scholarly journals Molecular Phylogenetic Analyses of Verticillium fungicola and Related Species Causing Dry Bubble Disease of the Cultivated Button Mushroom, Agaricus bisporus

2001 ◽  
Vol 91 (9) ◽  
pp. 905-912 ◽  
Author(s):  
P. D. Collopy ◽  
M. L. Largeteau-Mamoun ◽  
C. P. Romaine ◽  
D. J. Royse
Keyword(s):  
Sequence Analysis ◽  
North American ◽  
Type Strain ◽  
Phylogenetic Analyses ◽  
Rdna Sequence ◽  
Nuclear Ribosomal Dna ◽  
Transcriptional Unit ◽  
Korean Isolate ◽  
Verticillium Fungicola ◽  
Molecular Phylogenetic

Molecular phylogenetic analyses were performed on 40 isolates of Verticillium fungicola collected from various Pennsylvania mushroom farms in 1999 and 28 isolates of Verticillium spp. collected during the last 50 years from various geographic locations. Sequence analysis of internal transcribed spacers 1 and 2 (ITS1 and ITS2) and 5.8S regions of the nuclear ribosomal DNA (rDNA) transcriptional unit and analysis of random amplified polymorphic DNA (RAPD) data were performed for the 68 isolates of Verticillium spp. Identical rDNA sequences were obtained for all 40 Pennsylvania isolates collected during 1999, 13 North American isolates collected during the last 50 years, and the ex-type strain of V. fungicola var. aleophilum. Sequence analysis of European isolates revealed a close relationship to the ex-type strain V. fungicola var. fungicola. No European-like isolates of V. fungicola var. fungicola were detected in the collection of North American isolates examined. Results from six decamer RAPD primers strongly indicate the presence of a clonal population of V. fungicola among Pennsylvania isolates. In addition, RAPD data delineated a Korean isolate (DC130) and ex-type strain V. fungicola var. aleophilum from the North American group. Virulence assays, based on spore inoculation of mushroom pilei, revealed variation corresponding to each neighbor-joining and RAPD grouping. All isolates with rDNA sequence and RAPD grouping similarity to ex-type strains V. fungicola var. aleophilum and V. fungicola var. fungicola displayed the highest level of virulence. Based on rDNA sequence and RAPD analyses, isolates displaying reduced or no virulence were distantly related to these two varieties. All results obtained for the analyses of ex-type strain V. fungicola var. flavidum suggested that this fungal isolate should not be considered a variety of V. fungicola, but rather a distinct species.

A molecular phylogenetic and DNA barcode assessment of the tribe Pterosiphonieae (Ceramiales, Rhodophyta) emphasizing the Northeast Pacific

Botany ◽  
2016 ◽  
Vol 94 (10) ◽  
pp. 917-939 ◽  
Author(s):  
Amanda M. Savoie ◽  
Gary W. Saunders
Keyword(s):  
South African ◽  
North American ◽  
New Genus ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Dna Barcode ◽  
Sensu Stricto ◽  
North American Species ◽  
African Species ◽  
Molecular Phylogenetic

Sequence data (COI-5P and rbcL) for North American members of the tribe Pterosiphonieae were compared with collections from around the world. Phylogenetic analyses resolved Pterosiphonia as polyphyletic and many species required transfer to other genera. In our analyses Pterosiphonia sensu stricto included only the type species P. cloiophylla (C. Agardh) Falkenberg and P. complanata (Clemente) Falkenberg, as well as the South African species P. stegengae sp. nov. A new genus, Xiphosiphonia gen. nov., was described for X. ardreana (Maggs & Hommersand) comb. nov., X. pennata (C. Agardh) comb. nov., and X. pinnulata (Kützing) comb. nov. Some Asian, European and North American species previously attributed to Pterosiphonia were transferred to Symphyocladia including S. baileyi (Harvey) comb. nov., S. dendroidea (Montagne) comb. nov., S. plumosa nom. nov. (for P. gracilis Kylin), and S. tanakae (S. Uwai & M. Masuda) comb. nov. We also described two new North American species, Symphyocladia brevicaulis sp. nov. and S. rosea sp. nov. Other species formed a well-supported clade for which the genus name Polyostea Ruprecht was resurrected. Included in Polyostea were P. arctica (J. Agardh) comb. nov., P. bipinnata (Postels & Ruprecht) Ruprecht, P. hamata (E.S. Sinova) comb. nov., and P. robusta (N.L. Gardner) comb. nov.

