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J. De Gruyter - One of the best experts on this subject based on the ideXlab platform.

  • Revised taxonomy of Phoma and allied genera
    2012
    Co-Authors: J. De Gruyter
    Abstract:

    The anamorphic genus Phoma includes many important plant pathogens. The identification of Phoma species based on studies in pure culture is difficult and time consuming and the in vitro characters are often variable. Moreover, the present classification of Phoma species into sections is ambiguous and morphological characters are shared with related genera. In the present study the molecular phylogeny of species of Phoma and allied genera was examined and the results obtained were used to revise the taxonomy. The DNA sequence data obtained provide tools for the development of detection and identification methods. Chapter 1 provides a general introduction of the anamorph genus Phoma and the research that has been performed in The Netherlands during the last decades is described. Phoma is characterised by producing hyaline conidia in fruiting bodies called pycnidia. The genus includes many important plant pathogens. The taxonomy of Phoma has been studied intensively at the Plant Protection Service in the Netherlands for more than 50 years, resulting in the development of a generic concept in 1997 as an outline for identification of Phoma species. In this concept species of the genus Phoma are classified based on their morphological characters into the nine sections Phoma, Heterospora, Macrospora, Paraphoma, Peyronellaea, Phyllostictoides, Pilosa, Plenodomus and Sclerophomella. The species placed in each of the sections were systematically described culminating in the publication of the “Phoma Identification Manual” in 2004, with the descriptions of 223 specific and infra-specific taxa of Phoma, and more than 1000 synonyms in other coelomycetous genera. In the Netherlands the late Gerhard Boerema, former head of the Mycology Department at the Plant Protection Service, has been the driving force behind this Phoma research for decades. The Phoma Identification Manual is a valuable tool for the morphological identification of isolates, but in vitro studies are very time consuming and need a high level of expertise. Moreover, the classification of Phoma species in sections based on morphological characters appeared artificial and several species can be classified in more than one section because of their multiple “section-specific” characters. In addition, distinctive characters of Phoma sections are shared among morphologically related coelomycetous genera including Ascochyta, Asteromella, Microsphaeropsis, Phomopsis, Phyllosticta, Pleurophoma, Pyrenochaeta and Stagonospora. Phoma sections are related to diverse teleomorph genera including Didymella, Leptosphaeria, Mycosphaerella and Pleospora. Synanamorphs of Phoma species have been recognised amongst the genera Phaeomoniella, Stagonosporopsis, Epicoccum, Phialophora and Sclerotium illustrating their heterogeneity. A large, well-studied Phoma culture collection established at the Plant Protection Service and the “Centraalbureau voor Schimmelcultures” includes more than 1100 strains of Phoma species. This collection formed the basis of an intensive molecular phylogenetic study of the genus Phoma and morphologically similar genera, which commenced in 2006. Furthermore, a literature study identified sequences of genes that are suitable for phylogenic studies and elucidation of the evolutionary history of the genus Phoma. Several potentially informative regions of the genome were sequenced in the first phase of the project as has been described in chapters 2–4. The phylogeny and DNA sequence data obtained have provided tools for the development of fast and reliable molecular detection and identification methods. The development of Real-time TaqMan PCR methods for the detection and identification of two important plant pathogenic (quarantine) species formerly described in Phoma, Stagonosporopsis andigena and S. crystalliniformis, is described in Chapter 