Lineages in Nectriaceae: re-evaluating the generic status of Ilyonectria and allied genera

Genera with cylindrocarpon-like asexual morphs are important pathogens of various herbaceous and woody plant hosts globally. Recent multi-gene studies of this generic complex indicated that the genus Ilyonectria is paraphyletic. The present study was therefore initiated to re-evaluate the generic status of Ilyonectria and at the same time address some taxonomic irregularities in the genera Cylindrodendrum and Neonectria. Using multi-gene DNA data and morphological comparisons, the genus Dactylonectria is introduced with 10 new combinations, several of which were previously treated in Ilyonectria. Two new species, D. hordeicola and D. pinicola, are also described. Furthermore, one new combination is provided in the genus Cylindrodendrum, and three new combinations in the genus Neonectria, for species previously treated in the genera Acremonium, Cylindrocarpon, Nectria and Neonectria. The aquatic genus Heliscus is reduced to synonymy under Neonectria.

First fungal genome sequence from Africa : a preliminary analysis

Some of the most significant breakthroughs in the biological sciences this century will emerge from the development of next generation sequencing technologies. The ease of availability of DNA sequence made possible through these new technologies has given researchers opportunities to study organisms in a manner that was not possible with Sanger sequencing. Scientists will, therefore, need to embrace genomics, as well as develop and nurture the human capacity to sequence genomes and utilise the ’tsunami‘ of data that emerge from genome sequencing. In response to these challenges, we sequenced the genome of Fusarium circinatum, a fungal pathogen of pine that causes pitch canker, a disease of great concern to the South African forestry industry. The sequencing work was conducted in South Africa, making F. circinatum the first eukaryotic organism for which the complete genome has been sequenced locally. Here we report on the process that was followed to sequence, assemble and perform a preliminary characterisation of the genome. Furthermore, details of the computer annotation and manual curation of this genome are presented. The F. circinatum genome was found to be nearly 44 million bases in size, which is similar to that of four other Fusarium genomes that have been sequenced elsewhere. The genome contains just over 15 000 open reading frames, which is less than that of the related species, Fusarium oxysporum, but more than that for Fusarium verticillioides. Amongst the various putative gene clusters identified in F. circinatum, those encoding the secondary metabolites fumosin and fusarin appeared to harbour evidence of gene translocation. It is anticipated that similar comparisons of other loci will provide insights into the genetic basis for pathogenicity of the pitch canker pathogen. Perhaps more importantly, this project has engaged a relatively large group of scientists including students in a significant genome project that is certain to provide a platform for growth in this important area of research in the future.We thank the National Research Foundation (NRF) of South Africa, members of the Tree Protection Co-operative Programme, the THRIP initiative of the Department of Trade and Industry and the Department of Science and Technology (DST)/NRF Centre of Excellence in Tree Health Biotechnology and the Oppenheimer Foundation for funding.http://www.sajs.co.zanf201

Fungal Planet description sheets : 320–370

Novel species of fungi described in the present study include the following from Malaysia: Castanediella eucalypti from Eucalyptus pellita, Codinaea acacia from Acacia mangium, Emarcea eucalyptigena from Eucalyptus brassiana, Myrtapenidiella eucalyptorum from Eucalyptus pellita, Pilidiella eucalyptigena from Eucalyptus brassiana and Strelitziana malaysiana from Acacia mangium. Furthermore, Stachybotrys sansevieriicola is described from Sansevieria ehrenbergii (Tanzania), Phacidium grevilleae from Grevillea robusta (Uganda), Graphium jumulu from Adansonia gregorii and Ophiostoma eucalyptigena from Eucalyptus marginata (Australia), Pleurophoma ossicola from bone and Plectosphaerella populi from Populus nigra (Germany), Colletotrichum neosansevieriae from Sansevieria trifasciata, Elsinoë othonnae from Othonna quinquedentata and Zeloasperisporium cliviae (Zeloasperisporiaceae fam. nov.) from Clivia sp. (South Africa), Neodevriesia pakbiae, Phaeophleospora hymenocallidis and Phaeophleospora hymenocallidicola on leaves of a fern (Thailand), Melanconium elaeidicola from Elaeis guineensis (Indonesia), Hormonema viticola from Vitis vinifera (Canary Islands), Chlorophyllum pseudoglobossum from a grassland (India), Triadelphia disseminata from an immunocompromised patient (Saudi Arabia), Colletotrichum abscissum from Citrus (Brazil), Polyschema sclerotigenum and Phialemonium limoniforme from human patients (USA), Cadophora vitícola from Vitis vinifera (Spain), Entoloma flavovelutinum and Bolbitius aurantiorugosus from soil (Vietnam), Rhizopogon granuloflavus from soil (Cape Verde Islands), Tulasnella eremophila from Euphorbia officinarum subsp. echinus (Morocco), Verrucostoma martinicensis from Danaea elliptica (French West Indies), Metschnikowia colchici from Colchicum autumnale (Bulgaria), Thelebolus microcarpus from soil (Argentina) and Ceratocystis adelpha from Theobroma cacao (Ecuador). Myrmecridium iridis (Myrmecridiales ord. nov., Myrmecridiaceae fam. nov.) is also described from Iris sp. (The Netherlands). Novel genera include (Ascomycetes): Budhanggurabania from Cynodon dactylon (Australia), Soloacrosporiella, Xenocamarosporium, Neostrelitziana and Castanediella from Acacia mangium and Sabahriopsis from Eucalyptus brassiana (Malaysia), Readerielliopsis from basidiomata of Fuscoporia wahlbergii (French Guyana), Neoplatysporoides from Aloe ferox (Tanzania), Wojnowiciella, Chrysofolia and Neoeriomycopsis from Eucalyptus (Colombia), Neophaeomoniella from Eucalyptus globulus (USA), Pseudophaeomoniella from Olea europaea (Italy), Paraphaeomoniella from Encephalartos altensteinii, Aequabiliella, Celerioriella and Minutiella from Prunus (South Africa). Tephrocybella (Basidiomycetes) represents a novel genus from wood (Italy). Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.Alina V. Alexandrova was supported by the Russian Science Foundation (project N 14-50-00029). Ekaterina F. Malysheva, Olga V. Morozova, Alexander E. Kovalenko and Eugene S. Popov acknowledge financial support from the Russian Foundation for Basic Research (project 13-04-00838a and 15-04-04645a). Margarita Dueñas, María P. Martín and M. Teresa Telleria acknowledge financial support from the Plan Nacional I+D+I projects No. CGL2009-07231 and CGL2012-3559. Cony Decock gratefully acknowledges the financial support received from the FNRS / FRFC (convention FRFC 2.4544.10), the CNRS-French Guiana and the Nouragues staff, which enabled fieldwork in French Guiana, and the Belgian State – Belgian Federal Science Policy through the BCCMTM research programme.http://www.ingentaconnect.com/content/nhn/pimjam201

