Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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Evolution of Plant Parasitism in the Phylum Nematoda
Quist, C.W. ; Smant, G. ; Helder, J. - \ 2015
Annual Review of Phytopathology 53 (2015). - ISSN 0066-4286 - p. 289 - 310.
root-knot nematode - rna gene-sequences - small-subunit rdna - n. sp nematoda - ribosomal-rna - molecular phylogeny - cyst nematodes - beta-1,4-endoglucanase genes - tylenchoidea nematoda - aphelenchus-avenae
Within the species-rich and trophically diverse phylum Nematoda, at least four independent major lineages of plant parasites have evolved, and in at least one of these major lineages plant parasitism arose independently multiple times. Ribosomal DNA data, sequence information from nematode-produced, plant cell wall–modifying enzymes, and the morphology and origin of the style(t), a protrusible piercing device used to penetrate the plant cell wall, all suggest that facultative and obligate plant parasites originate from fungivorous ancestors. Data on the nature and diversification of plant cell wall–modifying enzymes point at multiple horizontal gene transfer events from soil bacteria to bacterivorous nematodes resulting in several distinct lineages of fungal or oomycete-feeding nematodes. Ribosomal DNA frameworks with sequence data from more than 2,700 nematode taxa combined with detailed morphological information allow for explicit hypotheses on the origin of agronomically important plant parasites, such as root-knot, cyst, and lesion nematodes.
Using multi-locus allelic sequence data to estimate genetic divergence among four Lilium (Liliaceae) cultivars
Shahin, A. ; Smulders, M.J.M. ; Tuyl, J.M. van; Arens, P.F.P. ; Bakker, F.T. - \ 2014
Frontiers in Plant Science 5 (2014). - ISSN 1664-462X
nuclear ribosomal dna - transcribed spacer region - phylogeny group classification - species trees - reticulate evolution - molecular phylogeny - flowering plants - genus lilium - apg iii - networks
Next Generation Sequencing (NGS) may enable estimating relationships among genotypes using allelic variation of multiple nuclear genes simultaneously. We explored the potential and caveats of this strategy in four genetically distant Lilium cultivars to estimate their genetic divergence from transcriptome sequences using three approaches: POFAD (Phylogeny of Organisms from Allelic Data, uses allelic information of sequence data), RAxML (Randomized Accelerated Maximum Likelihood, tree building based on concatenated consensus sequences) and Consensus Network (constructing a network summarizing among gene tree conflicts). Twenty six gene contigs were chosen based on the presence of orthologous sequences in all cultivars, seven of which also had an orthologous sequence in Tulipa, used as out-group. The three approaches generated the same topology. Although the resolution offered by these approaches is high, in this case there was no extra benefit in using allelic information. We conclude that these 26 genes can be widely applied to construct a species tree for the genus Lilium.
Isolated with persistence or dynamically connected? Genetic patterns in a common granite outcrop endemic
Tapper, S.L. ; Byrne, M. ; Yates, C.J. ; Keppel, G. ; Hopper, S.D. ; Niel, K.P. Van; Schut, A.G.T. ; Mucina, L. ; Wardell-Johnson, G.W. - \ 2014
Diversity and Distributions (2014). - ISSN 1366-9516 - p. 1 - 15.
population-structure - western-australia - climate-change - microsatellite markers - pleistocene refugia - molecular phylogeny - dna polymorphism - cpdna variation - phylogeography - myrtaceae
Aim Granite outcrops are prominent throughout the world and harbour many endemic species. Their topographic complexity and range of environments have led to the hypothesis that they act as refugia facilitating the persistence of species through climate change. We evaluate this hypothesis by investigating the phylogeographic patterns in a common granite endemic shrub. Location Granite outcrops of the Southwest Australian Floristic Region. Methods Chloroplast haplotypes of 89 Kunzea pulchella individuals from 16 granite outcrops were determined from sequences of three chloroplast intergenic spacer regions. Phylogenetic reconstruction and divergence dating was inferred using Bayesian and Parsimony analyses and phylogenetic relationships between haplotypes were examined in relation to geographic distributions. Nuclear diversity and differentiation of populations were assessed through analysis of 11 nuclear microsatellite loci across 384 individuals from the 16 granite outcrops. Results Kunzea pulchella exhibited low haplotype and allelic diversity within outcrops and high levels of divergence among outcrops, indicating an ancient restriction to specific outcrops with genetic drift as the main driver of evolution. Two divergent lineages were revealed in the chloroplast phylogeny dating to the Pliocene and potentially reflecting the initial impact of increased aridity prior to isolation on individual outcrops. Main conclusions Rather than uncovering the typical pattern for Pleistocene refugia with contraction to, and expansion from particular granite outcrops, we observed persistence, prolonged isolation and divergence of populations. We suggest the persistence of K. pulchella on multiple outcrops through a period of considerable climatic change may be a result of broad climatic tolerances or contraction and expansion dynamics operating at microrefugial scales within outcrops. Our observations of low haplotype and allelic diversity within populations of K. pulchella provide some support for the latter. The enduring nature of K. pulchella and evolutionary potential of populations on individual outcrops accentuates the value of these environments for biodiversity conservation planning in a changing climate.
