We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All ...currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon.
To identify gene loci associated with steroid-resistant nephrotic syndrome (SRNS), we utilized homozygosity mapping and exome sequencing in a consanguineous pedigree with three affected siblings. ...High-density genotyping identified three segments of homozygosity spanning 33.6Mb on chromosomes 5, 10, and 15 containing 296 candidate genes. Exome sequencing identified two homozygous missense variants within the chromosome 15 segment; an A159P substitution in myosin 1E (MYO1E), encoding a podocyte cytoskeletal protein; and an E181K substitution in nei endonuclease VIII-like 1 (NEIL1), encoding a base-excision DNA repair enzyme. Both variants disrupt highly conserved protein sequences and were absent in public databases, 247 healthy controls, and 286 patients with nephrotic syndrome. The MYO1E A159P variant is noteworthy, as it is expected to impair ligand binding and actin interaction in the MYO1E motor domain. The predicted loss of function is consistent with the previous demonstration that Myo1e inactivation produces nephrotic syndrome in mice. Screening 71 additional patients with SRNS, however, did not identify independent NEIL1 or MYO1E mutations, suggesting larger sequencing efforts are needed to uncover which mutation is responsible for the phenotype. Our findings demonstrate the utility of exome sequencing for rapidly identifying candidate genes for human SRNS.
The Teratosphaeriaceae represents a recently established family that includes numerous saprobic, extremophilic, human opportunistic, and plant pathogenic fungi. Partial DNA sequence data of the 28S ...rRNA and RPB2 genes strongly support a separation of the Mycosphaerellaceae
from the Teratosphaeriaceae, and also provide support for the Extremaceae and Neodevriesiaceae, two novel families including many extremophilic fungi that occur on a diversity of substrates. In addition, a multi-locus DNA sequence dataset was generated (ITS, LSU, Btub,
Act, RPB2, EF-1α and Cal) to distinguish taxa in Mycosphaerella and Teratosphaeria associated with leaf disease of Eucalyptus, leading to the introduction of 23 novel genera, five species and 48 new combinations. Species are distinguished based on a polyphasic approach,
combining morphological, ecological and phylogenetic species concepts, named here as the Consolidated Species Concept (CSC). From the DNA sequence data generated, we show that each one of the five coding genes tested, reliably identify most of the species present in this dataset (except species
of Pseudocercospora). The ITS gene serves as a primary barcode locus as it is easily generated and has the most extensive dataset available, while either Btub, EF-1α or RPB2 provide a useful secondary barcode locus.
Foliar pathogens of eucalypts Crous, P.W.; Wingfield, M.J.; Cheewangkoon, R. ...
Studies in mycology,
09/2019, Volume:
94, Issue:
1
Journal Article
Peer reviewed
Open access
Species of eucalypts are commonly cultivated for solid wood and pulp products. The expansion of commercially managed eucalypt plantations has chiefly been driven by their rapid growth and suitability ...for propagation across a very wide variety of sites and climatic conditions. Infection of foliar fungal pathogens of eucalypts is resulting in increasingly negative impacts on commercial forest industries globally. To assist in evaluating this threat, the present study provides a global perspective on foliar pathogens of eucalypts. We treat 110 different genera including species associated with foliar disease symptoms of these hosts. The vast majority of these fungi have been grown in axenic culture, and subjected to DNA sequence analysis, resolving their phylogeny. During the course of this study several new genera and species were encountered, and these are described. New genera include: Lembosiniella (L. eucalyptorum on E. dunnii, Australia), Neosonderhenia (N. eucalypti on E. costata, Australia), Neothyriopsis (N. sphaerospora on E. camaldulensis, South Africa), Neotrichosphaeria (N. eucalypticola on E. deglupta, Australia), Nothotrimmatostroma (N. bifarium on E. dalrympleana, Australia), Nowamyces (incl. Nowamycetaceae fam. nov., N. globulus on E. globulus, Australia), and Walkaminomyces (W. medusae on E. alba, Australia). New species include (all from Australia): Disculoides fraxinoides on E. fraxinoides, Elsinoe piperitae on E. piperita, Fusculina regnans on E. regnans, Marthamyces johnstonii on E. dunnii, Neofusicoccum corticosae on E. corticosa, Neotrimmatostroma dalrympleanae on E. dalrympleana, Nowamyces piperitae on E. piperita, Phaeothyriolum dunnii on E. dunnii, Pseudophloeospora eucalyptigena on E. obliqua, Pseudophloeospora jollyi on Eucalyptus sp., Quambalaria tasmaniae on Eucalyptus sp., Q. rugosae on E. rugosa, Sonderhenia radiata on E. radiata, Teratosphaeria pseudonubilosa on E. globulus and Thyrinula dunnii on E. dunnii. A new name is also proposed for Heteroconium eucalypti as Thyrinula uruguayensis on E. dunnii, Uruguay. Although many of these genera and species are commonly associated with disease problems, several appear to be opportunists developing on stressed or dying tissues. For the majority of these fungi, pathogenicity remains to be determined. This represents an important goal for forest pathologists and biologists in the future. Consequently, this study will promote renewed interest in foliar pathogens of eucalypts, leading to investigations that will provide an improved understanding of the biology of these fungi.