The Unique Homothallic Mating-Type Loci of the Fungal Tree Pathogens <i>Chrysoporthe syzygiicola</i> and <i>Chrysoporthe zambiensis</i> from Africa

Chrysoporthe syzygiicola and C. zambiensis are ascomycete tree pathogens first described from Zambia, causing stem canker on Syzygium guineense and Eucalyptus grandis, respectively. The taxonomic descriptions of these two species were based on their anamorphic states, as no sexual states are known. The main purpose of this work was to use whole genome sequences to identify and define the mating-type (MAT1) loci of these two species. The unique MAT1 loci for C. zambiensis and C. syzygiicola consist of the MAT1-1-1, MAT1-1-2, and MAT1-2-1 genes, but the MAT1-1-3 gene is absent. Genes canonically associated with opposite mating types were present at the single mating-type locus, suggesting that C. zambiensis and C. syzygiicola have homothallic mating systems

SNP Analysis Infers that Recombination Is Involved in the Evolution of Amitraz Resistance in Rhipicephalus microplus.

Rhipicephalus microplus, better known as the Asiatic cattle tick, is a largely invasive ectoparasite of great economic importance due to the negative effect it has on agricultural livestock on a global scale, particularly cattle. Tick-borne diseases (babesiosis and anaplasmosis) transmitted by R. microplus are alarming as they decrease the quality of livestock health and production. In sub-Saharan Africa, cattle represent a major source of meat and milk, but this region of the world is severely affected by the Rhipicephalus microplus tick. The principal method for tick control is the use of chemical acaricides, notably amitraz, which was implemented in the 1990's after resistance to other acaricides surfaced. However, the efficiency of chemical control is hindered by an increase in the frequency of mutant resistance alleles to amitraz in tick populations. Presently, the only way to assess amitraz resistance is by means of larval packet tests, but this technique is time-consuming and not particularly cost effective. The main aims of this study were three-fold. First, we attempted to correlate two known SNPs in the octopamine/tyramine (OCT/Tyr) receptor with amitraz resistance in South African field samples of R. microplus. Second, we calculated gametic disequilibrium for these SNPs to determine whether they are randomly associated. Lastly, we conducted a study to assess the evolutionary effects of recombination within the OCT/Tyr receptor. Our results confirmed that the two SNPs are associated with amitraz resistance in the South African tick strain, and that they are in gametic disequilibrium. Additionally, recombination was detected in the OCT/Tyr receptor generating two recombinant haplotypes. These results are of concern to farmers in sub-Saharan Africa, and the emergence of amitraz resistance should be closely monitored in future. Therefore, we present a quick and affordable RFLP based diagnostic technique to assess amitraz resistance in field samples of R. microplus

SNP Analysis Infers that Recombination Is Involved in the Evolution of Amitraz Resistance in <i>Rhipicephalus microplus</i>

