Browsing by Author "Chebii, Vivien"

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Genome scan for signatures of adaptive evolution in wild African goat (capra nubiana)
(NM-AIST, 2021-08) Chebii, Vivien
Nubian ibex (Capra nubiana) is a wild goat species inhabiting the Sahara and Arabia deserts. C. nubiana thrives well in its habitat which is characterized by intense solar radiation, high temperatures, little feed, and water supply. The genetic basis of C. nubiana adaptation to its environment remains unknown. Adaptive signatures of evolution in C. nubiana genome were investigated using comparative genomics approaches. Paired-end sequence reads of three C. nubiana individuals and other publicly available genome data were used for comparative genomic analysis. Positive selection signals were detected from sequence alignment by comparing the rates of synonymous versus non-synonymous substitutions (dN/dS) in orthologous protein-coding genes shared by C. nubiana and related species using CodeML program in PAML package. Copy number variations were detected from the sequence data using read-depth method, with the domestic goat genome data acting as the reference. Genes involved in the skin barrier and hair follicle development, such as ATP binding cassette subfamily A member 12 and UV stimulated scaffold protein A, were found to be positively selected, suggesting that C. nubiana has evolved adaptive mechanisms to cope with solar radiation and temperature extremes in its environment. Additionally, a DNA repair gene (UV stimulated scaffold protein A) was reported to be under strong selection signals, further supporting the assertion that C. nubiana has acquired adaptive mechanisms to deal with possible DNA damages induced by prolonged exposure to solar radiation. Similarly, duplications of viral response genes such as UL16 binding protein 3, Cluster of Differentiation 48, Natural Killer Group 2D ligand 1-like, Bactericidal/permeability-increasing fold containing family A, member 1, and Natural Killer Group 2D ligand 4-like were reported in C. nubiana, indicating that it has acquired adaptive strategies to cope with viral stressors in its environment. Additionally, xenobiotic compounds metabolism genes involved in biotransformation (Cytochrome P450 2D6, carboxylesterase 1 and cytochrome P450 family 2 subfamily B member 6), conjugation (UDP Glucuronosyltransferase-2B7 and Glutathione S transferase Mu 4), and transport (Multidrug resistance protein 4) of toxic compounds were found to be expanded in C. nubiana, suggesting possible adaptative mechanisms to desert diets that are affluent in toxic compounds. This work represents the first effort to understand the genomic of adaptations in C. nubiana, a wild African goat. The C. nubiana genomic information generated in this study is an important resource for researchers seeking to find genes of interest for breeding purposes among small ruminants of economic importance.
Genome Scan for Variable Genes Involved in Environmental Adaptations of Nubian Ibex
(Springer Nature Switzerland AG., 2021-06-17) Chebii, Vivien; Mpolya, Emmanuel; Oyola, Samuel; Kotze, Antoinette; Entfellner, Jean-Baka; Mutuku, J.
The Nubian ibex (Capra nubiana) is a wild goat species that inhabits the Sahara and Arabian deserts and is adapted to extreme ambient temperatures, intense solar radiation, and scarcity of food and water resources. To investigate desert adaptation, we explored the possible role of copy number variations (CNVs) in the evolution of Capra species with a specifc focus on the environment of Capra nubiana. CNVs are structural genomic variations that have been implicated in phenotypic dif ferences between species and could play a role in species adaptation. CNVs were inferred from Capra nubiana sequence data relative to the domestic goat reference genome using read-depth approach. We identifed 191 CNVs overlapping with protein-coding genes mainly involved in biological processes such as innate immune response, xenobiotic metabolisms, and energy metabolisms. We found copy number variable genes involved in defense response to viral infections (Cluster of Diferentiation 48, UL16 binding protein 3, Natural Killer Group 2D ligand 1-like, and Interferon-induced transmembrane protein 3), possibly suggesting their roles in Nubian ibex adaptations to viral infections. Additionally, we found copy num ber variable xenobiotic metabolism genes (carboxylesterase 1, Cytochrome P450 2D6, Glutathione S-transferase Mu 4, and UDP Glucuronosyltransferase-2B7), which are probably an adaptation of Nubian ibex to desert diets that are rich in plant secondary metabolites. Collectively, this study’s results advance our understanding of CNVs and their possible roles in the adaptation of Nubian ibex to its environment. The copy number variable genes identifed in Nubian ibex could be considered as subjects for further functional characterizations.
Genomics of Adaptations in Ungulates
(MDPI, 2021-05-29) Chebii, Vivien; Mpolya, Emmanuel; Muchadeyi, Farai; Entfellner, Jean-Baka
Ungulates are a group of hoofed animals that have long interacted with humans as essential sources of food, labor, clothing, and transportation. These consist of domesticated, feral, and wild species raised in a wide range of habitats and biomes. Given the diverse and extreme environments inhabited by ungulates, unique adaptive traits are fundamental for fitness. The documentation of genes that underlie their genomic signatures of selection is crucial in this regard. The increasing availability of advanced sequencing technologies has seen the rapid growth of ungulate genomic resources, which offers an exceptional opportunity to understand their adaptive evolution. Here, we summarize the current knowledge on evolutionary genetic signatures underlying the adaptations of ungulates to different habitats.