Many members of the Oomycota genus Phytophthora cause economic and environmental impact diseases in nurseries, horticulture, forest, and natural ecosystems and many are of regulatory concern around ...the world. At present, there are 223 described species, including eight unculturable and three lost species. Twenty-eight species need to be redescribed or validated. A lectotype, epitype or neotype was selected for 20 species, and a redescription based on the morphological/molecular characters and phylogenetic placement is provided. In addition, the names of five species are validated: P. cajani , P. honggalleglyana (Synonym: P. hydropathica ), P. megakarya , P. pisi and P. pseudopolonica for which morphology and phylogeny are given. Two species, P. ×multiformis and P. uniformis are presented as new combinations. Phytophthora palmivora is treated with a representative strain as both lecto- and epitypification are pending. This manuscript provides the updated multigene phylogeny and molecular toolbox with seven genes (ITS rDNA, β-tub , COI , EF1α , HSP90 , L10 , and YPT1 ) generated from the type specimens of 212 validly published, and culturable species (including nine hybrid taxa). The genome information of 23 types published to date is also included. Several aspects of the taxonomic revision and phylogenetic re-evaluation of the genus including species concepts, concept and position of the phylogenetic clades recognized within Phytophthora are discussed. Some of the contents of this manuscript, including factsheets for the 212 species, are associated with the “ IDphy : molecular and morphological identification of Phytophthora based on the types” online resource (https://idtools.org/tools/1056/index.cfm). The first version of the IDphy online resource released to the public in September 2019 contained 161 species. In conjunction with this publication, we are updating the IDphy online resource to version 2 to include the 51 species recently described. The current status of the 223 described species is provided along with information on type specimens with details of the host (substrate), location, year of collection and publications. Additional information is provided regarding the ex-type culture(s) for the 212 valid culturable species and the diagnostic molecular toolbox with seven genes that includes the two metabarcoding genes (ITS and COI ) that are important for Sanger sequencing and also very valuable Molecular Operational Taxonomic Units (MOTU) for second and third generation metabarcoding High-throughput sequencing (HTS) technologies. The IDphy online resource will continue to be updated annually to include new descriptions. This manuscript in conjunction with IDphy represents a monographic study and the most updated revision of the taxonomy and phylogeny of Phytophthora , widely considered one of the most important genera of plant pathogens.
During large-scale surveys for soilborne Phytophthora species in forests and semi-natural stands and nurseries in Europe during the last decade, homothallic Phytophthora isolates with paragynous ...antheridia, semi-papillate persistent sporangia and a growth optimum around
25 °C which did not form catenulate hyphal swellings, were recovered from 39 host species in 16 families. Based on their morphological and physiological characters and the similarity of their ITS DNA sequences with P. citricola as designated on GenBank, these isolates were routinely
identified as P. citricola. In this study DNA sequence data from the internal transcribed spacer regions (ITS1 and ITS2) and 5.8S gene of the rRNA operon, the mitochondrial cox1 and β-tubulin genes were used in combination with morphological and physiological characteristics
to characterise these isolates and compare them to the ex-type and the authentic type isolates of P. citricola, and two other taxa of the P. citricola complex, P. citricola I and the recently described P. multivora. Due to their unique combination of morphological,
physiological and molecular characters these semipapillate homothallic isolates are described here as a new species, P. plurivora sp. nov.