5. In chapter 2 several genes were studied to elucidate the molecular phylogeny of Phoma and allied genera. Sequence data of the 18S nrDNA (SSU) and 28S nrDNA (LSU) regions of the type species of the Phoma sections and morphologically similar coelomycetes and related teleomorphs were compared. The results justified the introduction of the new family Didymellaceae to accommodate the generic type species Didymella exigua and Phoma herbarum. The type species of the Phoma sections Phyllostictoides, Sclerophomella, Macrospora and Peyronellaea also grouped in Didymellaceae. The generic type species Ascochyta pisi and Microsphaeropsis olivacea also grouped in Didymellaceae and it shows that these genera are closely allied to Phoma. The type species of  Phoma sections Heterospora, Paraphoma, Pilosa and Plenodomus grouped in various families outside Didymellaceae and were subject of following studies. Chapter 3 provides a molecular phylogenetic re-evaluation on Phoma-like species that appeared only distantly related to the generic type species Phoma herbarum and its related Didymella teleomorph (Didymellaceae). Phoma section Paraphoma, characterised by setose pycnidia, resembles species of Pyrenochaeta and Pleurophoma. Sequence data from the SSU and LSU regions of the species classified in Phoma section Paraphoma were compared with those of representative isolates of Pyrenochaeta and Pleurophoma, and with those of the type species of the Phoma sections Phoma, Pilosa and Plenodomus. Unnamed, often sterile Phomalike strains in the collections were included. The molecular phylogeny of species that were classified in Phoma section Paraphoma appeared to be highly polyphyletic and a thorough reclassification of the species is provided. Paraphoma was reinstalled and grouped with the new genera Neosetophoma and Setophoma in Phaeosphaeriaceae. Pyrenochaeta and the new genus Pyrenochaetopsis, including mainly taxa formerly described in Phoma section Paraphoma, were closely allied in Cucurbitariaceae. In chapter 4 the molecular phylogeny of species of Phoma sections Plenodomus, Pleospora and Heterospora was determined using LSU, SSU and ITS. In a “one species = one name” approach, the species described in Phoma section Plenodomus and its teleomorph Leptosphaeria were reclassified in Leptosphaeria, Plenodomus and the new genera Paraleptosphaeria and Subplenodomus in Leptosphaeriaceae. Two species of Phoma section Heterospora, the type species Phoma heteromorphospora and its allied species Ph. dimorphospora, were transferred to the new genus Heterospora that also grouped in Leptosphaeriaceae. Leptosphaeria doliolum comprises a species complex that was revised based on multilocus sequence data of LSU, ITS, SSU, s-tubulin, and chitin synthase 1. The molecular phylogeny of species classified in Ascochyta and Phoma, section Pilosa in Pleosporaceae that produce morphologically similar pilose pycnidia, was determined based on analysis of actin sequence data. Several Phoma-like species grouped outside the suborder Pleosporineae in a LSU sequence analysis and were transferred to the genera Aposphaeria (Melanommataceae), Paraconiothyrium (Montagnulaceae) and Westerdykella (Sporormiaceae). Coniothyrium palmarum and related species were described in Coniothyriaceae. The new genera Medicopsis (Trematosphaeriaceae) and Nigrograna, of which the family is still unknown, are introduced to accommodate two medically important species formerly classified in Pyrenochaeta. In chapter 5 specific real-time (TaqMan) PCR assays were developed for the detection of the pathogens Stagonosporopsis andigena and S. crystalliniformis in leaves of potato and tomato. The molecular phylogeny with related species of Stagonosporopsis, Boeremia and Phoma based on sequence polymorphisms in the actine gene, was determined. The reliability of the DNA extraction and TaqMan PCRs for the detection of S. andigena and S. crystalliniformis in leaf material was tested in performance studies and demonstrated the specificity, analytical sensitivity, reproducibility, repeatability and robustness of both assays.

