confirmed the position of Phaius delavayi in the genus Calanthe as opposed to its previous placement in Phaius. CONCLUSION: This study provides a report on the complete plastomes of 6 Calanthe and 2 Phaius species and elucidates the structural characteristics of the plastomes. It also highlights the power of plastome data to resolve phylogenetic relationships and clarifies taxonomic disputes among closely related species to improve our understanding of their systematics and evolution. Furthermore, it also provides valuable genetic resources and a basis for studying evolutionary relationships and population genetics among orchid species.

Giraffe lineages are shaped by major ancient admixture events.

Strong genetic structure has prompted discussion regarding giraffe taxonomy,1,2,3 including a suggestion to split the giraffe into four species: Northern (Giraffa c. camelopardalis), Reticulated (G. c. reticulata), Masai (G. c. tippelskirchi), and Southern giraffes (G. c. giraffa).4,5,6 However, their evolutionary history is not yet fully resolved, as previous studies used a simple bifurcating model and did not explore the presence or extent of gene flow between lineages. We therefore inferred a model that incorporates various evolutionary processes to assess the drivers of contemporary giraffe diversity. We analyzed whole-genome sequencing data from 90 wild giraffes from 29 localities across their current distribution. The most basal divergence was dated to 280 kya. Genetic differentiation, FST, among major lineages ranged between 0.28 and 0.62, and we found significant levels of ancient gene flow between them. In particular, several analyses suggested that the Reticulated lineage evolved through admixture, with almost equal contribution from the Northern lineage and an ancestral lineage related to Masai and Southern giraffes. These new results highlight a scenario of strong differentiation despite gene flow, providing further context for the interpretation of giraffe diversity and the process of speciation in general. They also illustrate that conservation measures need to target various lineages and sublineages and that separate management strategies are needed to conserve giraffe diversity effectively. Given local extinctions and recent dramatic declines in many giraffe populations, this improved understanding of giraffe evolutionary history is relevant for conservation interventions, including reintroductions and reinforcements of existing populations.

Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations.

The blue wildebeest (Connochaetes taurinus) is a keystone species in savanna ecosystems from southern to eastern Africa, and is well known for its spectacular migrations and locally extreme abundance. In contrast, the black wildebeest (C. gnou) is endemic to southern Africa, barely escaped extinction in the 1900s and is feared to be in danger of genetic swamping from the blue wildebeest. Despite the ecological importance of the wildebeest, there is a lack of understanding of how its unique migratory ecology has affected its gene flow, genetic structure and phylogeography. Here, we analyze whole genomes from 121 blue and 22 black wildebeest across the genus' range. We find discrete genetic structure consistent with the morphologically defined subspecies. Unexpectedly, our analyses reveal no signs of recent interspecific admixture, but rather a late Pleistocene introgression of black wildebeest into the southern blue wildebeest populations. Finally, we find that migratory blue wildebeest populations exhibit a combination of long-range panmixia, higher genetic diversity and lower inbreeding levels compared to neighboring populations whose migration has recently been disrupted. These findings provide crucial insights into the evolutionary history of the wildebeest, and tangible genetic evidence for the negative effects of anthropogenic activities on highly migratory ungulates.

African bushpigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival.

Several African mammals exhibit a phylogeographic pattern where closely related taxa are split between West/Central and East/Southern Africa, but their evolutionary relationships and histories remain controversial. Bushpigs (Potamochoerus larvatus) and red river hogs (P. porcus) are recognised as separate species due to morphological distinctions, a perceived lack of interbreeding at contact, and putatively old divergence times, but historically, they were considered conspecific. Moreover, the presence of Malagasy bushpigs as the sole large terrestrial mammal shared with the African mainland raises intriguing questions about its origin and arrival in Madagascar. Analyses of 67 whole genomes revealed a genetic continuum between the two species, with putative signatures of historical gene flow, variable FST values, and a recent divergence time (<500,000 years). Thus, our study challenges key arguments for splitting Potamochoerus into two species and suggests their speciation might be incomplete. Our findings also indicate that Malagasy bushpigs diverged from southern African populations and underwent a limited bottleneck 1000-5000 years ago, concurrent with human arrival in Madagascar. These results shed light on the evolutionary history of an iconic and widespread African mammal and provide insight into the longstanding biogeographic puzzle surrounding the bushpig's presence in Madagascar.

Establishing African genomics and bioinformatics programs through annual regional workshops.

The African BioGenome Project (AfricaBP) Open Institute for Genomics and Bioinformatics aims to overcome barriers to capacity building through its distributed African regional workshops and prioritizes the exchange of grassroots knowledge and innovation in biodiversity genomics and bioinformatics. In 2023, we implemented 28 workshops on biodiversity genomics and bioinformatics, covering 11 African countries across the 5 African geographical regions. These regional workshops trained 408 African scientists in hands-on molecular biology, genomics and bioinformatics techniques as well as the ethical, legal and social issues associated with acquiring genetic resources. Here, we discuss the implementation of transformative strategies, such as expanding the regional workshop model of AfricaBP to involve multiple countries, institutions and partners, including the proposed creation of an African digital database with sequence information relating to both biodiversity and agriculture. This will ultimately help create a critical mass of skilled genomics and bioinformatics scientists across Africa.