scholarly journals Taxonomic revision of Russula subsection Amoeninae from South Korea

MycoKeys ◽  
2020 ◽  
Vol 75 ◽  
pp. 1-29
Author(s):  
Komsit Wisitrassameewong ◽  
Myung Soo Park ◽  
Hyun Lee ◽  
Aniket Ghosh ◽  
Kanad Das ◽  
...  
Keyword(s):  
New Species ◽  
South Korea ◽  
Central America ◽  
North American ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Taxonomic Revision ◽  
Molecular Phylogenetic ◽  
Pileus Surface ◽  
A New Species

Russula subsection Amoeninae is morphologically defined by a dry velvety pileus surface, a complete absence of cystidia with heteromorphous contents in all tissues, and spores without amyloid suprahilar spot. Thirty-four species within subsection Amoeninae have been published worldwide. Although most Russula species in South Korea have been assigned European or North American names, recent molecular studies have shown that Russula species from different continents are not conspecific. Therefore, the present study aims to: 1) define which species of Russula subsection Amoeninae occur on each continent using molecular phylogenetic analyses; 2) revise the taxonomy of Korean Amoeninae. The phylogenetic analyses using the internal transcribed spacer (ITS) and multilocus sequences showed that subsection Amoeninae is monophyletic within subgenus Heterophyllidiae section Heterophyllae. A total of 21 Russula subsection Amoeninae species were confirmed from Asia, Australia, Europe, North America, and Central America, and species from different continents formed separate clades. Three species were recognized from South Korea and were clearly separated from the European and North American species. These species are R. bella, also reported from Japan, a new species described herein, Russula orientipurpurea, and a new species undescribed due to insufficient material.

scholarly journals Six new species and reports of Hydnum (Cantharellales) from eastern North America

MycoKeys ◽  
2018 ◽  
Vol 42 ◽  
pp. 35-72 ◽  
Author(s):  
Rachel A. Swenie ◽  
Timothy J. Baroni ◽  
P. Brandon Matheny
Keyword(s):  
North America ◽  
North American ◽  
Phylogenetic Analyses ◽  
Eastern North America ◽  
Phylogenetic Species ◽  
Additional Species ◽  
Taxonomic Descriptions ◽  
Molecular Phylogenetic ◽  
Herbarium Collections ◽  
Environmental Sequences

Five species of Hydnum have been generally recognized from eastern North America based on morphological recognition: H.albidum, H.albomagnum, H.repandum and varieties, H.rufescens, and H.umbilicatum. Other unique North American species, such as H.caespitosum and H.washingtonianum, are either illegitimately named or considered synonymous with European taxa. Here, seventeen phylogenetic species of Hydnum are detected from eastern North America based on a molecular phylogenetic survey of ITS sequences from herbarium collections and GenBank data, including environmental sequences. Based on current distribution results, sixteen of these species appear endemic to North America. Of these, six species are described as new: H.alboaurantiacum, H.cuspidatum, H.ferruginescens, H.subconnatum, H.subtilior, and H.vagabundum. Geographic range extensions and taxonomic notes are provided for five additional species recently described as new from eastern North America. A new name, H.geminum, is proposed for H.caespitosum Banning ex Peck, non Valenti. Overall, species of Hydnum are best recognized by a combination of morphological and molecular phylogenetic analyses. Taxonomic descriptions are provided for seventeen species, including epitype designations for H.albidum, H.albomagnum, and H.umbilicatum, taxa described more than 100 years ago, and molecular annotation of the isotype of H.washingtonianum. Photographs and a key to eastern North American Hydnum species are presented.

