Baobab Index

Whole-genome sequencing (WGS) data on resistance patterns in western Kenya remain limited. We evaluated resistant patterns of In this cross-sectional study, 1,053 archived MTBC isolates from 12 counties in western Kenya were analyzed. An enriched subset of 316 isolates was selected for WGS, of which 290 produced high-quality genomes. Genomic data were analyzed to determine lineage distribution and identify drug resistance mutations using WHO mutation catalogue. Out of the 1,053 isolates, 127 (12%) showed resistance to at least one anti-TB drug. Isoniazid resistant-rifampicin susceptible (Hr-TB) isolates were the most common (52; 40%), followed by rifampicin-resistant (33;26%) and multidrug-resistant (23;18%). The predominance of Hr-TB is consistent with reports from Kenya and other high-burden settings. Enriched WGS subset identified resistance-associated mutations in 43/290 (14%) isolates, with similar resistance patterns. Rifampicin resistance was mainly associated with Western Kenya shows geographic DR-TB heterogeneity with predominant Hr-TB, which rifampicin-based diagnostics risk under-detection. Despite observed discordance, Integrating WGS with routine testing will strengthen surveillance, improve isoniazid resistance detection, and support appropriate treatment management in high-burden settings.

West Nile virus (WNV) is a mosquito-borne flavivirus of global public health importance, maintained in an enzootic cycle between birds and mosquitoes, with humans and other mammals as incidental hosts. Although WNV has been documented in Kenya, surveillance remains inconsistent, geographically fragmented, and largely dependent on serological methods. This limits understanding of circulating lineages, vector diversity, and transmission dynamics, particularly in coastal regions. This study aimed to address these gaps through systematic arboviral surveillance of mosquito populations across four ecologically distinct Kenyan counties using an integrated genomic approach. Mosquitoes were collected using CDC miniature light traps from Kwale, Kilifi, Mombasa, and Isiolo counties (

White star apple (Gambeya albida) is native to the lowland rainforests of Central, East, and West Africa. This species is highly valued for its nutritious fruits and offers medicinal, socio-cultural, and economic benefits. In West Africa, it contributes to food security for rural and urban communities alike. However, no genomic resources are available to untap the agronomic and medicinal traits of the white star apple. Here, we present its first chromosome-scale genome, generated using PacBio HiFi and Omni-C sequencing. The white star apple genome is highly homozygous, and we assembled 98.9% of the estimated haploid genome size (822 Mbp) into 13 pseudochromosomes. It has a base-level accuracy (QV) of 58.14, an N50 of 57 Mbp, and 97.5% BUSCO completeness, representing a reference-quality assembly. About 58.5% of the genome constitutes repetitive sequences, and ab initio gene prediction identified 33,602 gene models. This reference-quality genome of the white star apple will serve as a valuable resource to enhance our understanding of its nutritional and pharmacological traits and facilitate improvement research.

Nguni sheep (Ovis aries) are indigenous to the Southern Africa region and common within the smallholder and poor resources farming systems. They are well adapted to different agroecological regions. However, limited genomic resources such as high-quality reference genomes have hindered our understanding of its adaptation and establishment of an effective breeding program. To address this, we assembled a chromosomal-level genome of Nguni sheep using a combination of PacBio HiFi reads and Omni-C reads. The genome size was estimated to be 2.9 Gb with a contig/scaffold N50 74 Mb and 99.6 Mb and a genome completeness of 96.1%, as estimated by the Benchmarking Universal Single-Copy Orthologs (BUSCO) program. The final genome encompassed a total of 25,926 protein-coding genes. The findings of this study provide a valuable genomic resource for understanding the adaptability of the Nguni sheep and the establishment of effective breeding programs.

The Kolbroek pig is indigenous to South Africa and a breed of choice for smallholder farmers. This is mainly due to its characteristics, such as disease resistance and adaptability to tropical agroecological environments. Despite these desirable traits, the genomic architecture of this breed has not been explored. In this study, we report a high-quality genome assembly of the South African Kolbroek pig sequenced at 31 X coverage through a combination of PacBio Sequel IIe HiFi and Illumina Novaseq 6000 Omni-C sequencing. The assembled genome resulted in a length of 2.6 Gb in size, including 83 Scaffolds, which consist of 19 chromosome-size scaffolds with 138.7 Mb. The BUSCO completeness at 95.5%. Genome annotation and structure prediction identified 22,025 genes with protein-coding potential. The genome provides an opportunity to investigate genetic variation across multiple pig breeds and serves as a genetic resource to develop breeding programs for the conservation and improvement of the Kolbroek pig.

Nguni goat is an indigenous goat breed of South Africa characterised by small body frame, variable coat colours and exceptional tolerance to harsh environmental conditions. This breed is utilised for meat and milk production thus sustaining the livelihood of communal farmers and is important for cultural purposes. We assembled a high-quality genome using HiFi and Omni-C reads. For HiFi and Omni-C, we used PacBio sequel IIe and the Illumina NovaSeq 6000, respectively. The total HiFi generated was 106 Gb and Omni-C generated 300 million reads. The assembly length was 2.85 Gb, comprising of 114 scaffolds and 127 contigs; with N50/L50 of 97.7 Mb/12 and 81.34 Mb/12, respectively. BUSCO showed 96% completeness with 3% missing genes making it the most complete genome. The genome contained 42.86% repetitive elements, with LINEs being the most abundant, representing 28.82% and accounting for 67% of total repeats. The annotation predicted 22,507 genes with an average length of 33,847.2 bp. The genome assembly of the Nguni goat will advance genomic research and enhance breeding programs to improve both production and conservation.