Biology subjects

Mapholi, N.

Publications and source records attributed to Mapholi, N..

5 recordsLinked to original sources

bioRxiv2026

Draft genome assembly of the Woolly bottlebrush (Greyia radlkoferi) using Pacbio long-read sequencing technology.

The Woolly bottlebrush (Greyia radlkoferi) is an indigenous South African plant known for its ornamental appeal and potential medicinal uses. It naturally grows on rocky hillsides and grasslands and highly resilient to drought, temperature fluctuations, and nutrient-poor soils. Its flavonoid-rich compounds with anti-tyrosinase activity support its traditional use to treat skin pigmentation disorders in humans. Despite its outstanding ecological and biochemical characteristics, no reference genome is available for Greyia radlkoferi. Therefore, this study aimed to generate the first draft genome of the Greyia Radlkofleri using PacBio Sequel IIe HiFi long read sequencing. A total of 56.07 Gb HiFi data was generated, providing a total genome coverage of 270X. The assembled genome size was 206Mb, with the longest scaffold being 13.9 Mb. The assembly statistics yielded a scaffold and contig N50 of 10.1 Mb, and an L50 of 9, and with an overall GC content of 34.9 %. The genome scope profile set at kmer = 17 indicated that the genome is triploid. The genome annotation predicted 17,804 protein-coding genes and 17,804 transcripts with an average gene length of 3,116.03 bp. This is the first draft genome of its kind for the Greyia genus and provides a foundation for future studies aimed at elucidating the genetic basis of its environmental resilience and the biosynthetic pathways underlying its medicinal properties.

genomics↗

bioRxiv2026

Chromosome-level Genome Assembly of the South African Lion (Panthera leo melanochaita)

The lion (Panthera leo melanochaita) is one of the most iconic species and part of the big five, maintaining ecological balance and a major wildlife-based tourism attraction in South Africa. Despite its importance, it is currently threatened by rapid population decline and increasing population fragmentation. Therefore, there is a need for a high-quality genomic resource that captures the diverse genetic landscape of South African lion populations. To address this, we present a high-quality genome assembly of the lion, generated using PacBio HiFi and Omni-C sequencing technologies. The final assembly comprises 2.45 Gb, with a scaffold N50 of 148 Mb and a contig N50 of 22 Mb. Remarkably, 94.8% of the genome is anchored to 19 scaffolds, reflecting the high degree of contiguity and near-complete chromosomal level. Completeness assessment of the genome showed 98.2% BUSCO, 98.2% k-mer completeness and QV of 65.6 underscoring high accuracy and biological integrity. Genome annotation predicted 831.4 Mb (33.9%) of repetitive sequences and 21 739 protein-coding genes. This work provides high-quality genomic resource to establish a foundation for future population genomic and conservation-focused investigations of the lion populations in South Africa.

genomics↗

bioRxiv2025

Chromosome-Level Genome Assembly of Southern Africa Mozambique Tilapia (Oreochromis mossambicus) using PacBio HiFi and Omni-C sequencing

The Mozambique tilapia (Oreochromis mossambicus) is a species of significant ecological and economic importance in Southern Africa. However, urbanization and water management challenges have led to the species being classified as threatened by the International Union for Conservation of Nature. Despite its widespread distribution and significance as a key food source, the genetic architecture of Southern African O. mossambicus remains inadequately characterized. This gap in knowledge hinders efforts to conserve and manage the species effectively. This study presents a high-quality chromosome-level genome assembly for a South African O. mossambicus assembled using both PacBio HiFi and Dovetail Omni-C sequencing. The 1.09 Gb assembly is highly contiguous, with 99.4% of sequences anchored into 22 chromosomes and a BUSCO completeness of 99.5%. We annotated 27,544 protein-coding genes. This genome provides an essential resource for preserving native biodiversity and enabling genomic selection for traits like disease resistance and growth performance within the South African aquaculture context.

genomics↗

bioRxiv2025

A Near Telomere-to-Telomere Reference Genome for Drakensberger Cattle Achieved Through Trio-Binned Long-Read Sequencing

Drakensberger cattle is indigenous to South Africa and represent a unique genetic resource which is known for its quality beef production and adapted to the harsh climatic conditions. Despite its significance within the beef industry, no high-quality chromosomal level genome has been reported for this breed, limiting genomic selection and conservation efforts. Although there is a bovine genome reference, we need a breed specific reference to identify breed-unique alleles and structural variants that might not be explained by a distant reference. To address this, we generated a haplotype resolved assembly for Drakensberger cattle using a trio-binning where we employed PacBio HiFi reads for sire and dam, a combination of PacBio HiFi reads, Oxford Nanopore Technologies reads and Omni-C reads for the offspring. The assembled diploid genome size is 2.89 Gb with a scaffold N50 of 111 Mb and contig N50 of 61 Mb. The consensus accuracy was exceptionally high (QV = 70.23) and a genome completeness of 97.5 %, as analysed by the Benchmarking Universal Single-Copy Orthologs (BUSCO). The k-mer profiling suggested one of the strong haplotype separation for livestock with the paternity assembly containing 97.1% and maternity with 99.0%, combined diploid genome recovered 99.46% of all the solid read k-mers. We identified 14 telomeric ends across 13 scaffolds. The final genome encompassed a total of 22,854 protein-coding genes. This is the first high-quality, haplotype resolved genome assembly of the Drakensberger breed. This assembly high accuracy, contiguity and completeness place the genome among the highest-quality cattle genomes produced to date. This genomic resource is essential in designing programs to studies for breed evolution, adaptation, genomic selection and for conservation of the South African indigenous resources.

genomics↗

bioRxiv2025

High quality genome assemblies of African cattle breeds using PacBio HiFi sequencing

Africa has a uniquely rich cattle diversity of [~]150 breeds comprising the Bos taurus indicus sub-species, Bos taurus taurus, and their crosses. These represent [~]23% of the global cattle population. However, high quality, representative assemblies are limited for African cattle and especially for indicine breeds. Here we built high quality de novo assemblies for five important African indigenous cattle breeds using PacBio HiFi sequencing: Lagune (Bos taurus taurus), Gudali, Iringa Red and Singida White (Bos taurus indicus), and Mpwapwa (Bos taurus taurus x Bos taurus indicus). These new assemblies are the most contiguous and complete African cattle assemblies produced so far, with genome sizes of 3.25 - 3.36Gb, contiguity N50s ranging from 83.59Mb to 97.87Mb and scaffold N50s from 100.30Mb to 113.37Mb. BUSCO genome completeness scores were also higher than 99.68%, indicative of highly contiguous assemblies. These improved and highly contiguous genome assemblies are consequently a valuable resource for future African and global livestock genomic studies.

genomics↗