Phylogeny and systematics of Demospongiae in light of new small-subunit ribosomal DNA (18S) sequences
Redmond, N.E. ; Morrow, C. ; Thacker, R.W. ; Diaz, M.C. ; Boury-Esnaul, N. ; Cardenas, P.D. ; Hajdu, E. ; Lobo-Hajdu, G. ; Picton, B.E. ; Pomponi, S.A. ; Kayal, E. ; Collins, A.G. - \ 2013
Integrative and Comparative Biology 53 (2013)3. - ISSN 1540-7063 - p. 388 - 415.
glass sponges porifera - phylum porifera - molecular phylogeny - animal phylogeny - gene-sequences - fossil record - evolution - hexactinellida - classification - verongida
The most diverse and species-rich class of the phylum Porifera is Demospongiae. In recent years, the systematics of this clade, which contains more than 7000 species, has developed rapidly in light of new studies combining molecular and morphological observations. We add more than 500 new, nearly complete 18S sequences (an increase of more than 200%) in an attempt to further enhance understanding of the phylogeny of Demospongiae. Our study specifically targets representation of type species and genera that have never been sampled for any molecular data in an effort to accelerate progress in classifying this diverse lineage. Our analyses recover four highly supported subclasses of Demospongiae: Keratosa, Myxospongiae, Haploscleromorpha, and Heteroscleromorpha. Within Keratosa, neither Dendroceratida, nor its two families, Darwinellidae and Dictyodendrillidae, are monophyletic and Dictyoceratida is divided into two lineages, one predominantly composed of Dysideidae and the second containing the remaining families (Irciniidae, Spongiidae, Thorectidae, and Verticillitidae). Within Myxospongiae, we find Chondrosida to be paraphyletic with respect to the Verongida. We amend the latter to include species of the genus Chondrosia and erect a new order Chondrillida to contain remaining taxa from Chondrosida, which we now discard. Even with increased taxon sampling of Haploscleromorpha, our analyses are consistent with previous studies; however, Haliclona species are interspersed in even more clades. Haploscleromorpha contains five highly supported clades, each more diverse than previously recognized, and current families are mostly polyphyletic. In addition, we reassign Janulum spinispiculum to Haploscleromorpha and resurrect Reniera filholi as Janulum filholi comb. nov. Within the large clade Heteroscleromorpha, we confirmed 12 recently identified clades based on alternative data, as well as a sister-group relationship between the freshwater Spongillida and the family Vetulinidae. We transfer Stylissa flabelliformis to the genus Scopalina within the family Scopalinidae, which is of uncertain position. Our analyses uncover a large, strongly supported clade containing all heteroscleromorphs other than Spongillida, Vetulinidae, and Scopalinidae. Within this clade, there is a major division separating Axinellidae, Biemnida, Tetractinellida, Bubaridae, Stelligeridae, Raspailiidae, and some species of Petromica, Topsentia, and Axinyssa from Agelasida, Polymastiidae, Placospongiidae, Clionaidae, Spirastrellidae, Tethyidae, Poecilosclerida, Halichondriidae, Suberitidae, and Trachycladus. Among numerous results: (1) Spirophorina and its family Tetillidae are paraphyletic with respect to a strongly supported Astrophorina within Tetractinellida; (2) Agelasida is the earliest diverging lineage within the second clade listed above; and (3) Merlia and Desmacella appear to be the earliest diverging lineages of Poecilosclerida.
