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A monograph of Allantonectria, Nectria, and Pleonectria (Nectriaceae, Hypocreales, Ascomycota) and their pycnidial, sporodochial, and synnematous anamorphs  [cached]
Y. Hirooka,A.Y Rossman,G.J Samuels,C. Lechat
Studies in Mycology , 2012,
Abstract: Although Nectria is the type genus of Nectriaceae (Hypocreales, Sordariomycetes, Pezizomycotina, Ascomycota), the systematics of the teleomorphic and anamorphic state of Nectria sensu Rossman has not been studied in detail. The objectives of this study are to 1) provide a phylogenetic overview to determine if species of Nectria with Gyrostroma, Tubercularia, and Zythiostroma anamorphs form a monophyletic group; 2) define Nectria, segregate genera, and their species using morphologically informative characters of teleomorphic and anamorphic states; and 3) provide descriptions and illustrations of these genera and species. To accomplish these objectives, results of phylogenetic analyses of DNA sequence data from six loci (act, ITS, LSU, rpb1, tef1 and tub), were integrated with morphological characterisations of anamorphs and teleomorphs. Results from the phylogenetic analyses demonstrate that species previously regarded as the genus Nectria having Gyrostroma, Tubercularia, and Zythiostroma anamorphs belong in two major paraphyletic clades. The first major clade regarded as the genus Pleonectria contains 26 species with ascoconidia produced by ascospores in asci, perithecial walls having bright yellow scurf, and immersed or superficial pycnidial anamorphs (Zythiostroma = Gyrostroma). A lineage basal to the Pleonectria clade includes Nectria miltina having very small, aseptate ascospores, and trichoderma-like conidiophores and occurring on monocotyledonous plants. These characteristics are unusual in Pleonectria, thus we recognise the monotypic genus Allantonectria with Allantonectria miltina. The second major clade comprises the genus Nectria sensu stricto including the type species, N. cinnabarina, and 28 additional species. Within the genus Nectria, four subclades exist. One subclade includes species with sporodochial anamorphs and another with synnematous anamorphs. The other two paraphyletic subclades include species that produce abundant stromata in which the large perithecia are immersed, large ascospores, and peculiar anamorphs that form pycnidia or sporodochia either on their natural substrate or in culture. In this study the evolution of species, morphology, and ecology of the three genera, Allantonectria, Nectria, and Pleonectria, are discussed based on the phylogenetic analyses. In addition, descriptions, illustrations, and keys for identification are presented for the 56 species in Allantonectria, Nectria, and Pleonectria.
European species of Hypocrea Part 1. The green-spored species
Walter M. Jaklitsch
Studies in Mycology , 2009,
Abstract: At present 75 species of Hypocrea have been identified in temperate Europe. Nineteen green-spored species and their Trichoderma asexual states are here described in detail. Extensive searches for Hypocrea teleomorphs in 14 European countries, with emphasis on Central Europe, yielded more than 620 specimens within five years. The morphology of fresh and dry stromata was studied. In addition, available types of species described from Europe were examined. Cultures were prepared from ascospores and used to study the morphology of cultures and anamorphs, to determine growth rates, and to extract DNA that was used for amplification and sequencing of three genetic markers. ITS was used for identification, while RNA polymerase II subunit b (rpb2) and translation elongation factor 1 alpha (tef1) were analyzed for phylogenetic reconstruction of the genus.Several unexpected findings resulted from this project: 1) The previous view that only a small number of Trichoderma species form a teleomorph is erroneous. 2) All expectations concerning the number of species in Europe are by far exceeded. Seventy-five species of Hypocrea, two species of Protocrea, and Arachnocrea stipata, are herein identified in temperate Europe, based on the ITS identification routine using fresh material, on species described earlier without molecular data and on species recently described but not collected during this project. 