Fungal Genomics Challenges the Dogma of Name-Based Biosecurity

Microorganisms have inadvertently been spread via the global movement and trade of their substrates, such as animals, plants, and soil. This intercontinental exchange in the current era of globalisation has given rise to significant increases in the distribution of known pests and pathogens. Importantly, it has also resulted in many novel, emerging, infectious diseases. Biosecurity and quarantine, which aim to prevent the establishment of foreign or harmful organisms in a non-native area, are under significant pressure due to the massive increases in travel and trade. Traditionally, quarantine regulations have been implemented based on pathogens that already cause significant disease problems on congener hosts in other parts of the world (e.g., Q-bank, available at http://www.q-bank.eu). Well-known pathogens are described, named, and studied to determine their disease cycle, epidemiology, and impact. Their importance is assessed based on their risk of infection, establishment, and economic or environmental consequences. This then shapes phytosanitary practices.The Tree Protection Co-operative Programme (TPCP), THRIP initiative of the Department of Trade and Industry, Department of Science and Technology (DST)/ National Research Foundation (NRF), and Centre of Excellence in Tree Health Biotechnology (CTHB).http://www.plospathogens.orgam2016Forestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant PathologyPlant Scienc

Minimum Degree up to Local Complementation: Bounds, Parameterized Complexity, and Exact Algorithms

The local minimum degree of a graph is the minimum degree that can be reached by means of local complementation. For any n, there exist graphs of order n which have a local minimum degree at least 0.189n, or at least 0.110n when restricted to bipartite graphs. Regarding the upper bound, we show that for any graph of order n, its local minimum degree is at most 3n/8+o(n) and n/4+o(n) for bipartite graphs, improving the known n/2 upper bound. We also prove that the local minimum degree is smaller than half of the vertex cover number (up to a logarithmic term). The local minimum degree problem is NP-Complete and hard to approximate. We show that this problem, even when restricted to bipartite graphs, is in W[2] and FPT-equivalent to the EvenSet problem, which W[1]-hardness is a long standing open question. Finally, we show that the local minimum degree is computed by a O*(1.938^n)-algorithm, and a O*(1.466^n)-algorithm for the bipartite graphs

On the Exact Evaluation of Certain Instances of the Potts Partition Function by Quantum Computers

We present an efficient quantum algorithm for the exact evaluation of either the fully ferromagnetic or anti-ferromagnetic q-state Potts partition function Z for a family of graphs related to irreducible cyclic codes. This problem is related to the evaluation of the Jones and Tutte polynomials. We consider the connection between the weight enumerator polynomial from coding theory and Z and exploit the fact that there exists a quantum algorithm for efficiently estimating Gauss sums in order to obtain the weight enumerator for a certain class of linear codes. In this way we demonstrate that for a certain class of sparse graphs, which we call Irreducible Cyclic Cocycle Code (ICCC_\epsilon) graphs, quantum computers provide a polynomial speed up in the difference between the number of edges and vertices of the graph, and an exponential speed up in q, over the best classical algorithms known to date

IMA Genome - F16 – Draft genome assemblies of Fusarium marasasianum, Huntiella abstrusa, two Immersiporthe knoxdaviesiana isolates, Macrophomina pseudophaseolina, Macrophomina phaseolina, Naganishia randhawae, and Pseudocercospora cruenta

Draft genome assembly of Fusarium marasasianum Introduction Many plants are thought to have at least one Fusarium-associated disease with more than 80% of economically important plants affected by at least one Fusarium disease (Leslie and Summerell 2006). The socioeconomic importance of Fusarium is particularly evident when considering the Fusarium fujikuroi species complex (FFSC, sensu Geiser et al. 2021). This monophyletic group contains 65 species and numerous cryptic species (Yilmaz et al. 2021). More than 50 species in the FFSC have publicly available genomes (www.ncbi.nlm.nih.gov), indicative of their economic importance. A number of recent studies showed that the FFSC complex contains four large clades (Herron et al. 2015; Sandoval-Denis et al. 2018; Yilmaz et al. 2021). One of these corresponds to the so-called “American” clade that was initially proposed to reflect the biogeography of the species it contains (O’Donnell et al. 1998). For example, Fusarium circinatum, the pine pitch canker pathogen, is thought to be native to Mexico and Central America (Drenkhan et al. 2020), where it likely co-evolved with its Pinus hosts (Herron et al. 2015; O’Donnell et al. 1998; Wikler and Gordon 2000). The American clade also includes five additional species associated with Pinus species in Colombia. These species are F. fracticaudum, F. pininemorale, F. parvisorum, F. marasasianum, and F. sororula, of which F. parvisorum, F. marasasianum, and F. sororula displayed levels of pathogenicity that were comparable to those of F. circinatum on susceptible Pinus species (Herron et al. 2015). The risk that the various American clade species pose to forestry in Colombia and globally has provided the impetus for projects aiming to sequence their genomes. To complement the genomic resources available for F. circinatum (Fulton et al. 2020; van der Nest et al. 2014a; Van Wyk et al. 2018; Wingfield et al. 2012, 2018a), the genomes of F. pininemorale (Wingfield et al. 2017), F. fracticaudum (Wingfield et al. 2018b) and F. sororula (van der Nest et al. 2021) have been published. Here we present the whole genome sequence for the pine pathogen F. marasasianum, named after the late South African professor Walter “Wally” F.O. Marasas (Wingfield and Crous 2012) who specialised in the taxonomy of Fusarium species and their associated mycotoxins

