Faculty of Science (Research Outputs)

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    Draft genome sequence of the fungal pathogen Penicillium expansum (PPRI25879) isolated in South Africa
    (Elsevier, 2025-02) Chan, Wai Yin; Rauwane, Molemi; Figlan, Sandiswa; Ntushelo, Khayalethu
    Objectives: Penicillium expansum, a necrotrophic plant pathogen with a wide range of fruit hosts, is an important causal agent of blue mold rot. The fruit business suffers significant financial losses because of blue mold rot that occurs during fruit storage, transportation, and sale. The objective of this work was to generate a high-quality draft genome assembly of P. expansum, which will contribute to enhancing the management of blue mold, especially in stone and pome fruits, including grapes, by improving our understanding of the epidemiology of the pathogen and its interactions with the host. Data description: Here, we describe the genome sequence of Penicillium expansum isolate PPRI25879, one of the most virulent strains isolated from grapes in South Africa. Sequencing reads from P. expansum produced approximately 3.5 Gb. The assembly generated a draft genome of size 32.1 Mb, consisting of 1648 contigs, with an N50 of 508 KB. Examination of the genome completeness with Benchmarking Universal Single-Copy Orthologs (BUSCO) showed the draft genome carries 97.9% of the 746 genes in the Eurotiomycetes_odb10 database. The draft genome sequence will allow improved genomic comparisons among the most important pathogens belonging to the Penicillium genus, with the aim of improving our knowledge of their plant-pathogen interactions, population biology, and control.
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    Deep-crustal layered mafic complexes in the Mesoproterozoic oceanic-arc of the Tugela Terrane, South Africa
    (Elsevier, 2025-03) Wilson, Allan H.
    Layered mafic intrusions are important in understanding the generation of continental crust in oceanic arcs. The Mesoproterozoic (c. 1200 Ma) Tugela Terrane in southeast South Africa is made up of a series of thrust slices of varied rock-types purported to have been derived in oceanic arcs prior to accretion onto the southern margin of the Archean Kaapvaal Craton. They are not ophiolites. Mafic intrusions in two adjacent thrust slices are known as the Tugela Rand and Mambula Complexes. Both intrusions are intensely layered on scales of centimetres to several tens of metres but clear cyclic units are not apparent and crystal fractionation is limited indicating these were open systems with magma chamber through-flow. Tugela Rand is made up of dominantly olivine-bearing rocks ranging from dunite and pyroxenite to gabbro. In contrast, Mambula is dominantly gabbroic with only rare olivine-bearing rocks and is more evolved with layers of titaniferous-magnetite. Primary magmatic structures in both complexes include graded bedding, slumping and erosion features. Relatively high pressure of formation is indicated by the aluminous nature of the pyroxenes and corona textures by reaction between plagioclase and olivine. Chromitites in Tugela Rand range from massive to podiform with the rare orbicular variety indicating complex controls on chromite accretion. They include the high-Al compositional variety. There are no other similar chromitite occurrences in South Africa. The complexes, together with their enclosing rock-types, draw striking parallels with the lower arc crust observed in the late Cretaceous Kohistan arc complex in NE Pakistan. The Tugela Rand Complex shares many similarities with the Chilas Complex in that terrane, while the Mambula Complex is considered to be a more evolved derivative of the same magma. This study shows that generation of juvenile continental crust formation in mature island arc systems may have been firmly established by the Mesoproterozoic.
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    The Miocene primate Pliobates is a pliopithecoid
    (Nature Research, 2024-04) Amélie Beaudet; Zanolli, Clément; Urciuoli, Alessandro; Almécija, Sergio; Fortuny, Josep; Robles, Josep M.; Bouchet, Florian; Moyà-Solà, Salvador; Alba, David M.