3) Current data suggest that the biodiversity of Hypocrea / Trichoderma above soil exceeds the number of species isolated from soil. 4) The number of Trichoderma species forming hyaline conidia has been considered a small fraction. In Europe, 26 species of those forming teleomorphs produce hyaline conidia, while 42 green-conidial species are known. Three of the detected Hypocrea species do not form an anamorph in culture, while the anamorph is unknown in four species, because they have never been cultured.This work is a preliminary account of Hypocrea and their Trichoderma anamorphs in Europe. Of the hyaline-spored species, H. minutispora is by far the most common species in Europe, while of the green-spored species this is H. strictipilosa.General ecology of Hypocrea is discussed. Specific associations, either with host fungi or trees have been found, but the majority of species seems to be necrotrophic on diverse fungi on wood and bark.The taxonomy of the genus will be treated in two parts. In this first part 19 species of Hypocrea with green ascospores, including six new teleomorph and five new anamorph species, are described in detail. All green-spored species be
Selection of a DNA barcode for Nectriaceae from fungal whole-genomes
ZhaoQing Zeng,Peng Zhao,Jing Luo,WenYing Zhuang,ZhiHe Yu
Science China Life Sciences , 2012, DOI: 10.1007/s11427-012-4266-2
Abstract: A DNA barcode is a short segment of sequence that is able to distinguish species. A barcode must ideally contain enough variation to distinguish every individual species and be easily obtained. Fungi of Nectriaceae are economically important and show high species diversity. To establish a standard DNA barcode for this group of fungi, the genomes of Neurospora crassa and 30 other filamentous fungi were compared. The expect value was treated as a criterion to recognize homologous sequences. Four candidate markers, Hsp90, AAC, CDC48, and EF3, were tested for their feasibility as barcodes in the identification of 34 well-established species belonging to 13 genera of Nectriaceae. Two hundred and fifteen sequences were analyzed. Intra- and inter-specific variations and the success rate of PCR amplification and sequencing were considered as important criteria for estimation of the candidate markers. Ultimately, the partial EF3 gene met the requirements for a good DNA barcode: No overlap was found between the intra- and inter-specific pairwise distances. The smallest inter-specific distance of EF3 gene was 3.19%, while the largest intra-specific distance was 1.79%. In addition, there was a high success rate in PCR and sequencing for this gene (96.3%). CDC48 showed sufficiently high sequence variation among species, but the PCR and sequencing success rate was 84% using a single pair of primers. Although the Hsp90 and AAC genes had higher PCR and sequencing success rates (96.3% and 97.5%, respectively), overlapping occurred between the intra- and inter-specific variations, which could lead to misidentification. Therefore, we propose the EF3 gene as a possible DNA barcode for the nectriaceous fungi.
Acute/subacute cerebral infarction (ASCI) in HIV-negative adults with cryptococcal meningoencephalitis (CM): a MRI-based follow-up study and a clinical comparison to HIV-negative CM adults without ASCI
Shu-Fang Chen, Cheng-Hsien Lu, Chun-Chung Lui, Chi-Ren Huang, Yao-Chung Chuang, Teng-Yeow Tan, Nai-Wen Tsai, Chiung-Chih Chang, Wan-Chen Tsai, Wen-Neng Chang
BMC Neurology , 2011, DOI: 10.1186/1471-2377-11-12
Abstract: The clinical characteristics and a series of brain MRI findings of seven CM adults with ASCI were enrolled for analysis. The clinical characteristics of another 30 HIV-negative CM adults who did not have ASCI were also included for a comparative analysis.The seven HIV-negative CM adults with ASCI were four men and three women, aged 46-78 years. Lacunar infarction was the type of ASCI, and 86% (6/7) of the ACSI were multiple infarctions distributed in both the anterior and posterior cerebrovascular territories. The seven CM patients with ASCI were significantly older and had a higher rate of DM and previous stroke than the other 30 CM adults without ASCI. They also had a higher incidence of consciousness disturbance at presentation and had a poor prognosis.ASCI was found in 18.9% (7/37) of HIV-negative CM adults. Serial MRI follow-up studies