Limited genetic variations of the Rh5-CyRPA-Ripr invasion complex in Plasmodium falciparum parasite population in selected malaria-endemic regions, Kenya.

The invasion of human erythrocytes by Plasmodium falciparum merozoites requires interaction between parasite ligands and host receptors. Interaction of PfRh5-CyRPA-Ripr protein complex with basigin, an erythrocyte surface receptor, via PfRh5 is essential for erythrocyte invasion. Antibodies raised against each antigen component of the complex have demonstrated erythrocyte invasion inhibition, making these proteins potential blood-stage vaccine candidates. Genetic polymorphisms present a significant challenge in developing efficacious vaccines, leading to variant-specific immune responses. This study investigated the genetic variations of the PfRh5 complex proteins in P. falciparum isolates from Lake Victoria islands, Western Kenya. Here, twenty-nine microscopically confirmed P. falciparum field samples collected from islands in Lake Victoria between July 2014 and July 2016 were genotyped by whole genome sequencing, and results compared to sequences mined from the GenBank database, from a study conducted in Kilifi, as well as other sequences from the MalariaGEN repository. We analyzed the frequency of polymorphisms in the PfRh5 protein complex proteins, PfRh5, PfCyRPA, PfRipr, and PfP113, and their location mapped on the 3D protein complex structure. We identified a total of 58 variants in the PfRh5 protein complex. PfRh5 protein was the most polymorphic with 30 SNPs, while PfCyRPA was relatively conserved with 3 SNPs. The minor allele frequency of the SNPs ranged between 1.9% and 21.2%. Ten high-frequency alleles (>5%) were observed in PfRh5 at codons 147, 148, 277, 410, and 429 and in PfRipr at codons 190, 255, 259, and 1003. A SNP was located in protein-protein interaction region C203Y and F292V of PfRh5 and PfCyRPA, respectively. Put together, this study revealed low polymorphisms in the PfRh5 invasion complex in the Lake Victoria parasite population. However, the two mutations identified on the protein interaction regions prompts for investigation on their impacts on parasite invasion process to support the consideration of PfRh5 components as potential malaria vaccine candidates.

The soil microbiomes of forest ecosystems in Kenya: their diversity and environmental drivers.

Soil microbiomes in forest ecosystems act as both nutrient sources and sinks through a range of processes including organic matter decomposition, nutrient cycling, and humic compound incorporation into the soil. Most forest soil microbial diversity studies have been performed in the northern hemisphere, and very little has been done in forests within African continent. This study examined the composition, diversity and distribution of prokaryotes in Kenyan forests top soils using amplicon sequencing of V4-V5 hypervariable region of the 16S rRNA gene. Additionally, soil physicochemical characteristics were measured to identify abiotic drivers of prokaryotic distribution. Different forest soils were found to have statistically distinct microbiome compositions, with Proteobacteria and Crenarchaeota taxa being the most differentially abundant across regions within bacterial and archaeal phyla, respectively. Key bacterial community drivers included pH, Ca, K, Fe, and total N while archaeal diversity was shaped by Na, pH, Ca, total P and total N. To contextualize the prokaryote diversity of Kenyan forest soils on a global scale, the sample set was compared to amplicon data obtained from forest biomes across the globe; displaying them to harbor distinct microbiomes with an over-representation of uncultured taxa such as TK-10 and Ellin6067 genera.

Lactic Acid Bacteria from African Fermented Cereal-Based Products: Potential Biological Control Agents for Mycotoxins in Kenya.

Cereals play an important role in global food security. Data from the UN Food and Agriculture Organization projects increased consumption of cereals from 2.6 billion tonnes in 2017 to approximately 2.9 billion tonnes by 2027. However, cereals are prone to contamination by toxigenic fungi, which lead to mycotoxicosis. The current methods for mycotoxin control involve the use of chemical preservatives. However, there are concerns about the use of chemicals in food preservation due to their effects on the health, nutritional quality, and organoleptic properties of food. Therefore, alternative methods are needed that are affordable and simple to use. The fermentation technique is based on the use of microorganisms mainly to impart desirable sensory properties and shelf-life extension. The lactic acid bacteria (LAB) are generally regarded as safe (GRAS) due to their long history of application in food fermentation systems and ability to produce antimicrobial compounds (hydroxyl fatty acids, organic acids, phenyllactic acid, hydrogen peroxide, bacteriocins, and carbon dioxide) with a broad range of antifungal activity. Hence, LAB can inhibit the growth of mycotoxin-producing fungi, thereby preventing the production of mycotoxins. Fermentation is also an efficient technique for improving nutrient bioavailability and other functional properties of cereal-based products. This review seeks to provide evidence of the potential of LAB from African fermented cereal-based products as potential biological agents against mycotoxin-producing fungi.