The occurrence of haplosporidian parasites, Haplosporidium nelsoni and Haplosporidium sp., in oysters in Ireland
Lynch, S.A. ; Villalba, A. ; Abollo, E. ; Engelsma, M.Y. ; Stokes, N. ; Culloty, S.C. - \ 2013
Journal of Invertebrate Pathology 112 (2013)3. - ISSN 0022-2011 - p. 208 - 212.
crassostrea-gigas - pacific oyster - ostrea-edulis - delaware bay - molecular phylogeny - bonamia-ostreae - eastern oyster - flat oyster - disease - msx
The phylum Haplosporidia is a group of obligate protozoan parasites that infect a number of freshwater and marine invertebrates. Haplosporidian parasites have caused significant mortalities in commercially important shellfish species worldwide. In this study, haplosporidia were detected in Pacific oysters Crassostrea gigas originating in Ireland and were subsequently identified independently in laboratories both in Ireland and in Spain as Haplosporidium nelsoni. In Ireland, H. nelsoni plasmodia were also observed in the heart tissue of a single Ostrea edulis. A range of techniques including heart smear screening, histology, standard polymerase chain reaction (PCR), direct sequencing and in situ hybridisation with an H. nelsoni specific DNA probe were carried out to confirm diagnosis. This is the first reporting of H. nelsoni in oysters in Ireland and this is the first reporting of the detection of this haplosporidian in O. edulis. In Ireland, another haplosporidian was also observed in a single O. edulis during heart smear screening. PCR and DNA sequencing were carried out and indicated the presence of a Haplosporidium sp., most likely Haplosporidium armoricanum. The low prevalence and intensity of infection of both haplosporidian species in Irish C. gigas and in particular O. edulis may indicate that their presence is inconsequential.
Redisposition of Phoma-like anamorphs in Pleosporales
Gruyter, J. de; Woudenberg, J.H.C. ; Aveskamp, M.M. ; Verkley, G.J.M. ; Groenewald, J.Z. ; Crous, P.W. - \ 2013
Studies in Mycology 75 (2013). - ISSN 0166-0616 - p. 1 - 36.
ribosomal dna-sequences - winter oilseed rape - 7 mu-m - leptosphaeria-maculans - stem canker - molecular phylogeny - section plenodomus - small conidia - monograph - taxa
The anamorphic genus Phoma was subdivided into nine sections based on morphological characters, and included teleomorphs in Didymella, Leptosphaeria, Pleospora and Mycosphaerella, suggesting the polyphyly of the genus. Recent molecular, phylogenetic studies led to the conclusion that Phoma should be restricted to Didymellaceae. The present study focuses on the taxonomy of excluded Phoma species, currently classified in Phoma sections Plenodomus, Heterospora and Pilosa. Species of Leptosphaeria and Phoma section Plenodomus are reclassified in Plenodomus, Subplenodomus gen. nov., Leptosphaeria and Paraleptosphaeria gen. nov., based on the phylogeny determined by analysis of sequence data of the large subunit 28S nrDNA (LSU) and Internal Transcribed Spacer regions 1 & 2 and 5.8S nrDNA (ITS). Phoma heteromorphospora, type species of Phoma section Heterospora, and its allied species Phoma dimorphospora, are transferred to the genus Heterospora stat. nov. The Phoma acuta complex (teleomorph Leptosphaeria doliolum), is revised based on a multilocus sequence analysis of the LSU, ITS, small subunit 18S nrDNA (SSU), ß-tubulin (TUB), and chitin synthase 1 (CHS-1) regions. Species of Phoma section Pilosa and allied Ascochyta species were determined to belong to Pleosporaceae based on analysis of actin (ACT) sequence data. Anamorphs that are similar morphologically to Phoma and described in Ascochyta, Asteromella, Coniothyrium, Plectophomella, Pleurophoma and Pyrenochaeta are included in this study. Phoma-like species, which grouped outside the Pleosporineae based on a LSU sequence analysis, are transferred to the genera Aposphaeria, Paraconiothyrium and Westerdykella. The genera Medicopsis gen. nov. and Nigrograna gen. nov. are introduced to accommodate the medically important species formerly known as Pyrenochaeta romeroi and Pyrenochaeta mackinnonii, respectively.
The Phytophthora Genus Anno 2012
Kroon, L.P.N.M. ; Brouwer, H. ; Cock, A.W.A.M. de; Govers, F. - \ 2012
Phytopathology 102 (2012)4. - ISSN 0031-949X - p. 348 - 364.
