On the phylogeny of members of Ceratocystis s.s. and Ophiostoma that possess different anamorphic states, with emphasis on the anamorph genus Leptographium, based on partial ribosomal DNA sequences

2000 ◽  
Vol 78 (7) ◽  
pp. 903-916 ◽  
Author(s):  
Georg Hausner ◽  
James Reid ◽  
Glen R Klassen
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Phylogenetic Distribution ◽  
Rdna Sequences ◽  
Molecular Characters

Phylogenetic analysis of partial ribosomal DNA sequences was undertaken to assess the phylogenetic distribution of ophiostomatoid anamorphs with an emphasis on members of Leptographium and the generic limits of Ceratocystis sensu lato Ell. & Halst. Molecular data identified one group of Ophiostoma species with anamorphs assignable to Pesotum and Leptographium that appears to be monophyletic. This study also showed that, based on molecular characters, Pesotum pini (Hutchison & Reid) Okada and all Leptographium strains tested, including L. terebrantis Barras & Perry, L. lundbergii Lag. & Melin, and L. procerum (Kendr.) Wingf., could be placed among Ophiostoma species. With regard to the anamorphs of Ophiostoma, we determined that the separation of Leptographium from Pesotum, although convenient, is artificial. The partial ribosomal DNA sequences also confirm that Europhium should be considered a synonym of Ophiostoma. The phylogenetic position of species of Ceratocystis sensu lato with Chalara-like, Knoxdaviesia, and Gabarnaudia anamorphs is also discussed.Key words: Ceratocystis, Ophiostoma, Leptographium, partial rDNA sequences, phylogeny.

scholarly journals Sequences of psychrophilic fungi amplified from glacier-preserved ascolichens

2000 ◽  
Vol 78 (11) ◽  
pp. 1450-1459 ◽  
Author(s):  
Paula T DePriest ◽  
Natalia V Ivanova ◽  
Dianne Fahselt ◽  
Vagn Alstrup ◽  
Andrea Gargas
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Large Subunit ◽  
Ice Core ◽  
Small Subunit ◽  
Rdna Sequences ◽  
Three Samples ◽  
Tyrolean Iceman ◽  
Small Subunit Ribosomal Dna

Ribosomal DNA sequences were amplified from subfossils of the ascolichen Umbilicaria cylindrica (L.) Delise ex Duby collected at the ablating edges of Greenland glaciers. Surprisingly, phylogenetic analysis indicated that the amplified rDNA sequences were not closely related to those of the lichen-forming fungus but rather represented two groups of psychrophilic basidiomycetes (orders Cystofilobasidiales and Sporidiales) and one group of ascomycetes (order Leotiales). Two of these groups, the Sporidiales and the Leotiales, include other fungi previously detected in DNA extracted from the grass clothing of the Tyrolean Iceman desiccated and frozen for over 3000 years and also in 2000- and 4000-year-old ice core samples from northern Greenland. Large subunit ribosomal DNA sequences representing the group Cystofilobasidiales were nearly identical to those of the basidioyeast saprobe Mrakia frigida. The adjacent internal transcribed spacer sequence was more than 98% similar to those from three samples of U. cylindrica from different sites that had been subjected to ice burial for various lengths of time, suggesting they also were Mrakia sequences. Although ancient contamination of multiple U. cylindrica specimens with fungi such as Mrakia cannot be ruled out, it is more probable that saprobic colonization of the subfossil tissues by psychrophilic fungi proceeded during recent ice melt.Key words: ancient DNA, small subunit ribosomal DNA, 18S ribosomal DNA, phylogenetic analysis, psychrophilic fungi, lichen-forming fungi.

A phylogeny inferred from large-subunit (26S) ribosomal DNA sequences suggests that the family Dasypogonaceae is closely aligned with the Restionaceae allies

2002 ◽  
Vol 15 (6) ◽  
pp. 749 ◽  
Author(s):  
Ray Neyland
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Large Subunit ◽  
Monophyletic Group ◽  
26S Rdna ◽  
Rdna Sequences ◽  
Australian Family ◽  
The Family

The Dasypogonaceae is a small Australian family composed of four genera. Previous systematic studies have failed to place the Dasypogonaceae with confidence. The present phylogenetic analysis, inferred from large-subunit (26S) rDNA sequences, strongly suggests that the Dasypogonaceae form a monophyletic group with the taxa referred to as the Restionaceae allies (i.e. Anarthriaceae, Centrolepidaceae, Ecdeiocoleaceae).