Aim: Cryptic species in the Neofusicoccum parvum—N. ribis species complex have only recently been described, invalidating previous interpretations on host and geographical distribution. This study ...aimed to characterize the diversity and distribution of these species and to understand the patterns of host association, likely origins and their patterns of spread. Location: Australia, Brazil, Cameroon, Chile, China, Colombia, Ethiopia, France, Greece, India, Indonesia, Iran, Italy, Japan, Kenya, Mexico, New Zealand, Panama, Portugal, Puerto Rico, South Africa, South Korea, Spain, Swaziland, Taiwan, Thailand, Uganda, United States of America, Uruguay, Zambia and Zimbabwe. Methods: Using the unique polymorphisms that separate species within the complex, we evaluated sequence search results available in public and in our own databases. In addition, the global distribution of diversity of N. parvum was analysed using seven microsatellite markers. Results: Neofusicoccum parvum is found in 90 hosts across six continents and 29 countries. Neofusicoccum kwambonambiense is found on four continents, six countries and on 14 hosts; N. occulatum is found on four continents, four countries and on 11 hosts; N. umdonicola is found on two continents, countries and hosts; N. cordaticola is found on three continents, countries and hosts; N. batangarum is found on two continents, three countries and three hosts; and N. ribis is found on one host in one country. Population genetic analysis of the global N. parvum population reflects admixture and repeat introductions. Main conclusions: This study illustrates the unfettered and frequent movement of latent pathogens across international borders. Amongst the species in the N. parvum—N. ribis complex, N. parvum is the most widespread and has been reported on the majority of the hosts studied. The current dispersal of N. parvum and its sister species is probably due to repeated introductions of plant material into new growing areas, with Eucalyptus and Vitis vinifera being two prominent candidates for material transfer.
New and Interesting Fungi. 1 Crous, P W; Schumacher, R K; Wingfield, M J ...
Fungal Systematics and Evolution,
06/2018, Volume:
1, Issue:
1
Journal Article
Peer reviewed
Open access
This study introduces two new families, one new genus, 22 new species, 10 new combinations, four epitypes, and 16 interesting new host and / or geographical records. Cylindriaceae (based on ...Cylindrium elongatum) is introduced as new family, with three new combinations.
Xyladictyochaetaceae (based on Xyladictyochaeta lusitanica) is introduced to accommodate Xyladictyochaeta. Pseudoanungitea gen. nov. (based on P. syzygii) is described on stems of Vaccinium myrtillus (Germany). New species include: Exophiala eucalypticola
on Eucalyptus obliqua leaf litter, Phyllosticta hakeicola on leaves of Hakea sp., Setophaeosphaeria citricola on leaves of Citrus australasica, and Sirastachys cyperacearum on leaves of Cyperaceae (Australia); Polyscytalum chilense
on leaves of Eucalyptus urophylla (Chile); Pseudoanungitea vaccinii on Vaccinium myrtillus (Germany); Teichospora quercus on branch tissue of Quercus sp. (France); Fusiconidium lycopodiellae on stems of Lycopodiella inundata, Monochaetia
junipericola on twig of Juniperus communis, Myrmecridium sorbicola on branch tissues of Sorbus aucuparia, Parathyridaria philadelphi on twigs of Philadelphus coronarius, and Wettsteinina philadelphi on twigs of Philadelphus coronarius (Germany);
Zygosporium pseudogibbum on leaves of Eucalyptus pellita (Malaysia); Pseudoanungitea variabilis on dead wood (Spain); Alfaria acaciae on leaves of Acacia propinqua, Dictyochaeta mimusopis on leaves of Mimusops caffra, and Pseudocercospora breonadiae
on leaves of Breonadia microcephala (South Africa); Colletotrichum kniphofiae on leaves of Kniphofia uvaria, Subplenodomus iridicola on Iris sp., and Trochila viburnicola on twig cankers on Viburnum sp.(UK); Polyscytalum neofecundissimum
on Quercus robur leaf litter, and Roussoella euonymi on fallen branches of Euonymus europaeus (Ukraine). New combinations include: Cylindrium algarvense on leaves of Eucalyptus sp. (Portugal), Cylindrium purgamentum on leaf litter (USA),
Cylindrium syzygii on leaves of Syzygium sp. (Australia), Microdochium musae on leaves of Musa sp. (Malaysia), Polyscytalum eucalyptigenum on Eucalyptus grandis × pellita (Malaysia), P. eucalyptorum on leaves of Eucalyptus
(Australia), P. grevilleae on leaves of Grevillea (Australia), P. nullicananum on leaves of Eucalyptus (Australia), Pseudoanungitea syzygii on Syzygium cordatum leaf litter (South Africa), and Setophaeosphaeria sidae on leaves of