Draft genome sequences for Ceratocystis fagacearum, C. harringtonii, Grosmannia penicillata, and Huntiella bhutanensis

Draft genomes for the fungi Ceratocystis fagacearum, C. harringtonii, Grosmannia penicillata, and Huntiella bhutanensis are presented. Ceratocystis fagacearum is a major causal agent of vascular wilt of oaks and other trees in the family Fagaceae. Ceratocystis harringtonii, previously known as C. populicola, causes disease in Populus species in the USA and Canada. Grosmannia penicillata is the causal agent of bluestain of sapwood on various conifers, including Picea spp. and Pinus spp. in Europe. Huntiella bhutanensis is a fungus in Ceratocystidaceae and known only in association with the bark beetle Ips schmutzenhorferi that infests Picea spinulosa in Bhutan. The availability of these genomes will facilitate further studies on these fungi.The Genomics Research Institute (University of Pretoria), the University of Pretoria Research Development Programme, the DST/NRF Center of Excellence in Tree Health Biotechnology (FABI, University of Pretoria), and the National Research Foundation (NRF) (Grant number 87332). Sequencing the genomes of Ceratocystis fagacearum, C. harringtonii, Huntiella bhutanensis was made possible through the Improving Academics Qualifications (IAQ) grant from the NRF.http://www.imafungus.orgam2017Forestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Draft genomes of Amanita jacksonii, Ceratocystis albifundus, Fusarium circinatum, Huntiella omanensis, Leptographium procerum, Rutstroemia sydowiana, and Sclerotinia echinophila

The genomes of fungi provide an important resource to resolve issues pertaining to their taxonomy, biology, and evolution. The genomes of Amanita jacksonii, Ceratocystis albifundus, a Fusarium circinatum variant, Huntiella omanensis, Leptographium procerum, Sclerotinia echinophila, and Rutstroemia sydowiana are presented in this genome announcement. These seven genomes are from a number of fungal pathogens and economically important species. The genome sizes range from 27 Mb in the case of Ceratocystis albifundus to 51.9 Mb for Rutstroemia sydowiana. The latter also encodes for a predicted 17 350 genes, more than double that of Ceratocystis albifundus. These genomes will add to the growing body of knowledge of these fungi and provide a value resource to researchers studying these fungi.The US Department of Agriculture (USDA) Agricultural Research Service, grants from the Natural Sciences and Engineering Research Council of Canada (NSERC) and the Royal Ontario Museum to J.M.M.; Graduate Scholarships from the Consejo Nacional de Ciencia y Tecnologia (Mexico) and the University of Toronto to SSR; and a Undergraduate Student Research Award from NSERC to M.S. Financial support was provided by members of the Tree Protection Cooperative Program (TPCP), the Department of Science and Technology (DST)/ National Research Foundation (NRF) Centre of Excellence in Tree Health Biotechnology, and the Genomics Research Institute of the University of Pretoria. This project was supported by multiple grants from the NRF, South Africa, including the grant specific unique reference number (UID) 83924.http://www.imafungus.orgam201

Renaissance and Enlightenment Philosophy: PHL 211

Renaissance and Enlightenment Philosophy: PHL 211, examination June 2011

Introduction to Philosophy: PHL 111F

Introduction to Philosophy: PHL 111F, examinations June 2011

Introduction to Philosoph/Elementary Logic: PHL 112

Introduction to Philosoph/Elementary Logic: PHL 112, examination June 2011