A review on ethnobotany, phytochemistry, and pharmacology of the genus Didymocarpus wall. (Gesneriaceae).

ETHNOPHARMACOLOGICAL RELEVANCE: Medicinal plants have been extensively used to treat various illnesses since the dawn of civilization. The genus Didymorcapus Wall. comprises 100 species widely distributed in the tropical regions of Asia, with a few found scattered in Africa and Australia. Species in this genus have long been used in folk medicine to treat various illnesses, including wounds, kidney stones, inflammations, asthma, flu, eczema, dysentery, fractures, colic etc. Some species have applications as weight loss agents, laxatives, and protective medication after childbirth. AIM: To provide comprehensive information on the current knowledge of the ethnobotanical uses, phytochemical compounds, pharmacological applications, and toxicology of genus Didymocarpus to reveal its therapeutic potential, offering insights into future research opportunities. MATERIALS AND METHODS: Data were systematically obtained from books and online databases such as PubMed, Web of Science, Scopus, Sci Finder, Google Scholar, Science direct, ACS Publications, Elsevier, Wiley Online Library. RESULTS: Seventeen Didymocarpus species have applications in traditional medicine in different Asian countries. A total of 166 compounds have been isolated from the genus Didymocarpus including terpenoids, flavonoids, phenolic compounds, fatty acids, chalcones, steroids, and others. Among these constituents, terpenoids, flavonoids, chalcones, and phenolics are the significant contributors to pharmacological activities of the genus Didymocarpus, possessing wide-reaching biological activities both in vivo and in vitro. The crude extracts and isolated phytochemical compounds from this genus have been shown to exhibit various pharmacological activities, including antiurolithiatic, nephro-protective, antimicrobial, anticancer, antidiabetic, cytotoxic, wound healing, and antioxidant activities. CONCLUSIONS: Traditional uses and scientific evaluation of Didymocarpus indicate that Didymocarpus pedicellata is one of the most widely used species in some parts of the world. Although substantial progress on the chemical and pharmacological properties of Didymocarpus species has been made, further studies on the pharmacology and toxicology of these species are needed to ensure safety, efficacy, and quality. Also, further research on the structure-activity relationship of some of the isolated phytocompounds may improve their biological potency and scientific exploitation of traditional uses of the Didymocarpus taxa.

Prokaryotic diversity and composition within equatorial lakes Olbolosat and Oloiden in Kenya (Africa).

Total community 16S rDNA was used to determine the diversity and composition of bacteria and archaea within lakes Olbolosat and Oloiden in Kenya. The V3-V4 hypervariable region of the 16S rRNA gene was targeted since it's highly conserved and has a higher resolution for lower rank taxa. High throughput sequencing was performed on 15 samples obtained from the two lakes using the Illumina Miseq platform. Lakes Olbolosat and Oloiden shared 280 of 10,523 Amplicon Sequence Variants (ASVs) recovered while the four sample types (water, microbial mats, dry and wet sediments) shared 4 ASVs. The composition of ASVs in lake Olbolosat was highly dependent on Cu+, Fe2+, NH4 +, and Mn2+, while L. Oloiden was dependent on Mg2+, Na+, Ca2+, and K+. All the alpha diversity indices except Simpson were highest in the dry sediment sample (EC1 and 2) both from lake Oloiden. The abundant phyla included Proteobacteria (33.8%), Firmicutes (27.3%), Actinobacteriota (21.2%), Chloroflexi (6.8%), Cyanobacteria (3.8%), Acidobacteriota (2.8%), Planctomycetota (1.9%) and Bacteroidota (1.1%). Analysis of similarity (ANOSIM) revealed a significant difference in ASV composition between the two lakes (r = 0.191, p = 0.048), and between the sample types (r = 0.6667, p = 0.001). The interaction network for prokaryotic communities within the two lakes displayed Proteobacteria to be highly positively connected with other microbes. PERMANOVA results suggest that temperature controls the functioning of the two ecosystems.

Rapid nectar-meal effects on a predator's capacity to kill mosquitoes.

Using Evarcha culicivora, an East African jumping spider (Salticidae), we investigate how nectar meals function in concert with predation specifically at the juvenile stage between emerging from the egg sac and the first encounter with prey. Using plants and using artificial nectar consisting of sugar alone or sugar plus amino acids, we show that the plant species (Lantana camara, Ricinus communis, Parthenium hysterophorus), the particular sugars in the artificial nectar (sucrose, fructose, glucose, maltose), the concentration of sugar (20%, 5%, 1%) and the duration of pre-feeding fasts (3 days, 6 days) influence the spider's prey-capture proficiency on the next day after the nectar meal. However, there were no significant effects of amino acids. Our findings suggest that benefits from nectar feeding are derived primarily from access to particular sugars, with fructose and sucrose being the most beneficial, glucose being intermediate and maltose being no better than a water-only control.