  • Systematic reappraisal of species in Phoma section Paraphoma, Pyrenochaeta and Pleurophoma
    Mycologia, 2010
    Co-Authors: J. De Gruyter, Maikel M Aveskamp, Joyce H C Woudenberg, Gerard J M Verkley, Johannes Z Groenewald, Pedro W Crous
    Abstract:

    Sequence data from the 18S nrDNA (SSU) and 28S nrDNA (LSU) regions of isolates of Phoma section Paraphoma were compared with those of representative isolates of the morphologically similar anamorph genera Pleurophoma and Pyrenochaeta and of the type species of Phoma sections Phoma, Pilosa and Plenodomus. Phoma section Paraphoma was found to be highly polyphyletic within the Pleosporales and only distantly related to Phoma section Phoma. The genus Paraphoma, which is based on Paraphoma radicina, is reintroduced in the Phaeosphaeriaceae with two additional taxa. The new genera Setophoma and Neosetophoma, type species Setophoma terrestris comb. nov. and Neosetophoma samarorum comb. nov., are introduced and represent species that are closely related to Paraphoma but differ based on morpho- logical characters and molecular phylogeny. Phoma coonsii is transferred to genus Chaetosphaeronema that also belongs to the Phaeosphaeriaceae. Pyrenochae- topsis gen. nov. is introduced to accommodate the type species Pyrenochaetopsis leptospora comb. nov., as well as several other species formerly accommodated in Phoma and Pyrenochaeta. Pyrenochaetopsis is closely related to Pyrenochaeta and classified in the Cucurbi- tariaceae. Pleurophoma cava is transferred to genus Pyrenochaeta. The new genera elucidate the confusing taxonomy of species in genera Phoma, Pyrenochaeta and Pleurophoma and recognize monophyletic genera with distinct teleomorph affinities.

  • Molecular phylogeny of Phoma and allied anamorph genera: towards a reclassification of the Phoma complex.
    Mycological research, 2009
    Co-Authors: J. De Gruyter, Maikel M Aveskamp, Joyce H C Woudenberg, Gerard J M Verkley, Johannes Z Groenewald, Pedro W Crous
    Abstract:

    The present generic concept of Phoma is broadly defined, with nine sections being recognised based on morphological characters. Teleomorph states of Phoma have been described in the genera Didymella, Leptosphaeria, Pleospora and Mycosphaerella, indicating that Phoma anamorphs represent a polyphyletic group. In an attempt to delineate generic boundaries, representative strains of the various Phoma sections and allied coelomycetous genera were included for study. Sequence data of the 18S nrDNA (SSU) and the 28S nrDNA (LSU) regions of 18 Phoma strains included were compared with those of representative strains of 39 allied anamorph genera, including Ascochyta, Coniothyrium, Deuterophoma, Microsphaeropsis, Pleurophoma, Pyrenochaeta, and 11 teleomorph genera. The type species of the Phoma sections Phoma, Phyllostictoides, Sclerophomella, Macrospora and Peyronellaea grouped in a subclade in the Pleosporales with the type species of Ascochyta and Microsphaeropsis. The new family Didymellaceae is proposed to accommodate these Phoma sections and related anamorph genera. The present study demonstrated that Phoma radicina, the type species of Phoma sect. Paraphoma and Phoma heteromorphospora, the type species of Phoma sect. Heterospora can be assigned to the Phaeosphaeriaceae and Leptosphaeriaceae respectively.

  • DNA phylogeny reveals polyphyly of Phoma section Peyronellaea and multiple taxonomic novelties
    Mycologia, 2009
    Co-Authors: Maikel M Aveskamp, J. De Gruyter, Joyce H C Woudenberg, Gerard J M Verkley, Johannes Z Groenewald, Mónica Adriana Murace, Analía Perelló, Pedro W Crous
    Abstract:

    Species of the anamorph genus Phoma are commonly isolated from a wide range of ecological niches. They are notoriously difficult to identify due to the paucity of morphological features and the plasticity of these when cultivated on agar media. Species linked to Phoma section Peyronellaea are typified by the production of dictyochlamydospores and thus have additional characters to use in taxon delineation. However, the taxonomy of this section is still not fully understood. Furthermore the production of such chlamydospores also is known in some other sections of Phoma. DNA sequences were generated from three loci, namely ITS, actin, and 3-tubulin, to clarify the phylogeny of Phoma taxa that produce dictyochlamydospores. Results were unable to support section Peyronellaea as a taxonomic entity. Dictyochlamydospore formation appears to be a feature that developed, or was lost, many times during the evolution of Phoma. Furthermore, based on the multigene analyses, five new Phoma species could be delineated while a further five required taxonomic revision to be consistent with the genetic variation observed.