species causing root - high-temperature tolerant - sudden oak death - sp-nov. - western-australia - interspecific hybridization - phylogenetic-relationships - lithocarpus-densiflorus - heterothallic pathogen - molecular phylogeny
Plant diseases caused by Phytophthora species will remain an ever increasing threat to agriculture and natural ecosystems. Phytophthora literally means plant destroyer, a name coined in the 19th century by Anton de Bary when he investigated the potato disease that set the stage for the Great Irish Famine. Phytophthora infestans, the causal agent of potato late blight, was the first species in a genus that at present has over 100 recognized members. In the last decade, the number of recognized Phytophthora species has nearly doubled and new species are added almost on a monthly basis. Here we present an overview of the 10 clades that are currently distinguished within the genus Phytophthora with special emphasis on new species that have been described since 1996 when Erwin and Ribeiro published the valuable monograph ‘Phytophthora diseases worldwide’ (35)
Zhang, Y. ; Crous, P.W. ; Schoch, C.L. ; Hyde, K.D. - \ 2012
Fungal Diversity 53 (2012)1. - ISSN 1560-2745 - p. 1 - 221.
ribosomal dna-sequences - australian fresh-water - intertidal mangrove wood - sp-nov - north-america - marine fungi - molecular phylogeny - trematosphaeria-circinans - shiraia-bambusicola - multigene phylogeny
One hundred and five generic types of Pleosporales are described and illustrated. A brief introduction and detailed history with short notes on morphology, molecular phylogeny as well as a general conclusion of each genus are provided. For those genera where the type or a representative specimen is unavailable, a brief note is given. Altogether 174 genera of Pleosporales are treated. Phaeotrichaceae as well as Kriegeriella, Zeuctomorpha and Muroia are excluded from Pleosporales. Based on the multigene phylogenetic analysis, the suborder Massarineae is emended to accommodate five families, viz. Lentitheciaceae, Massarinaceae, Montagnulaceae, Morosphaeriaceae and Trematosphaeriaceae.
Genome analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea
Amselem, J. ; Cuomo, C.A. ; Kan, J.A.L. van; Viaud, M. ; Benito, E.P. ; Couloux, A. ; Coutinho, P.M. ; Vries, R.P. de; Dyer, P.S. ; Fillinger, S. ; Fournier, E. ; Gout, L. ; Hahn, M. ; Kohn, L. ; Lapalu, N. ; Plummer, K.M. ; Pradier, J.M. ; Quévillon, E. ; Sharon, A. ; Simon, A. ; Have, A. ten; Tudzynski, B. ; Tudzynski, P. ; Wincker, P. ; Andrew, M. ; Anthouard, V. ; Beever, R.E. ; Beffa, R. ; Benoit, I. ; Bouzid, O. ; Brault, B. ; Chen, Z. ; Choquer, M. ; Collemare, J. ; Cotton, P. ; Danchin, E.G. ; Silva, C. Da; Gautier, A. ; Giraud, C. ; Giraud, T. ; Gonzalez, C. ; Grossetete, S. ; Güldener, U. ; Henrissat, B. ; Howlett, B.J. ; Kodira, C. ; Kretschmer, M. ; Lappartient, A. ; Leroch, M. ; Levis, C. ; Mauceli, E. ; Neuvéglise, C. ; Oeser, B. ; Pearson, M. ; Poulain, J. ; Poussereau, N. ; Quesneville, H. ; Rascle, C. ; Schumacher, J. ; Ségurens, B. ; Sexton, A. ; Silva, E. ; Sirven, C. ; Soanes, D.M. ; Talbot, N.J. ; Templeton, M. ; Yandava, C. ; Yarden, O. ; Zeng, Q. ; Rollins, J.A. ; Lebrun, M.H. ; Dickman, M. - \ 2011
Plos Genetics 7 (2011)8. - ISSN 1553-7404 - 27 p.
rice blast fungus - development-specific protein - expressed sequence tags - programmed cell-death - mating-type loci - oxalic-acid - neurospora-crassa - arabidopsis-thaliana - secondary metabolism - molecular phylogeny
Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38–39 Mb genomes include 11,860–14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to
DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer
Robideau, G.P. ; Cock, A.W.A.M. de; Coffey, M.D. ; Voglmayr, H. ; Brouwer, H. ; Bala, K. ; Chitty, D.W. ; Désaulniers, N. ; Eggertson, Q.A. ; Gachon, C.M.M. ; Hu, C.H. ; Küpper, F.C. ; Rintoul, T.L. ; Sarhan, E. ; Verstappen, E.C.P. ; Zhang, Y. ; Bonants, P.J.M. ; Ristaino, J.B. ; Lévesque, C.A. - \ 2011
Molecular Ecology Resources 11 (2011)6. - ISSN 1755-098X - p. 1002 - 1011.
