Colonialism in South Africa leaves a lasting legacy of reduced genetic diversity in Cape buffalo
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ABSTRACT:
PROVIDER: PRJEB58638 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR10772718_1.fastq.gz | Fastqsanger.gz | |||
| ERR10772718_2.fastq.gz | Fastqsanger.gz | |||
| ERR10772720_1.fastq.gz | Fastqsanger.gz | |||
| ERR10772720_2.fastq.gz | Fastqsanger.gz |
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Project description:Drivers of genetic diversity differences in Cape buffalo
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2010-08-11 | E-GEOD-19442 | biostudies-arrayexpress
Project description:The reduced cost of next-generation sequencing (NGS) has allowed researchers to generate nuclear and mitochondrial genome data to gain deeper insights into the phylogeography, evolutionary history and biology of non-model species. While the Cape buffalo (Syncerus caffer caffer) has been well-studied across its range with traditional genetic markers over the last 25 years, researchers are building on this knowledge by generating whole genome, population-level data sets to improve understanding of the genetic composition and evolutionary history of the species. Using publicly available NGS data, we assembled 40 Cape buffalo mitochondrial genomes (mitogenomes) from four protected areas in South Africa, expanding the geographical range and almost doubling the number of mitogenomes available for this species. Coverage of the mitogenomes ranged from 154 to 1036X. Haplotype and nucleotide diversity for Kruger National Park (n = 15) and Mokala National Park (n = 5) were similar to diversity levels in southern and eastern Africa. Hluhluwe-iMfolozi Park (n = 15) had low levels of genetic diversity, with only four haplotypes detected, reflecting its past bottleneck. Addo Elephant National Park (n = 5) had the highest nucleotide diversity of all populations across Africa, which was unexpected, as it is known to have low nuclear diversity. This diversity was driven by a highly divergent mitogenome from one sample, which was subsequently identified in another sample via Sanger sequencing of the cytochrome b gene. Using a fossil-calibrated phylogenetic analysis, we estimated that this lineage diverged from all other Cape buffalo lineages approximately 2.51 million years ago. We discuss several potential sources of this mitogenome but propose that it most likely originated through introgressive hybridisation with an extinct buffalo species, either S. acoelotus or S. antiquus. We conclude by discussing the conservation consequences of this finding for the Addo Elephant National Park population, proposing careful genetic management to prevent inbreeding depression while maintaining this highly unique diversity.
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Project description:Long non-coding RNAs (lncRNAs) have been identified in various tissues and cell types from human, monkey, porcine and mouse. However, expression profile of lncRNAs across Guangxi native cattle and swamp buffalo muscle development has never been investigated. Here, we examine the expression of lncRNA in cattle and buffalo muscle at adult stage(12 months), exhibiting the first report of lncRNA in the Guangxi native cattle and swamp buffalo muscle development of a large animal. 16,236 lncRNA candidates were obtained from buffalo skeletal muscle samples, of which a number of lncRNAs were highly abundant, and 2,161 lncRNAs were differentially expressed between buffalo and cattle. Real-time quantitative PCR (qPCR) analysis confirmed the expression profile of these lncRNAs, including several highly abundant lncRNAs, and a subset of differently expressed lncRNAs according to the high-throughput RNA sequencing (RNA-seq) data. These results indicate that abundant lncRNA is differentially expressed in bovine muscle, indicating important and diverse functions in mammalian muscle development.
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Project description:Mycobiome cape gooseberries Metagenome
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Project description:AimTo conduct a prospective assessment of anti-hepatitis E virus (HEV) IgG seroprevalence in the Western Cape Province of South Africa in conjunction with evaluating risk factors for exposure.MethodsConsenting participants attending clinics and wards of Groote Schuur, Red Cross Children's Hospital and their affiliated teaching hospitals in Cape Town, South Africa, were sampled. Healthy adults attending blood donor clinics were also recruited. Patients with known liver disease were excluded and all major ethnic/race groups were included to broadly represent local demographics. Relevant demographic data was captured at the time of sampling using an interviewer-administered confidential questionnaire. Human immunodeficiency virus (HIV) status was self-disclosed. HEV IgG testing was performed using the Wantai® assay.ResultsHEV is endemic in the region with a seroprevalence of 27.9% (n = 324/1161) 95%CI: 25.3%-30.5% (21.9% when age-adjusted) with no significant differences between ethnic groups or HIV status. Seroprevalence in children is low but rapidly increases in early adulthood. With univariate analysis, age ≥ 30 years old, pork and bacon/ham consumption suggested risk. In the multivariate analysis, the highest risk factor for HEV IgG seropositivity (OR = 7.679, 95%CI: 5.38-10.96, P < 0.001) was being 30 years or older followed by pork consumption (OR = 2.052, 95%CI: 1.39-3.03, P < 0.001). A recent clinical case demonstrates that HEV genotype 3 may be currently circulating in the Western Cape.ConclusionHepatitis E seroprevalence was considerably higher than previously thought suggesting that hepatitis E warrants consideration in any patient presenting with an unexplained hepatitis in the Western Cape, irrespective of travel history, age or ethnicity.
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