A revision of the Leptogium saturninum group in North America

2016 ◽  
Vol 48 (5) ◽  
pp. 387-421 ◽  
Author(s):  
Daphne F. STONE ◽  
James W. HINDS ◽  
Frances L. ANDERSON ◽  
James C. LENDEMER
Keyword(s):  
North American ◽  
Morphological Study ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Lower Surface ◽  
Molecular Data ◽  
The North ◽  
Molecular Phylogenetic ◽  
Nrits Sequence

AbstractA revision of the North American members of the Leptogium saturninum group (i.e. species with long lower-surface hairs, isidia, and usually smooth upper surface) is presented based on molecular phylogenetic analyses of mtSSU and nrITS sequence data, together with an extensive morphological study. Three species supported by both molecular and morphological characteristics are recognized: L. acadiense sp. nov. (distinguished by granular saturninum-type isidia, medulla composed of irregularly arranged or perpendicular hyphae), L. cookii sp. nov. (distinguished by cylindrical saturninum-type isidia) and L. hirsutum (distinguished by hirsutum-type isidia and medulla composed of loosely intertwined hyphae). One species supported by morphological characteristics, but for which no molecular data could be generated, is also recognized: L. compactum sp. nov. (distinguished by hirsutum-type isidia and medulla composed of tightly packed hyphae). Finally, L. saturninum (distinguished by granular saturninum-type isidia and medulla composed of perpendicular and parallel hyphae) is supported by morphological characteristics but molecular data from geographically diverse populations, including those near the type locality, indicate that the morphologically defined species is paraphyletic. Leptogium burnetiae is excluded from North American based on morphological study of the type. The species are described and illustrated in detail, and are distinguished morphologically by their isidium development, morphology of mature isidia, and pattern of hyphae in the medulla in transverse sections near lobe margins. A key to the members of the L. saturninum group and related species is also presented.

scholarly journals Ravenelia piepenbringiae and Ravenelia hernandezii, two new rust species on Senegalia (Fabaceae, Mimosoideae) from Panama and Costa Rica

MycoKeys ◽  
2018 ◽  
Vol 41 ◽  
pp. 51-63 ◽  
Author(s):  
M. Ebinghaus ◽  
D. Begerow
Keyword(s):  
South Africa ◽  
Costa Rica ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Rdna Sequence ◽  
28S Rdna ◽  
Host Genus ◽  
Rdna Sequence Data ◽  
Molecular Phylogenetic ◽  
28S Rdna Sequence

Two new rust species, Raveneliapiepenbringiae and R.hernandezii (Pucciniales) on Senegalia spp. (Fabaceae) are described from the Neotropics (Panama, Costa Rica). A key to the species on neotropical Senegalia spp. is provided. Molecular phylogenetic analyses based on 28S rDNA sequence data suggest that the representatives of Senegalia rusts distributed in the neotropics evolved independently from species known from South Africa. This is further supported by the teliospore morphology, which is characterised by uniseriate cysts in the neotropical Senegalia rusts and contrasting multiseriate cysts in the paleotropic Ravenelia species that infect this host genus.

scholarly journals Tamilnaduibacter salinus gen. nov., sp. nov., a halotolerant gammaproteobacterium within the family Alteromonadaceae, isolated from a salt pan in Tamilnadu, India

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3248-3255 ◽  
Author(s):  
Ashish Verma ◽  
Poonam Mual ◽  
Shanmugam Mayilraj ◽  
Srinivasan Krishnamurthi
Keyword(s):  
Type Strain ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Carbon Sources ◽  
Rrna Gene ◽  
The Novel ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Salt Pan ◽  
Slow Growing

Two novel Gram-stain-negative, slow-growing, halotolerant strains with rod-shaped cells, designated as strains Mi-7T and Mi-8, which formed pin-point colonies on halophilic media were isolated during a study into the microbial diversity of a salt pan in the state of Tamilnadu, India. Both the strains had an obligate requirement for 1 % (w/v) NaCl for growth and were halotolerant, growing at NaCl concentrations of up to 20 % (w/v) in media. The strains, however, showed an inability to utilize the majority of substrates tested as sole carbon sources for growth and in fermentation reactions. Molecular phylogenetic analyses, based on 16S rRNA gene sequence revealed their closest phylogenetic neighbours to be members of the genus Marinobacter, with whom they showed the highest sequence similarity of 93.6 % and even less with the type strain of the type species, Marinobacter hydrocarbonoclasticus DSM 8798T (91.1 %). Similarities with other genera within the family Alteromonadaceae were below 91.0 %. However, the two strains were very closely related to each other with 99.9 % sequence similarity, and DNA–DNA hybridization analyses confirmed their placement in the same species. The DNA G+C content of both strains was 65 mol%. Using the polyphasic taxonomic data obtained from this study, strains Mi-7T and Mi-8 represent two strains of the same species of a novel genus for which the name Tamilnaduibacter salinus gen. nov., sp. nov., is proposed; the type strain of the novel species is Mi-7T ( = MTCC 12009T = DSM 28688T).