multiple sequence alignment - phylogenetic-relationships - molecular phylogeny - ribosomal dna - genus phytophthora - filamentous fungi - lsu rdna - pythium - mitochondrial - identification
Oomycete species occupymany different environments andmany ecological niches. The genera Phytophthora and Pythium for example, contain many plant pathogens which cause enormous damage to a wide range of plant species. Proper identification to the species level is a critical first step in any investigation of oomycetes, whether it is research driven or compelled by the need for rapid and accurate diagnostics during a pathogen outbreak. The use of DNA for oomycete species identification is well established, but DNA barcoding with cytochrome c oxidase subunit I (COI) is a relatively new approach that has yet to be assessed over a significant sample of oomycete genera. In this study we have sequenced COI, from 1205 isolates representing 23 genera. A comparison to internal transcribed spacer (ITS) sequences from the same isolates showed that COI identification is a practical option; complementary because it uses the mitochondrial genome instead of nuclear DNA. In some cases COI was more discriminative than ITS at the species level. This is in contrast to the large ribosomal subunit, which showed poor species resolution when sequenced from a subset of the isolates used in this study. The results described in this paper indicate that COI sequencing and the dataset generated are a valuable addition to the currently available oomycete taxonomy resources, and that both COI, the default DNA barcode supported by GenBank, and ITS, the de facto barcode accepted by the oomycete and mycology community, are acceptable and complementary DNA barcodes to be used for identification of oomycetes
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis
Dalloul, R.A. ; Long, J.A. ; Zimin, A.V. ; Aslam, M.L. ; Crooijmans, R.P.M.A. ; Megens, H.J.W.C. ; Groenen, M. - \ 2010
PloS Biology 8 (2010)9. - ISSN 1545-7885 - 21 p.
high-throughput - monodelphis-domestica - molecular phylogeny - chicken genome - gene family - evolution - identification - diversity - birds - galliformes
A synergistic combination of two next-generation sequencing platforms with a detailed comparative BAC physical contig map provided a cost-effective assembly of the genome sequence of the domestic turkey (Meleagris gallopavo). Heterozygosity of the sequenced source genome allowed discovery of more than 600,000 high quality single nucleotide variants. Despite this heterozygosity, the current genome assembly (~1.1 Gb) includes 917 Mb of sequence assigned to specific turkey chromosomes. Annotation identified nearly 16,000 genes, with 15,093 recognized as protein coding and 611 as non-coding RNA genes. Comparative analysis of the turkey, chicken, and zebra finch genomes, and comparing avian to mammalian species, supports the characteristic stability of avian genomes and identifies genes unique to the avian lineage. Clear differences are seen in number and variety of genes of the avian immune system where expansions and novel genes are less frequent than examples of gene loss. The turkey genome sequence provides resources to further understand the evolution of vertebrate genomes and genetic variation underlying economically important quantitative traits in poultry. This integrated approach may be a model for providing both gene and chromosome level assemblies of other species with agricultural, ecological, and evolutionary interest.
Systematic reappraisal of species in Phoma section Paraphoma, Pyrenochaeta and Pleurophoma
Gruyter, J. de; Woudenberg, J.H.C. ; Aveskamp, M.M. ; Verkley, G.J.M. ; Groenewald, J.Z. ; Crous, P.W. - \ 2010
Mycologia 102 (2010)5. - ISSN 0027-5514 - p. 1066 - 1081.
molecular phylogeny - ribosomal dna - monograph - genus - peyronellaea - complex - genera
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 morphological characters and molecular phylogeny. Phoma coonsii is transferred to genus Chaetosphaeronema that also belongs to the Phaeosphaeriaceae. Pyrenochaetopsis 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 Cucurbitariaceae. 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.
A case for re-inventory of Australia’s plant pathogens
Hyde, K.D. ; Chomnunti, P. ; Crous, P.W. ; Groenewald, J.Z. ; Damm, U. ; Ko Ko, T.W. ; Shivas, R.G. ; Summerell, B.A. ; Tan, Y.P. - \ 2010
Persoonia 25 (2010). - ISSN 0031-5850 - p. 50 - 60.