    The systematic status of the small-bodied catarrhine primate Pliobates cataloniae, from the Miocene (11.6 Ma) of Spain, is controversial because it displays a mosaic of primitive and derived features compared with extant hominoids (apes and humans). Cladistic analyses have recovered Pliobates as either a stem hominoid or as a pliopithecoid stem catarrhine (i.e., preceding the cercopithecoid–hominoid divergence). Here, we describe additional dental remains of P. cataloniae from another locality that display unambiguous synapomorphies of crouzeliid pliopithecoids. Our cladistic analyses support a close phylogenetic link with poorly-known small crouzeliids from Europe based on (cranio)dental characters but recover pliopithecoids as stem hominoids when postcranial characters are included. We conclude that Pliobates is a derived stem catarrhine that shows postcranial convergences with modern apes in the elbow and wrist joints—thus clarifying pliopithecoid evolution and illustrating the plausibility of independent acquisition of postcranial similarities between hylobatids and hominids.
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    Confocal microscopy and molecular analyses reveal anal secretory apparatus in immatures and recover transcontinental Clade of Gall Mites (Eriophyoidea) from Tamarisks
    (MDPI, 2024-04) Sivu, Situngu; Chetverikov , Philipp E.; Ngubane-Ndhlovu, Nompumelelo P.; Elhalawan, Ashraf; Amrine, James
    Tamarisk is an invasive evergreen shrub native to arid regions of Africa and Eurasia and is considered a weed in some countries with dry climates. The complex of gall mites from tamarisks includes fourteen species from four genera of the family Eriophyidae. We reinvestigated the type species of the genus Dicruvasates, D. tamaricis from Egypt, described D. ngubani n. sp. from Tamarix usneoides from South Africa, and revised the generic concept of Dicruvasates. This genus possesses cuticular plates marking longitudinal opisthosomal ridges typical of various phyllocoptine genera, e.g., Echinacrus. We sequenced three genes of Dicruvasates and Phyllocoptes mites from Tamarix and Echinacrus from Frangula, combined our sequences with the data from GenBank, and performed single-gene phylogenetic analyses. All analyses inferred the following: (1) a transcontinental clade Tam comprising Dicruvasates + Aceria + Phyllocoptes from Tamarix; (2) Echinacrus distantly related to Dicruvasates, suggesting the homoplastic nature of the cuticular plates on the opisthosomal ridges, and (3) polyphyly of the genera Aceria and Phyllocoptes. We also investigated partially cleared specimens of Dicruvasates under CLSM and, for the first time, visualized a well-developed anal secretory apparatus (ASA) in the immatures of gall mites, which was previously shown to be a specialized system evolved in Eriophyoidea for silk production. We hypothesize that the ASA contributes to finding nymphs by conspecific males and advocate for the importance of the future molecular biology studies of gall mite silk for developing new methods for controlling mites based on the knowledge of their ecology, behavior, and silk gene genetics.
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    Temporal shifts in landscape connectivity for an ecosystem engineer, the roe deer, across a multiple-use landscape
    (Springer, 2018-04) Martin, Jodie; Vourc’h, Gwenae¨l; Bonnot, Nade`ge; Cargnelutti, Bruno; Chaval, Yannick; Lourte, Bruno; Goulard, Michel; Hoch, Thierry; Plantard, Olivier; Hewison, A. J. Mark; Morellet, Nicolas
    Context: Routine movements of large herbivores, often considered as ecosystem engineers, impact key ecological processes. Functional landscape connectivity for such species influences the spatial distribution of associated ecological services and disservices. Objectives: We studied how spatio-temporal variation in the risk-resource trade-off, generated by fluctuations in human activities and environmental conditions, influences the routine movements of roedeer across a heterogeneous landscape, generating shifts in functional connectivity at daily and seasonal time scales. Methods: We used GPS locations of 172 adult roedeer and step selection functions to infer landscape connectivity. In particular, we assessed the influence of six habitat features on fine scale movements across four biological seasons and three daily periods, based on variations in the risk-resource trade-off. Results: The influence of habitat features on roe deer movements was strongly dependent on proximity to refuge habitat, i.e. woodlands. Roe deer confined their movements to safe habitats during daytime and during the hunting season, when human activity is high.