Morphological characteristics and phylogenetic analyses revealed a new Calocybe (Lyophyllaceae, Basidiomycota) species from northeast China

Phytotaxa ◽  
2021 ◽  
Vol 490 (2) ◽  
pp. 203-210
Author(s):  
JIZE XU ◽  
XIAODONG YU ◽  
CHUNLAN ZHANG ◽  
YU LI
Keyword(s):  
New Species ◽  
Internal Transcribed Spacer ◽  
Northeast China ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Morphological Characteristics ◽  
Nuclear Ribosomal Dna ◽  
Full Description ◽  
Molecular Phylogenetic ◽  
A New Species

A new species, Calocybe decurrens, is illustrated and described in detail based on morphological characteristics and phylogenetic analyses. Calocybe decurrens is mainly characterized by its decurrent gills and by its stipe that discolors upon maturation. Molecular phylogenetic analyses were based on the internal transcribed spacer (ITS1-5.8S-ITS2) and the large subunit of the nuclear ribosomal DNA (nrLSU) sequences. The results indicated that its affiliation is in genus Calocybe, where it occupies an isolated position. A full description, color images, illustrations and a phylogenetic tree to show the placement of the new species are provided.

scholarly journals Bacillus novalis sp. nov., Bacillus vireti sp. nov., Bacillus soli sp. nov., Bacillus bataviensis sp. nov. and Bacillus drentensis sp. nov., from the Drentse A grasslands

2004 ◽  
Vol 54 (1) ◽  
pp. 47-57 ◽  
Author(s):  
Jeroen Heyrman ◽  
Bram Vanparys ◽  
Niall A. Logan ◽  
An Balcaen ◽  
Marina Rodríguez-Díaz ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rdna ◽  
Type Strain ◽  
Biochemical Characterization ◽  
Agricultural Research ◽  
Research Area ◽  
Fatty Acid Analysis ◽  
Rdna Sequence ◽  
16S Rdna Sequence ◽  
16S Rdna Sequence Analysis

A group of 42 isolates were isolated from the soil of several disused hay fields, in the Drentse A agricultural research area (The Netherlands), that were taken out of production at different times. The group represents hitherto-uncultured Bacillus lineages that have previously been found, by a non-cultural method, to be predominant in soil. The strains were subjected to a polyphasic taxonomic study, including (GTG)5-PCR, 16S rDNA sequence analysis, DNA–DNA hybridizations, DNA base-ratio determination, fatty acid analysis and morphological and biochemical characterization. By comparing the groupings obtained by (GTG)5-PCR and 16S rDNA sequence analysis, six clusters of similar strains could be recognized. A DNA–DNA relatedness study showed that these clusters represented five novel genospecies. Further analysis supported the proposal of five novel species in the genus Bacillus, namely Bacillus novalis sp. nov. (type strain IDA3307T=R-15439T=LMG 21837T=DSM 15603T), Bacillus vireti sp. nov. (type strain IDA3632T=R-15447T=LMG 21834T=DSM 15602T), Bacillus soli sp. nov. (type strain IDA0086T=R-16300T=LMG 21838T=DSM 15604T), Bacillus bataviensis sp. nov. (type strain IDA1115T=R-16315T=LMG 21833T=DSM 15601T) and Bacillus drentensis sp. nov. (type strain IDA1967T=R-16337T=LMG 21831T=DSM 15600T).

Sphingomonas yabuuchiae sp. nov. and Brevundimonas nasdae sp. nov., isolated from the Russian space laboratory Mir

2004 ◽  
Vol 54 (3) ◽  
pp. 819-825 ◽  
Author(s):  
Ying Li ◽  
Yoshiaki Kawamura ◽  
Nagatoshi Fujiwara ◽  
Takashi Naka ◽  
Hongsheng Liu ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rdna ◽  
Related Species ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Biochemical Properties ◽  
Rdna Sequence ◽  
Rrna Gene ◽  
16S Rdna Sequence