phenotypic characters differentiate - multiple gene genealogies - sp-nov - western-australia - south-africa - colletotrichum-gloeosporioides - mycosphaerella-spp. - molecular phylogeny - polyphasic approach - cryptic speciation
Australia has efficient and visible plant quarantine measures, which through various border controls and survey activities attempt to prevent the entry of unwanted pests and diseases. The ability to successfully perform this task relies heavily on determining what pathogens are present and established in Australia as well as those pathogens that are exotic and threatening. There are detailed checklists and databases of fungal plant pathogens in Australia, compiled, in part, from surveys over many years sponsored by Federal and State programmes. These checklists and databases are mostly specimen-based, which enables validation of records with reference herbarium specimens and sometimes associated cultures. Most of the identifications have been based on morphological examination. The use of molecular methods, particularly the analysis of DNA sequence data, has recently shown that several well-known and important plant pathogenic species are actually complexes of cryptic species. We provide examples of this in the important plant pathogenic genera Botryosphaeria and its anamorphs, Colletotrichum, Fusarium, Phomopsis / Diaporthe and Mycosphaerella and its anamorphs. The discovery of these cryptic species indicates that many of the fungal names in checklists need scrutiny. It is difficult, and often impossible, to extract DNA for sequence analysis from herbarium specimens in order to validate identifications that may now be considered suspect. This validation can only be done if specimens are recollected, re-isolated and subjected to DNA analysis. Where possible, herbarium specimens as well as living cultures are needed to support records. Accurate knowledge of the plant pathogens within Australia's borders is an essential prerequisite for the effective discharge of plant quarantine activities that will prevent or delay the arrival of unwanted plant pathogens.
Coniochaeta (Lecythophora), Collophora gen. nov. and Phaeomoniella species associated with wood necroses of Prunus trees
Damm, U. ; Fourie, P.H. ; Crous, P.W. - \ 2010
Persoonia 24 (2010). - ISSN 0031-5850 - p. 60 - 80.
molecular phylogeny - petri disease - phaeoacremonium - anamorph - key - phialophora - grapevines - acremonium - complex - fungi
Species of the genus Coniochaeta (anamorph: Lecythophora) are known as pathogens of woody hosts, but can also cause opportunistic human infections. Several fungi with conidial stages resembling Lecythophora were isolated from necrotic wood samples of Prunus trees in South Africa. In order to reveal their phylogenetic relationships, these fungi were studied on a morphological and molecular (5.8S nrDNA, ITS-1, ITS-2, GAPDH, EF-1a, 28S nrDNA, 18S nrDNA) basis. Some of the isolates were identified as Coniochaeta (Sordariomycetes), including C. velutina and two new species, C. africana and C. prunicola. The majority of the isolates, however, formed pycnidial or pseudopycnidial synanamorphs and were not closely related to Coniochaeta. According to their 28S nrDNA phylogeny, they formed two distinct groups, one of which was closely related to Helotiales (Leotiomycetes). The new genus Collophora is proposed, comprising five species that frequently occur in necrotic peach and nectarine wood, namely Co. africana, Co. capensis, Co. paarla, Co. pallida and Co. rubra. The second group was closely related to Phaeomoniella chlamydospora (Eurotiomycetes), occurring mainly in plum wood. Besides P. zymoides occurring on Prunus salicina, four new species are described, namely P. dura, P. effusa, P. prunicola and P. tardicola. In a preliminary inoculation study, pathogenicity was confirmed for some of the new species on apricot, peach or plum wood.
Virulence of soil-borne pathogens and invasion by Prunus serotina
Reinhart, K.O. ; Tytgat, T.O.G. ; Putten, W.H. van der; Clay, K. - \ 2010
New Phytologist 186 (2010)2. - ISSN 0028-646X - p. 484 - 495.
enemy release hypothesis - black-cherry - molecular phylogeny - ammophila-arenaria - species-diversity - plant invasions - temperate tree - native range - pythium - root
Globally, exotic invaders threaten biodiversity and ecosystem function. Studies often report that invading plants are less affected by enemies in their invaded vs home ranges, but few studies have investigated the underlying mechanisms. Here, we investigated the variation in prevalence, species composition and virulence of soil-borne Pythium pathogens associated with the tree Prunus serotina in its native US and non-native European ranges by culturing, DNA sequencing and controlled pathogenicity trials. Two controlled pathogenicity experiments showed that Pythium pathogens from the native range caused 38–462% more root rot and 80–583% more seedling mortality, and 19–45% less biomass production than Pythium from the non-native range. DNA sequencing indicated that the most virulent Pythium taxa were sampled only from the native range. The greater virulence of Pythium sampled from the native range therefore corresponded to shifts in species composition across ranges rather than variation within a common Pythium species. Prunus serotina still encounters Pythium in its non-native range but encounters less virulent taxa. Elucidating patterns of enemy virulence in native and nonnative ranges adds to our understanding of how invasive plants escape disease. Moreover, this strategy may identify resident enemies in the non-native range that could be used to manage invasive plants.
