Research Articles (Genetics)

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  • ItemOpen Access
    Birds of a feather flock together: a dataset for Clock and Adcyap1 genes from migration genetics studies
    (Nature Research, 2023) Le Clercq, Louis-Stéphane; Bazzi, Gaia; Obiol, Joan Ferrer; Cecere, Jacopo G.; Gianfranceschi, Luca; Grobler, J. Paul; Kotzé, Antoinette; Riutort León, Marta; González-Solís, Jacob; Rubolini, Diego; Liedvogel, Miriam; Dalton, Desiré Lee
    Birds in seasonal habitats rely on intricate strategies for optimal timing of migrations. This is governed by environmental cues, including photoperiod. Genetic factors affecting intrinsic timekeeping mechanisms, such as circadian clock genes, have been explored, yielding inconsistent findings with potential lineage-dependency. To clarify this evidence, a systematic review and phylogenetic reanalysis was done. This descriptor outlines the methodology for sourcing, screening, and processing relevant literature and data. PRISMA guidelines were followed, ultimately including 66 studies, with 34 focusing on candidate genes at the genotype-phenotype interface. Studies were clustered using bibliographic coupling and citation network analysis, alongside scientometric analyses by publication year and location. Data was retrieved for allele data from databases, article supplements, and direct author communications. The dataset, version 1.0.2, encompasses data from 52 species, with 46 species for the Clock gene and 43 for the Adcyap1 gene. This dataset, featuring data from over 8000 birds, constitutes the most extensive cross-species collection for these candidate genes, used in studies investigating gene polymorphisms and seasonal bird migration.
  • ItemOpen Access
    PAReTT: a Python package for the automated retrieval and management of divergence time data from the TimeTree resource for downstream analyses
    (Springer, 2023) Le Clercq, Louis-Stephane; Kotze, Antoinette; Grobler, J. Paul; Dalton, Desire Lee
    Evolutionary processes happen gradually over time and are, thus, considered time dependent. In addition, several evolutionary processes are either adaptations to local habitats or changing habitats, otherwise restricted thereby. Since evolutionary processes driving speciation take place within the landscape of environmental and temporal bounds, several published studies have aimed at providing accurate, fossil-calibrated, estimates of the divergence times of both extant and extinct species. Correct calibration is critical towards attributing evolutionary adaptations and speciation both to the time and paleogeography that contributed to it. Data from more than 4000 studies and nearly 1,50,000 species are available from a central TimeTree resource and provide opportunities of retrieving divergence times, evolutionary timelines, and time trees in various formats for most vertebrates. These data greatly enhance the ability of researchers to investigate evolution. However, there is limited functionality when studying lists of species that require batch retrieval. To overcome this, a PYTHON package termed Python-Automated Retrieval of TimeTree data (PAReTT) was created to facilitate a biologist-friendly interaction with the TimeTree resource. Here, we illustrate the use of the package through three examples that includes the use of timeline data, time tree data, and divergence time data. Furthermore, PAReTT was previously used in a meta-analysis of candidate genes to illustrate the relationship between divergence times and candidate genes of migration. The PAReTT package is available for download from GitHub or as a pre-compiled Windows executable, with extensive documentation on the package available on GitHub wiki pages regarding dependencies, installation, and implementation of the various functions.
  • ItemOpen Access
    Time trees and clock genes: a systematic review and comparative analysis of contemporary avian migration genetics
    (Wiley, 2023) Le Clercq, Louis-Stephane; Bazzi, Gaia; Cecere, Jacopo G.; Gianfranceschi, Luca; Grobler, Johannes Paul; Kotze, Antoinette; Rubolini, Diego; Liedvogel, Miriam; Dalton, Desire Lee
    Timing is a crucial aspect for survival and reproduction in seasonal environments leading to carefully scheduled annual programs of migration in many species. But what are the exact mechanisms through which birds (class: Aves) can keep track of time, anticipate seasonal changes, and adapt their behaviour? One proposed mechanism regulating annual behaviour is the circadian clock, controlled by a highly conserved set of genes, collectively called ‘clock genes’ which are well established in controlling the daily rhythmicity of physiology and behaviour. Due to diverse migration patterns observed within and among species, in a seemingly endogenously programmed manner, the field of migration genetics has sought and tested several candidate genes within the clock circuitry that may underlie the observed differences in breeding and migration behaviour. Among others, length polymorphisms within genes such as Clock and Adcyap1 have been hypothesised to play a putative role, although association and fitness studies in various species have yielded mixed results. To contextualise the existing body of data, here we conducted a systematic review of all published studies relating polymorphisms in clock genes to seasonality in a phylogenetically and taxonomically informed manner. This was complemented by a standardised comparative re-analysis of candidate gene polymorphisms of 76 bird species, of which 58 are migrants and 18 are residents, along with population genetics analyses for 40 species with available allele data. We tested genetic diversity estimates, used Mantel tests for spatial genetic analyses, and evaluated relationships between candidate gene allele length and population averages for geographic range (breeding- and non-breeding latitude), migration distance, timing of migration, taxonomic relationships, and divergence times. Our combined analysis provided evidence (i) of a putative association between Clock gene variation and autumn migration as well as a putative association between Adcyap1 gene variation and spring migration in migratory species; (ii) that these candidate genes are not diagnostic markers to distinguish migratory from sedentary birds; and (iii) of correlated variability in both genes with divergence time, potentially reflecting ancestrally inherited genotypes rather than contemporary changes driven by selection. These findings highlight a tentative association between these candidate genes and migration attributes as well as genetic constraints on evolutionary adaptation.