On the basis of phenotypic and genotypic characteristics and 16S rRNA gene sequence analysis, novel species belonging to the genera Sphingomonas and Brevundimonas were identified from samples taken from the Russian space laboratory Mir. Strain A1-18T was isolated from the air. 16S rDNA sequence analysis showed that strain A1-18T formed a coherent cluster with Sphingomonas sanguinis, Sphingomonas parapaucimobilis, Sphingomonas paucimobilis and Sphingomonas roseiflava with sequence similarity of 97·5–98·6 %. Similar to other Sphingomonas species, the G+C content was 66·1 mol%, but DNA–DNA hybridization rates at optimal temperatures among these related species were only 24·7–51·7 %. Strain A1-18T can be differentiated biochemically from related species. Strain W1-2BT was isolated from condensation water. It forms a distinct lineage within the genus Brevundimonas, forming a coherent cluster with Brevundimonas vesicularis, Brevundimonas aurantiaca and Brevundimonas intermedia. 16S rDNA sequence similarities were 98·6–99·5 % and the G+C content was 66·5 mol%, similar to other Brevundimonas species, but DNA–DNA relatedness was only 50·2–54·8 %. Strain W1-2BT also showed some differential biochemical properties from its related species. A series of polyphasic taxonomic studies led to the proposal of two novel species, Sphingomonas yabuuchiae sp. nov. (type strain A1-18T=GTC 868T=JCM 11416T=DSM 14562T) and Brevundimonas nasdae sp. nov. (type strain W1-2BT=GTC 1043T=JCM 11415T=DSM 14572T).

scholarly journals Lichens or endophytes? The enigmatic genus Leptosillia in the Leptosilliaceae fam. nov. (Xylariales), and Furfurella gen. nov. (Delonicicolaceae)

2019 ◽  
Vol 42 (1) ◽  
pp. 228-260 ◽  
Author(s):  
H. Voglmayr ◽  
M.B. Aguirre-Hudson ◽  
H.G. Wagner ◽  
S. Tello ◽  
W.M. Jaklitsch
Keyword(s):  
Dna Sequence ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Rdna Sequence ◽  
Lsu Rdna ◽  
Tropical Regions ◽  
Dna Sequence Data ◽  
New Family ◽  
Rdna Sequence Data ◽  
Molecular Phylogenetic

Based on DNA sequence data, the genus Leptosillia is shown to belong to the Xylariales. Molecular phylogenetic analyses of ITS-LSU rDNA sequence data and of a combined matrix of SSU-ITS-LSU rDNA, rpb1, rpb2, tef1 and tub2 reveal that the genera Cresporhaphis and Liberomyces are congeneric with Leptosillia. Coelosphaeria fusariospora, Leptorhaphis acerina, Leptorhaphis quercus f. macrospora, Leptorhaphis pinicola, Leptorhaphis wienkampii, Liberomyces pistaciae, Sphaeria muelleri and Zignoëlla slaptonensis are combined in Leptosillia, and all of these taxa except for C. fusariospora, L. pinicola and L. pistaciae are epitypified. Coelosphaeria fusariospora and Cresporhaphis rhoina are lectotypified. Liberomyces macrosporus and L. saliciphilus, which were isolated as phloem and sapwood endophytes, are shown to be synonyms of Leptosillia macrospora and L. wienkampii, respectively. All species formerly placed in Cresporhaphis that are now transferred to Leptosillia are revealed to be non-lichenized. Based on morphology and ecology, Cresporhaphis chibaensis is synonymised with Rhaphidicyrtis trichosporella, and C. rhoina is considered to be unrelated to the genus Leptosillia, but its generic affinities cannot be resolved in lack of DNA sequence data. Phylogenetic analyses place Leptosillia as sister taxon to Delonicicolaceae, and based on morphological and ecological differences, the new family Leptosilliaceae is established. Furfurella, a new genus with the three new species, F. luteostiolata, F. nigrescens and F. stromatica, growing on dead branches of mediterranean fabaceous shrubs from tribe Genisteae, is revealed to be the closest relative of Delonicicola in the family Delonicicolaceae, which is emended. ITS rDNA sequence data retrieved from GenBank demonstrate that the Leptosilliaceae were frequently isolated or sequenced as endophytes from temperate to tropical regions, and show that the genus Leptosillia represents a widely distributed component of endophyte communities of woody plants.

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