Burrowing nematodes from Colombia and their relationship with Radopholus similis populations,R. arabocoffeae and R. duriophilus
Múnera Uribe, G.E. ; Bert, W. ; Vierstraete, A.R. ; Peña, E. de la; Moens, M. ; Decraemer, W. - \ 2010
Nematology 12 (2010)4. - ISSN 1388-5545 - p. 619 - 629.
fragment-length-polymorphism - multiple sequence alignment - plant-parasitic nematodes - sp-n. nematoda - phylogenetic analysis - molecular phylogeny - ribosomal-rna - dna - pratylenchidae - tylenchida
Two burrowing nematode populations from Colombia were characterised using morphological, morphometric and molecular criteria. The morphological and morphometric characters of the two populations did not differ from those of Radopholus similis. The phylogenetic analysis based on sequence comparison of 18S, D2D3 regions of these populations with those of Radopholus sp., R. similis and other Tylenchomorpha from GenBank confirmed the close molecular relationship between the genus Radopholus and the Hoplolaimidae. The consensus tree based on the comparison of ITS1-5.8-ITS2 rDNA sequences of the Colombian populations with R. similis (many sources), R. arabocoffeae and R. duriophilus from GenBank grouped the Colombian populations in a clade which also included R. similis from different localities. Other R. similis populations grouped in separated clades, which were closely related to the clade containing R. arabocoffeae and R. duriophilus. The high genetic variability among the R. similis populations was observed and confirmed by the high ITS1-5.8-ITS2 sequence divergence within the R. similis populations studied (5.4%) which was comparable to the divergence (4.2-6.9%) between the Radopholus species included in the analysis. These findings and the unresolved phylogenetic placement of R. arabocoffeae and R. duriophilus among R. similis suggests that the burrowing nematode could be a species complex. Limited information on the variability of the 18S and D2D3 region gives an indication of their possible value, besides ITS1-5.8-ITS, as molecular markers within Radopholus. No complete and comprehensible relation was found between the phylogenetic position of the Radopholus populations and their geographical origin or host
Preliminary insight into the age and origin of the Labeobarbus fish species flock from Lake Tana (Ethiopia) using the mtDNA cytochrome b gene
Graaf, M. de; Megens, H.J.W.C. ; Samallo, J. ; Sibbing, F.A. - \ 2010
Molecular Phylogenetics and Evolution 54 (2010)2. - ISSN 1055-7903 - p. 336 - 343.
late pleistocene desiccation - barbus-intermedius complex - cichlid fishes - molecular phylogeny - reproductive segregation - ecological divergence - dna-sequences - east-africa - cyprinidae - speciation
The high diversity of Cyprinid fish in Ethiopia’s Lake Tana appears to be an example of ecological differentiation and assortative mating leading to rapid sympatric speciation. Lake Tana’s Labeobarbus species flock consists of 15 morphological and ecological distinct species. This is the first attempt to determine the age and origin and inter-species relationships of Lake Tana’s Labeobarbus species using the mtDNA cytochrome b gene. Analysis of cytchrome b sequences shows that Lake Tana’s species flock appears to be young but the present dataset did not unequivocally support monophyly of Lake Tana’s species. Additional markers are needed to determine whether Lake Tana’s labeobarbs originated from a single or multiple incursion(s) of ancestral L. intermedius in the Lake Tana drainage basin, or the disruption of an ancient continuous riverine population by the emergence of the Tissisat waterfalls. Adaptive radiation and speciation within Lake Tana’s Labeobarbus species flock may have occurred in the last 10,000–25,000 years, following the desiccation of Lake Tana around 17,000 years ago, at the same time as Lake Victoria, however, obtaining more data using other (nuclear) markers is urgently required
Multi-locus phylogeny of Pleosporales: a taxonomic, ecological and evolutionary re-evaluation
Zhang, Y. ; Schoch, C.L. ; Fournier, J. ; Crous, P.W. ; Gruyter, J. de; Woudenberg, J.H.C. ; Hirayama, K. ; Tanaka, K. ; Pointing, S.B. ; Spatafora, J.W. ; Hyde, K.D. - \ 2009
Studies in Mycology 64 (2009)1. - ISSN 0166-0616 - p. 85 - 102.
