School of Animal, Plant and Environmental Sciences (Journal Articles)

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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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    Spatio-temporal trends in daily precipitation extremes over the Enkangala escarpment of South Africa: 1961–2021
    (Springer, 2025-02) Abubakar, Hadisu Bello; Scholes, Mary C.; Engelbrecht, Francois A.
    The Intergovernmental Panel on Climate Change in its Sixth Assessment Report reported that increases in extreme weather events can already be detected in every region in the world. For eastern southern Africa the report provides evidence of an increasing trend in extreme precipitation events, but more research is needed to understand how this change is manifesting over regions as diverse as South Africa’s eastern escarpment and northern Mozambique. This study evaluates the trends in extreme precipitation over the Enkangala Escarpment, part of South Africa’s eastern escarpment, over the period 1961 to 2021. Daily precipitation data covering 22 stations with fewer than 10% missing values over 61 years were obtained from the South African Weather Service. A total of twelve extreme events precipitation indices were computed using the ClimPACT2 package, and a time series trend analysis was performed using the Trend Free Whitening Mann Kendal test and a field significance test. The results indicate significant increasing trends in nine out of the twelve extreme events indices that were investigated. The three indices which have shown significant decreasing trends include Consecutive Wet days (CWD) at (0.03 day/year total annual rainfall (PRCPTOT) (0.61 mm/decade) and the annual count of days when precipitation≥10 mm (R10mm) of 0.32 days/decade. Indices such Rx1 days, Rx3 days and Rx5 days exhibited increasing trends of 0.2 days/decade each. Other indices with an increasing trend are CDD (3.6 day/decade), R20mm (0.2 days/decade) and R30mm (0.2 days/decade). The R95p (11.2 mm/decade) and R99p (6.0 mm/decade) indices, and Simple Daily Intensity Index(0.4 mm/decade) also exhibit positive trends over the study period. Overall the analysis is indicative of a change in the nature of rainfall over the Enkangala escarpment of South Africa, with annual rainfall totals, the number of consecutive wet days and the frequency of events with smaller thresholds such as 10 mm/day decreasing, but with extreme events of larger thresholds occurring more frequently. That is, when it rains, it tends to rain more intensely than in the past. The use of a field significance test was useful to formalise when relatively small but spatially homogeneous trends detected at separate weather stations yield statistical significance. The findings of the paper are relevant to decision and policy in multiple of socio-economic sectors active in South Africa’s eastern escarpment.
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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.
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    A metagenomic viral discovery approach identifies potential zoonotic and novel mammalian viruses in Neoromicia bats within South Africa
    (Public Library of Science, 2018-03) Geldenhuys, M.; Mortlock, M.; Weyer, J.; Bezuidt, O.; Seamark, E.C.J.; Kearney, T.
    Species within the Neoromicia bat genus are abundant and widely distributed in Africa. It is common for these insectivorous bats to roost in anthropogenic structures in urban regions. Additionally, Neoromicia capensis have previously been identified as potential hosts for Middle East respiratory syndrome (MERS)-related coronaviruses. This study aimed to ascertain the gastrointestinal virome of these bats, as viruses excreted in fecal material or which may be replicating in rectal or intestinal tissues have the greatest opportunities of coming into contact with other hosts. Samples were collected in five regions of South Africa over eight years. Initial virome composition was determined by viral metagenomic sequencing by pooling samples and enriching for viral particles. Libraries were sequenced on the Illumina MiSeq and NextSeq500 platforms, producing a combined 37 million reads. Bioinformatics analysis of the high throughput sequencing data detected the full genome of a novel species of the Circoviridae family, and also identified sequence data from the Adenoviridae, Coronaviridae, Herpesviridae, Parvoviridae, Papillomaviridae, Phenuiviridae, and Picornaviridae families. Metagenomic sequencing data was insufficient to determine the viral diversity of certain families due to the fragmented coverage of genomes and lack of suitable sequencing depth, as some viruses were detected from the analysis of reads-data only. Follow up conventional PCR assays targeting conserved gene regions for the Adenoviridae, Coronaviridae, and Herpesviridae families were used to confirm metagenomic data and generate additional sequences to determine genetic diversity. The complete coding genome of a MERS-related coronavirus was recovered with additional amplicon sequencing on the MiSeq platform. The new genome shared 97.2% overall nucleotide identity to a previous Neoromicia-associated MERS-related virus, also from South Africa. Conventional PCR analysis detected diverse adenovirus and herpesvirus sequences that were widespread throughout Neoromicia populations in South Africa. Furthermore, similar adenovirus sequences were detected within these populations throughout several years. With the exception of the coronaviruses, the study represents the first report of sequence data from several viral families within a Southern African insectivorous bat genus; highlighting the need for continued investigations in this regard.