Sida sp. (Brazil). New records include: Sphaerellopsis paraphysata on leaves of Phragmites sp., Vermiculariopsiella dichapetali on leaves of Melaleuca sp. and Eucalyptus regnans, and Xyladictyochaeta lusitanica on leaf litter of Eucalyptus
sp. (Australia); Camarosporidiella mackenziei on twigs of Caragana sp. (Finland); Cyclothyriella rubronotata on twigs of Ailanthus altissima, Rhinocladiella quercus on Sorbus aucuparia branches (Germany); Cytospora viticola on stems of
Vitis vinifera (Hungary); Echinocatena arthrinioides on leaves of Acacia crassicarpa (Malaysia); Varicosporellopsis aquatilis from garden soil (Netherlands); Pestalotiopsis hollandica on needles of Cupressus sempervirens (Spain), Pseudocamarosporium
africanum on twigs of Erica sp. (South Africa), Pseudocamarosporium brabeji on branch of Platanus sp. (Switzerland); Neocucurbitaria cava on leaves of Quercus ilex (UK); Chaetosphaeria myriocarpa on decaying wood of Carpinus betulus, Haplograhium
delicatum on decaying Carpinus betulus wood (Ukraine). Epitypes are designated for: Elsinoë mimosae on leaves of Mimosa diplotricha (Brazil), Neohendersonia kickxii on Fagus sylvatica twig bark (Italy), Caliciopsis maxima on fronds of
Niphidium crassifolium (Brazil), Dictyochaeta septata on leaves of Eucalyptus grandis × urophylla (Chile), and Microdochium musae on leaves of Musa sp. (Malaysia).
During routine vegetation health surveys in the southwest of Western Australia (SWWA), several Phytophthora isolates with affinity to Clade 6a have been recovered. In this study, all known taxa from ...Clade 6a, P. inundata, P. humicola, P. gemini, P.
'walnut' and P. 'personii', and the new isolates were compared based on morphology and DNA sequence data from three nuclear genes and two mitochondrial genes resulting in the description of five new species, P. balyanboodja, P. condilina, P. cooljarloo, P. kwongonina
and P. pseudorosacearum. With the exception of P. gemini and P. humicola, all species from Clade 6a have been recovered from natural ecosystems in SWWA. These species are morphologically similar, with predominantly ovoid sporangia and nested and extended internal
proliferation. If oospores are present, they tend to be aplerotic with paragynous antheridia mostly attached adjacent to the oogonial stalk. They can all grow at 35°C and have a fast growth rate on most agar media. These species have all been recovered from the rhizosphere soil and dead
and dying plants within dry kwongon heathlands, often from water gaining sites and frequently from very isolated areas. The radiation, origin and potential ecological role of these species are discussed.
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•A new tree decline/recovery model for eucalypts was developed.•Model based on prediction of increased drought periods in regions with eucalypt plantations.•The model incorporates ...recovery from the effect of drought and secondary biological stressors.•Biological stressors include both insect pests and pathogens.•This model could be expanded to other types of tree plantations and to other stress events.
Worldwide tree plantations face prolonged drought periods that are predicted to increase in duration and intensity under climate change scenarios. Trees stressed by drought are susceptible to secondary stressors including pests and pathogens. Depending on the timing and intensity of these stressors, their impact may be persistent or acute, with varied temporal and spatial responses by different hosts. There are complex processes involved in tree performance and mortality, and often it can be difficult to identify the leading cause of growth decline and death. However, it is important to recognise that often death can be a gradual process with periods of recovery. While previous models have focussed on the decline of the tree in response to stress, there has been little focus on the recovery from stress. Hence, the development here of the Tree Decline Recovery Seesaw model. This conceptual model is based on the premise that drought stressed trees may alternate between different stages of health through time, particularly those facing intermittent drought over extended periods. This approach takes into account that recovery periods allow for the tree to regain health, and potentially create new opportunities for pest and disease outbreaks. The Tree Decline Recovery Seesaw model provides researchers with the understanding of the complexity of drought/pest/pathogen interactions, allowing them to assess the order and severity of the stressors to determine the likely outcome. This paper provides a vital step towards the development of predictive tools for plantation managers. While our model has focussed on eucalypt plantation trees, there is potential to apply the model to other tree species and forms of plant stress.