may allow a better delineation of ASCI in this specific group of infectious disease and multiple lacunar infarctions was the most common type. Older in age and presence of DM and previous stroke were the significant underlying conditions. CM patients with ASCI also had a poor therapeutic outcome.Cryptococcal meningoencephalitis (CM) caused by Cryptococcus neoformans infection is a serious central nervous system (CNS) infection in immunocompromised patients [1]. Among the immunocompromised states, human immunodeficiency virus (HIV) infection is an important one [1], but CM also occurs in individuals with an apparently immunocompetent state [2-5]. Disturbed cerebral blood flow in the early stages of CM has been noted [6], and the occurrence of cerebral infarct may influence the therapeutic outcome [6,7]. There are case reports of cerebral infarction in CM [8-12], but cranial magnetic resonance imaging (MRI)-based assessment has been rarely examined solely. Cerebrovascular diseases are also important neurologic complications in HIV-infected patients [8,13], therefore, the HIV-positive status may interfere with the interpretation of
Two-Gene Phylogeny of Bright-Spored Myxomycetes (Slime Moulds, Superorder Lucisporidia)  [PDF]
Anna Maria Fiore-Donno, Fionn Clissmann, Marianne Meyer, Martin Schnittler, Thomas Cavalier-Smith
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0062586
Abstract: Myxomycetes, or plasmodial slime-moulds, are one of the largest groups in phylum Amoebozoa. Nonetheless, only ~10% are in the database for the small subunit (SSU) ribosomal RNA gene, the most widely used gene for phylogenetics and barcoding. Most sequences belong to dark-spored Myxomycetes (order Fuscisporida); the 318 species of superorder Lucisporidia (bright-spored) are represented by only eleven genuine sequences. To compensate for this, we provide 66 new sequences, 37 SSU rRNA and 29 elongation factor 1-alpha (EF-1α), for 82% of the genera of Lucisporidia. Phylogenetic analyses of single- and two-gene alignments produce congruent topologies and reveal both morphological characters that have been overemphasised and those that have been overlooked in past classifications. Both classical orders, Liceida and Trichiida, and several families and genera are para/polyphyletic; some previously unrecognised clades emerge. We discuss possible evolutionary pathways. Our study fills a gap in the phylogeny of Amoebozoa and provides an extensive SSU rRNA sequence reference database for environmental sampling and barcoding. We report a new group I intron insertion site for Myxomycetes in one Licea.
Not as Ubiquitous as We Thought: Taxonomic Crypsis, Hidden Diversity and Cryptic Speciation in the Cosmopolitan Fungus Thelonectria discophora (Nectriaceae, Hypocreales, Ascomycota)  [PDF]
Catalina Salgado-Salazar, Amy Y. Rossman, Priscila Chaverri
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0076737
Abstract: The distribution of microbial species, including fungi, has long been considered cosmopolitan. Recently, this perception has been challenged by molecular studies in historical biogeography, phylogeny and population genetics. Here we explore this issue using the fungal morphological species Thelonectria discophora, one of the most common species of fungi in the family Nectriaceae, encountered in almost all geographic regions and considered as a cosmopolitan taxon. In order to determine if T. discophora is a single cosmopolitan species or an assemblage of sibling species, we conducted various phylogenetic analyses, including standard gene concatenation, Bayesian concordance methods, and coalescent-based species tree reconstruction on isolates collected from a wide geographic range. Results show that diversity among isolates referred as T. discophora is greatly underestimated and that it represents a species complex. Within this complex, sixteen distinct highly supported lineages were recovered, each of which has a restricted geographic distribution and ecology. The taxonomic status of isolates regarded as T. discophora is reconsidered, and the assumed cosmopolitan distribution of this species is rejected. We discuss how assumptions about geographically widespread species have implications regarding their taxonomy, true diversity, biological diversity conservation, and ecological functions.