  • Contributions towards a monograph of Phoma (Coelomycetes) VIII. Section Paraphoma: Taxa with setose pycnidia
    Persoonia, 2002
    Co-Authors: J. De Gruyter, G. H. Boerema
    Abstract:

    In this paper eleven species of Phoma with obvious setose pycnidia, grouped in the section Paraphoma, are documented and described. Most of these species were formerly classified in Pyrenochaeta. The following new taxa have been proposed: Phoma briardii nom. nov., Phoma carteri nom. nov., Phoma glycinicola nom. nov., Phoma indica (T.S. Viswan.) comb, nov., Phoma setariae (H.C. Greene) comb. nov. and Phoma leveillei var. microspora var. nov. Indices on host/substratum-fungus and fungus-host relations are included and short comments on the ecology and distribution of the taxa are given.

John J Burns - One of the best experts on this subject based on the ideXlab platform.

  • Spotted Seal: Phoca largha
    Encyclopedia of Marine Mammals, 2018
    Co-Authors: Kathryn J. Frost, John J Burns
    Abstract:

    Summary Spotted seals (Phoca largha) occur primarily in seasonally ice-covered seas of the North Pacific Ocean. Breeding populations occur in the Bering Sea, Sea of Okhotsk, Yellow Sea, and Sea of Japan. This species is closely related to the harbor seal (Phoca vitulina). However, these sibling species have adapted very differently to their environments; spotted seals primarily breed and molt on sea ice and harbor seals on land.

  • comparative morphology of the skull of the ribbon seal histrioPhoca fasciata with remarks on systematics of phocidae
    Journal of Zoology, 2010
    Co-Authors: John J Burns
    Abstract:

    Study of skulls from 145 Ribbon seals, mainly from the Bering Sea, disclosed much greater variation in form than was indicated by earlier descriptions. The characters of greatest diagnostic value in the Ribbon seal are the short rostrum, broad cranium with reduced temporal fossae. short, wide palate with small, widely spaced teeth, and the elongate, thickwalled bullae with massive, widely exposed petrosals. Comparison of these skulls with examples from each of the other recognized genera of Phocidae revealed several deficiencies in the referred cranial characteristics of taxa at all ranks below the family. Provisional support for J. E. King's recently proposed division of the Phocidae into two subfamilies, Phocinae and Monachinae, is reported; the distinctions formerly employed for diagnosis of a third subfamily, Cystophorinae, can be ascribed to convergent evolution. Craniologically, the subfamily Phocinae is divisible into three tribes: Erignathini, Cystophorini, and Phocini. The first two are monotypic; the third is polytypic. The subtribes Phocina and Histriophocina are untenable; while HistrioPhoca's nearest structural relative is Pagophilus, the latter shows equal or closer relationship with Phocu. Within the tribe Phocini, only the Grey seal, Hlichoerus grypus, shows sufficient cranial differentiation for recognition as a monotypic genus. The other four major taxa within that tribe show a complex system of intergrading characters that disallows generic recognition, other than as a polytypic group. Therefore, the Ribbon, Harp, Harbor, and Ringed seals are re-assigned to subgeneric rank, under the inclusive genus Phoca (sensu luto).

G. H. Boerema - One of the best experts on this subject based on the ideXlab platform.

Nobuyuki Miyazaki - One of the best experts on this subject based on the ideXlab platform.

  • Antibodies to human-related H3 influenza A virus in Baikal seals (Phoca sibirica) and ringed seals (Phoca hispida) in Russia.
    Microbiology and immunology, 2004
    Co-Authors: Kazue Ohishi, Nobuyuki Miyazaki, Noriko Kishida, Ai Ninomiya, Hiroshi Kida, Yoshitake Takada, Andrei N. Boltunov, Tadashi Maruyama
    Abstract:

    Antibodies to influenza A virus were detected using enzyme-linked immunosorbent assay (ELISA) in the sera from two of seven Baikal seals (Phoca sibrica) and from five of six ringed seals (Phoca hispida) in Russia. In a hemagglutination-inhibition test using H1-H15 reference influenza A viruses, ELISA-positive sera from one Baikal seal and four ringed seals reacted to A/Aichi/2/68 (H3N2) and A/Bangkok/1/79 (H3N2) strains. One ringed seal serum sample reacted to A/seal/Massachusetts/1/80 (H7N7). The present results suggested that human-related H3 viruses were prevalent in Baikal seals and ringed seals inhabiting the central Russian Arctic.