  • ItemOpen Access
    Filamentous fungi for sustainable remediation of pharmaceutical compounds, heavy metal and oil hydrocarbons
    (Frontiers, 2023) Ghosh, Soumya; Rusyn, Iryna; Dmytruk, Olena V.; Dmytruk, Kostyantyn V.; Onyeaka, Helen; Gryzenhout, Marieka; Gafforov, Yusufjon
    This review presents a comprehensive summary of the latest research in the field of bioremediation with filamentous fungi. The main focus is on the issue of recent progress in remediation of pharmaceutical compounds, heavy metal treatment and oil hydrocarbons mycoremediation that are usually insufficiently represented in other reviews. It encompasses a variety of cellular mechanisms involved in bioremediation used by filamentous fungi, including bio-adsorption, bio-surfactant production, bio-mineralization, bio-precipitation, as well as extracellular and intracellular enzymatic processes. Processes for wastewater treatment accomplished through physical, biological, and chemical processes are briefly described. The species diversity of filamentous fungi used in pollutant removal, including widely studied species of Aspergillus, Penicillium, Fusarium, Verticillium, Phanerochaete and other species of Basidiomycota and Zygomycota are summarized. The removal efficiency of filamentous fungi and time of elimination of a wide variety of pollutant compounds and their easy handling make them excellent tools for the bioremediation of emerging contaminants. Various types of beneficial byproducts made by filamentous fungi, such as raw material for feed and food production, chitosan, ethanol, lignocellulolytic enzymes, organic acids, as well as nanoparticles, are discussed. Finally, challenges faced, future prospects, and how innovative technologies can be used to further exploit and enhance the abilities of fungi in wastewater remediation, are mentioned.
  • ItemOpen Access
    Characterization of the endophytic mycobiome in cowpea (Vigna unguiculata) from a single location using illumina sequencing
    (MDPI, 2022) Kinge, Tonjock Rosemary; Ghosh, Soumya; Cason, Errol D.; Gryzenhout, Marieka
    Cowpea is an important crop for small-scale farmers in poor areas but is also being developed for commercial agriculture as a possible substitute for commercial legumes. Endophytic fungi are omnipresent and play crucial but diverse roles in plants. This study characterized the endophyte component of the cowpea mycobiome from leaves, main and crown stems and roots using Illumina MiSeq of the ITS2 region of the ribosomal operon. Ascomycetes exhibited the highest diversity, with Molecular Operational Taxonomic Units (MOTUs) assigned as Macrophomina, Cladosporium, Phoma, Fusarium and Cryptococcus, among the most dominant genera. Certain MOTUS showed preferential colonization patterns for above or below ground tissues. Several MOTU generic groups known to include phytopathogenic species were found, with relative abundances ranging from high to very low. Phylogenetic analyses of reads for some MOTUs showed that a level of identification could be obtained to species level. It also confirmed the absences of other species, including phytopathogens. This is the first study that adopted a holistic metagenomic typing approach to study the fungal endophytes of cowpea from a single location, a crop that is so integral for low-income households of the world.
  • ItemOpen Access
    Fusarium casha sp. nov. and F. curculicola sp. nov. in the Fusarium fujikuroi species complex isolated from Amaranthus cruentus and three weevil species in South Africa
    (MDPI, 2021) Vermeulen, Marcele; Rothmann, Lisa A.; Swart, Wijnand J.; Gryzenhout, Marieka
    Trials are currently being conducted in South Africa to establish Amaranthus cruentus as a new pseudocereal crop. During recent surveys, Fusarium species were associated with weevil damage in A. cruentus fields. Preliminary studies showed that some of these Fusarium species grouped into two distinct clades within the F. fujikuroi species complex. The aim of this study was to characterize these isolates based on the morphology and phylogeny of the translation elongation factor 1  (TEF1 ) gene region, ß-tubulin 2 (ßT) gene region and RNA polymerase II subunit (RPB2), and to determine if these isolates are pathogenic to A. cruentus. Phylogenetic and morphological studies showed that these two clades represent two novel species described here as F. casha and F. curculicola. Both species were shown to have the potential to be pathogenic to A. cruentus during routine greenhouse inoculation tests. While isolations indicate a possible association between these two species and weevils, further research is needed to understand this association and the role of weevils in disease development involving F. casha and F. curculicola in A. cruentus.