Delimitation of Neonectria and Cylindrocarpon (Nectriaceae, Hypocreales, Ascomycota) and related genera with Cylindrocarpon-like anamorphs
P. Chaverri,C. Salgado,Y. Hirooka,A.Y. Rossman
Studies in Mycology , 2011,
Abstract: Neonectria is a cosmopolitan genus and it is, in part, defined by its link to the anamorph genus Cylindrocarpon. Neonectria has been divided into informal groups on the basis of combined morphology of anamorph and teleomorph. Previously, Cylindrocarpon was divided into four groups defined by presence or absence of microconidia and chlamydospores. Molecular phylogenetic analyses have indicated that Neonectria sensu stricto and Cylindrocarpon sensu stricto are phylogenetically congeneric. In addition, morphological and molecular data accumulated over several years have indicated that Neonectria sensu lato and Cylindrocarpon sensu lato do not form a monophyletic group and that the respective informal groups may represent distinct genera. In the present work, a multilocus analysis (act, ITS, LSU, rpb1, tef1, tub) was applied to representatives of the informal groups to determine their level of phylogenetic support as a first step towards taxonomic revision of Neonectria sensu lato. Results show five distinct highly supported clades that correspond to some extent with the informal Neonectria and Cylindrocarpon groups that are here recognised as genera: (1) N. coccinea-group and Cylindrocarpon groups 1 & 4 (Neonectria/Cylindrocarpon sensu stricto); (2) N. rugulosa-group (Rugonectria gen. nov.); (3) N. mammoidea/N. veuillotiana-groups and Cylindrocarpon group 2 (Thelonectria gen. nov.); (4) N. radicicola-group and Cylindrocarpon group 3 (Ilyonectria gen. nov.); and (5) anamorph genus Campylocarpon. Characteristics of the anamorphs and teleomorphs correlate with the five genera, three of which are newly described. New combinations are made for species where their classification is confirmed by phylogenetic data
Phylogeny of some genera in the Nectriaceae (Hypocreales,Ascomycetes) inferred from 28S nrDNA partial sequences
丛赤壳科部分属之间的系统学关系

ZHANG Xiang-Min,ZHUANG Wen-Ying,
张向民
,庄文颖

菌物学报 , 2006,
Abstract: Phylogenetic relationships among 11 genera in the family Nectriaceae, Hypocreales were studied by using analysis of partial sequences of the nuclear large subunit rDNA. The results showed that Cosmospora is possibly not monophyletic, species of the genus tested showed close relationships to 3 different genera i.e. Nectria, Haematonectria, and Neocosmospora; species of Haematonectria and Neocosmospora are very closely related; Lanatonectria is a tenable genus; and Neonectria represented by N. discophora var. discophora is distinct at the generic level.
Sequence and phylogenetic analysis of endopolygalacturonase genes from Alternaria small-spored species
小孢子链格孢endoPG基因核苷酸序列分析及系统发育研究

YUE Hai-Mei,ZHANG Rong,SUN Guang-Yu,
岳海梅
,张荣,孙广宇

微生物学报 , 2007,
Abstract: EndoPG genes of small-spored Alternaria species were amplified with specific primer pairs,most of strains could produce a single same size band.Nucleotide acid and amino acid sequences were compared.It was found that there were some differences in nucleotide and amino acid sequences among the species,such as Alternaria longipes and A.vaisen.Phylogenetic tree were constructed using neighbor-joining method,all of the isolates were distributed in eight eludes.Isolates of A.alternata were clustered into different groups,but A.tenuissima,A.mali,Acitri,A.limoniasperae,A.citriarbusti were assembled to a same group,it showed the species segregation incongruence based on unstable morphologycal characters and molecular data.There are great variations among the small-spored Alternaria species of the endoPG gene sequences,which could provide useful information for phylogenetics of small-spored Alternaria species.
Sequence and phylogenetic analysis of endopolygalacturonase genes from Alternaria small-spored species
小孢子链格孢endoPG基因核苷酸序列分析及系统发育研究

YUE Hai-Mei,ZHANG Rong,SUN Guang-Yu,
岳海梅
,张荣,孙广宇

菌物学报 , 2007,
Abstract: EndoPG genes of small-spored Alternaria species were amplified with specific primer pairs,most of strains could produce a single same size band.Nucleotide acid and amino acid sequences were compared.It was found that there were some differences in nucleotide and amino acid sequences among the species,such as Alternaria longipes and A.vaisen.Phylogenetic tree were constructed using neighbor-joining method,all of the isolates were distributed in eight eludes.Isolates of A.alternata were clustered into different groups,but A. tenuissima,A.mali,A.citri,A.limoniasperae,A.citriarbusti were assembled to a same group,it showed the species segregation incongruence based on unstable morphological characters and molecular data.There are great variations among the small-spored Alternaria species of the endoPG gene sequences,which could provide useful information for phylogenetics of small-spored Alternaria species.
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