  • The muscles of mastication in the caspian seal (Phoca caspica).
    Anatomia histologia embryologia, 2002
    Co-Authors: Hideki Endo, S. Sakata, Takaomi Arai, Nobuyuki Miyazaki
    Abstract:

    The muscles of mastication and their related skull characters in the Caspian seal (Phoca caspica) were anatomically examined and compared with those of the Baikal (Phoca sibirica) and ringed (Phoca hispida) seals. A well-developed masseter muscle was observed in the Caspian seal, whereas the temporal muscle consisted of thin bundles. The skull of the Caspian seal possessed the same thin frontal bone and the dorso-ventrally developed zygomatic arch found in the Baikal seal that are required to install the enlarged eyeball into the orbit. The temporal bone was not robust, and the digastric muscle was well-developed in the ventral space of the auditory bulla. The present results suggest that the skull form of the Caspian seal has changed morphologically from its ringed seal-like ancestors, and suggest that the evolutionary strategy of the muscles of mastication in the Caspian seal is principally consistent with that of the Baikal seal.

  • Age determination and growth of Baikal seals (Phoca sibirica)
    Advances in Ecological Research, 2000
    Co-Authors: Masao Amano, Nobuyuki Miyazaki, E. A. Petrov
    Abstract:

    Abstract The ages of 75 Baikal seals (Phoca sibirica) were determined in order to study the growth pattern of body length and body weight in this species. Longitudinal decalcified and stained sections of canine teeth were prepared, and growth layer groups (GLGs) in the dentine and cementum were counted. In those specimens with fewer than 10 GLGs, the GLG counts in dentine agreed well with those in cementum. However, in specimens with more than 10 GLGs, the cemental GLGs tended to exceed dentinal ones. Individuals of 4–5 years old were absent from the sample population, suggesting that the recorded mass mortality of Baikal seals in 1987–1988 (4–5 years before sampling) had affected the age composition. Growth of body length, body weight and core weight ceased at around 20 years of age. The growth pattern was similar to that of ringed seals (Phoca hispida), but differed from that of other Phoca species. Asymptotic body length and core weight were significantly different between sexes, but body weight was not. In the spring sampling period, female body weights tended to be heavier than those of males of the same body length, a feature attributed to the thicker blubber of females. Sexual dimorphism, and the large fluctuation in body weight and presence of secondary sexual characters reported in males, suggested the presence of intermale competition in the Baikal seal, presumably for access to females.

Jesse C Vermaire - One of the best experts on this subject based on the ideXlab platform.

  • no plastics detected in seal phocidae stomachs harvested in the eastern canadian arctic
    Marine Pollution Bulletin, 2020
    Co-Authors: Madelaine P T Bourdages, Enooyaq Sudlovenick, Nicolas Pelletier, Michael J J Murphy, Alexa Daddario, Brent G Young, Jennifer F. Provencher, Steven H. Ferguson, Jesse C Vermaire
    Abstract:

    Abstract Through collaboration with Inuit hunters, we examined the stomach contents of 142 seals (ringed seals [Phoca hispida; n = 135], bearded seals [Erignathus barbatus; n = 6], and one harbour seal [Phoca vitualina; n = 1]) hunted between 2007 and 2019 from communities around Nunavut to assess whether seals in the eastern Canadian Arctic ingest and retain plastics in their stomachs. The seals in this study ranged from juveniles to adults of up to 30 years of age, and 55% of the seals were males. We found no evidence of plastic ingestion in any of the seals suggesting that seals in Nunavut are not accumulating plastics (>425 μm) in their stomachs. These data provide important baseline information for future plastic pollution monitoring programs in the Arctic.

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