ribosomal dna-sequences - stagonospora-nodorum - molecular phylogeny - leptosphaeria-maculans - phaeosphaeria-nodorum - multigene phylogeny - multiple alignment - endophytic fungi - sp-nov - ascomycota
Five loci, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, are used for analysing 129 pleosporalean taxa representing 59 genera and 15 families in the current classification of Pleosporales. The suborder Pleosporineae is emended to include four families, viz. Didymellaceae, Leptosphaeriaceae, Phaeosphaeriaceae and Pleosporaceae. In addition, two new families are introduced, i.e. Amniculicolaceae and Lentitheciaceae. Pleomassariaceae is treated as a synonym of Melanommataceae, and new circumscriptions of Lophiostomataceae s. str, Massarinaceae and Lophiotrema are proposed. Familial positions of Entodesmium and Setomelanomma in Phaeosphaeriaceae, Neophaeosphaeria in Leptosphaeriaceae, Leptosphaerulina, Macroventuria and Platychora in Didymellaceae, Pleomassaria in Melanommataceae and Bimuria, Didymocrea, Karstenula and Paraphaeosphaeria in Montagnulaceae are clarified. Both ecological and morphological characters show varying degrees of phylogenetic significance. Pleosporales is most likely derived from a saprobic ancestor with fissitunicate asci containing conspicuous ocular chambers and apical rings. Nutritional shifts in Pleosporales likely occured from saprotrophic to hemibiotrophic or biotrophic.
A class-wide phylogenetic assessment of Dothideomycetes
Schoch, C.L. ; Crous, P.W. ; Groenewald, J.Z. ; Boehm, E.W.A. ; Burgess, T.I. ; Gruyter, J. de; Hoog, G.S. de; Dixon, L.J. ; Grube, M. ; Gueidan, C. ; Harada, Y. ; Hatakeyama, S. ; Hirayama, K. ; Hosoya, T. ; Huhndorf, S.M. ; Hyde, K.D. ; Jones, E.B.G. ; Kohlmeyer, J. ; Kruys, Å. ; Li, Y.M. ; Lücking, R. ; Lumbsch, H.T. ; Marvanová, L. ; Mbatchou, J.S. ; McVay, A.H. ; Miller, A.N. ; Mugambi, G.K. ; Muggia, L. ; Nelsen, M.P. ; Nelson, P. ; Owensby, C.A. ; Phillips, A.J.L. ; Phongpaichit, S. ; Pointing, S.B. ; Pujade-Renaud, V. ; Raja, H.A. ; Rivas Plata, E. ; Robbertse, B. ; Ruibal, C. ; Sakayaroj, J. ; Sano, T. ; Selbmann, L. ; Shearer, C.A. ; Shirouzu, T. ; Slippers, B. ; Suetrong, S. ; Tanaka, K. ; Volkmann-Kohlmeyer, B. ; Wingfield, M.J. ; Wood, A.R. ; Woudenberg, J.H.C. ; Yonezawa, H. ; Zhang, Y. ; Spatafora, J.W. - \ 2009
Studies in Mycology 64 (2009)1. - ISSN 0166-0616 - p. 1 - 15.
ribosomal dna-sequences - multigene phylogenies - molecular phylogeny - maximum-likelihood - multiple alignment - marine ascomycota - rdna sequences - fungi - evolution - classification
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
A phylogenetic tree of nematodes based on about 1200 full-length small subunit ribosomal DNA sequences
Megen, H.H.B. van; Elsen, S.J.J. van den; Holterman, M.H.M. ; Karssen, G. ; Mooijman, P.J.W. ; Bongers, A.M.T. ; Holovachov, O.V. ; Bakker, J. ; Helder, J. - \ 2009
Nematology 11 (2009)6. - ISSN 1388-5545 - p. 927 - 950.
n.-sp nematoda - molecular phylogeny - species nematoda - 18s rdna - rhabditidae - evolution - dorylaimida - longidoridae - cephalobina - coleoptera
As a result of the scarcity of informative morphological and anatomical characters, nematode systematics have always been volatile. Differences in the appreciation of these characters have resulted in numerous classifications and this greatly confuses scientific communication. An advantage of the use of molecular data is that it allows for an enormous expansion of the number of characters. Here we present a phylogenetic tree based on 1215 small subunit ribosomal DNA sequences (ca 1700 bp each) covering a wide range of nematode taxa. Of the 19 nematode orders mentioned by De Ley et al. (2006) 15 are represented here. Compared with Holterman et al. (2006) the number of taxa analysed has been tripled. This did not result in major changes in the clade subdivision of the phylum, although a decrease in the number of well supported nodes was observed. Especially at the family level and below we observed a considerable congruence between morphology and ribosomal DNA-based nematode systematics and, in case of discrepancies, morphological or anatomical support could be found for the alternative grouping in most instances. The extensiveness of convergent evolution is one of the most striking phenomena observed in the phylogenetic tree presented here - it is hard to find a morphological, ecological or biological characteristic that has not arisen at least twice during nematode evolution. Convergent evolution appears to be an important additional explanation for the seemingly persistent volatility of nematode systematics.
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