<div><p><i>Rhipicephalus microplus</i>, better known as the Asiatic cattle tick, is a largely invasive ectoparasite of great economic importance due to the negative effect it has on agricultural livestock on a global scale, particularly cattle. Tick-borne diseases (babesiosis and anaplasmosis) transmitted by <i>R</i>. <i>microplus</i> are alarming as they decrease the quality of livestock health and production. In sub-Saharan Africa, cattle represent a major source of meat and milk, but this region of the world is severely affected by the <i>Rhipicephalus microplus</i> tick. The principal method for tick control is the use of chemical acaricides, notably amitraz, which was implemented in the 1990’s after resistance to other acaricides surfaced. However, the efficiency of chemical control is hindered by an increase in the frequency of mutant resistance alleles to amitraz in tick populations. Presently, the only way to assess amitraz resistance is by means of larval packet tests, but this technique is time-consuming and not particularly cost effective. The main aims of this study were three-fold. First, we attempted to correlate two known SNPs in the octopamine/tyramine (OCT/Tyr) receptor with amitraz resistance in South African field samples of <i>R</i>. <i>microplus</i>. Second, we calculated gametic disequilibrium for these SNPs to determine whether they are randomly associated. Lastly, we conducted a study to assess the evolutionary effects of recombination within the OCT/Tyr receptor. Our results confirmed that the two SNPs are associated with amitraz resistance in the South African tick strain, and that they are in gametic disequilibrium. Additionally, recombination was detected in the OCT/Tyr receptor generating two recombinant haplotypes. These results are of concern to farmers in sub-Saharan Africa, and the emergence of amitraz resistance should be closely monitored in future. Therefore, we present a quick and affordable RFLP based diagnostic technique to assess amitraz resistance in field samples of <i>R</i>. <i>microplus</i>.</p></div

Population structure and genetic diversity of Rhipicephalus microplus in Zimbabwe

Recently there was an expansion in the geographic range of Rhipicephalus microplus in Zimbabwe. In order to understand gene flow patterns and population structure in this highly invasive and adaptable cattle tick, a population genetics study was carried out. Eighty-seven R. microplus tick samples drawn from 5 distinct populations were genotyped using eight polymorphic microsatellite loci. Genetic diversity (He) was high (0.755-0.802) in all the populations, suggesting high levels of gene flow with 97% of genetic variation found within populations and 3% amongst populations. No isolation by distance was observed with low but significant genetic differentiation amongst the populations (0-0.076). Most of the sampled individuals had admixed genetic backgrounds, except for those from Matabeleland North whose genetic makeup appeared different from the rest. Rhipicephalus microplus was recently recorded in this area and the environmental conditions do not support survival of the tick there. These results confirm recent range expansion of the tick and the lowest genetic diversity recorded in the Matabeleland North population is suggestive of a founder effect, which may lead to genetic drift. Generally, the very low levels of genetic differentiation amongst the populations could be a result of the frequent movement of livestock from one area to another, which will have implications for disease control. This study offers further opportunities to study evolutionary adaptation of R. microplus in Zimbabwe and southern Africa.https://doi.org/10.1016/j.actatropica.2018.01.00

Loci significantly associated with resistant loci 11 and 17.

<p>^a</p><p></p><p></p><p></p><p></p><p></p><p><mi>r</mi><mo>¯</mo></p><p></p><mi>d</mi><p></p><p></p><p></p><p></p> value represents the gametic disequilibrium that is observed between the two SNPs being compared to one another.<p></p><p>^b Aggregate value is the mean value of </p><p></p><p></p><p></p><p></p><p></p><p><mi>r</mi><mo>¯</mo></p><p></p><mi>d</mi><p></p><p></p><p></p><p></p> values that were obtained for loci 11 and 17 associated with the other loci to determine which association displayed the most gametic disequilibrium.<p></p><p>Loci significantly associated with resistant loci 11 and 17.</p

The r¯d density distribution for the OCT/Tyr receptor.

<p>The </p><p></p><p></p><p></p><p></p><p></p><p><mi>r</mi><mo>¯</mo></p><p></p><mi>d</mi><p></p><p></p><p></p><p></p> values are placed on the x-axis while the relative occurrence of each of these values is displayed on the y-axis. The observed value falls outside of the distribution range generated by the randomized data set indicating that there is gametic disequilibrium.<p></p

Ancestral recombination graph for homozygous amitraz resistant and susceptible <i>R</i>. <i>microplus</i> ticks in South Africa as well as characterized heterozygotes.

<p>H1 to H8 represent the infinite-sites-compatible haplotype sequences that were observed. Two recombination events were detected generating two recombinant haplotypes (H6 and H7). The H6 haplotype represented an intermediate (or heterozygous) state containing the SNP at nucleotide position 157 but not at 200. The two resistance-linked SNPs are shown in bold along with site 174 which is the potential biomarker for amitraz resistance. The numbers in brackets represent the nucleotide positions where mutations occurred within that haplotype. GenBank accession numbers and haplotype designations are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131341#pone.0131341.s002" target="_blank">S1 Table</a>.</p