Phylogenetic relationships in Neonectria species having Cylindrocarpon anamorphs inferred from mitochondrial ribosomal DNA sequences

2001 ◽  
Vol 79 (3) ◽  
pp. 334-340 ◽  
Author(s):  
Feky R Mantiri ◽  
Gary J Samuels ◽  
James E Rahe ◽  
Barry M Honda
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequence ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Sequence Divergence ◽  
Small Subunit ◽  
New Combinations ◽  
Rdna Sequences ◽  
Informal Groups

Mitochondrial small subunit (mtSSU) rDNA sequences elucidated phylogenetic relationships in Neonectria Wollenw. (anamorphs = Cylindrocarpon Wollenw.; Ascomycetes, Hypocreales). Twelve isolates representing seven species in five taxonomically informal groups of Neonectria were subjected to phylogenetic analysis. Fusarium inflexum R. Schneid. (teleomorph: Gibberella) and Nectria cinnabarina (Fr.) Fr. (= Nectria s.str.) were outgroups. All of the Neonectria species formed a strongly supported clade with respect to the outgroups, indicating a single ascomycete genus for the holomorphs of Cylindrocarpon. Within the Neonectria clade there were three well-supported subclades that only partially corresponded to phenotype-defined groups. DNA sequence divergence among the twelve Neonectria isolates, 2.3-7.4%, was sufficient to resolve them. The results suggest that the mtSSU rDNA region is appropriate for phylogenetic analysis of Neonectria and Cylindrocarpon. The following new combinations are proposed: Neonectria coronata, Neonectria discophora, Neonectria neomacrospora, Neonectria radicicola, Neonectria rugulosa, Neonectria veuillotiana.Key words: Ascomycetes, Hypocreales, Nectria, systematics, tree pathogens.

scholarly journals Characterization of the Complete Nuclear Ribosomal DNA Sequences ofParamphistomum cervi

2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
Author(s):  
Xu Zheng ◽  
Qiao-Cheng Chang ◽  
Yan Zhang ◽  
Si-Qin Tian ◽  
Yan Lou ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
18S Rdna ◽  
Internal Transcribed Spacer ◽  
Interspecific Variation ◽  
28S Rdna ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Position ◽  
Rdna Sequences ◽  
Length Range

Sequences of the complete nuclear ribosomal DNA (rDNA) gene from five individualParamphistomum cerviwere determined for the first time. The five complete rDNA sequences, which included the 18S rDNA, the internal transcribed spacer 1 (ITS1), the 5.8S rDNA, the internal transcribed spacer 2 (ITS2), the 28S rDNA, and the intergenic spacer (IGS) regions, had a length range of 8,493–10,221 bp. The lengths of the investigated 18S, ITS1, 5.8S, ITS2, and 28S rDNA sequences, which were 1,994 bp, 1,293 bp, 157 bp, 286 bp, and 4,186 bp, respectively, did not vary. However, the IGS rDNA sequences had a length range of 577–2,305 bp. The 5.8S and ITS-2 rDNA sequences had 100% identity among the five investigated samples, while the identities among the IGS had a range of 53.7–99.8%. A comparative analysis revealed that different types and numbers of repeats were found within each ITS1 and IGS region, which may be related to the length polymorphism of IGS. The phylogenetic position ofP. cerviin Paramphistomatidae was analyzed based on the 18S rDNA sequences. These results will aid in studying the intra- and interspecific variation of the Paramphistomatidae and the systematics and phylogenetics of Digenea.

Phylogenetic Analysis of Trichaptum Based on Nuclear 18S, 5.8S and ITS Ribosomal DNA Sequences

Mycologia ◽  
1997 ◽  
Vol 89 (5) ◽  
pp. 727 ◽  
Author(s):  
Kwan S. Ko ◽  
Soon G. Hong ◽  
Hack S. Jung
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Dna ◽  
Dna Sequences

scholarly journals A project for analyzing the ecology and phylogeny of western Pacific echinoids

Zoosymposia ◽  
2019 ◽  
Vol 15 (1) ◽  
pp. 83-87
Author(s):  
K. KANAZAWA ◽  
M. SAITOH ◽  
N. WAKAYAMA ◽  
M. OBUCHI ◽  
S. NAKACHI ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Sea Urchins ◽  
Molecular Data ◽  
Western Pacific ◽  
The West ◽  
The World ◽  
The Western Pacific ◽  
Gathering Data ◽  
Northern Japan

In 2017 we started a project to analyze the ecology and phylogeny of western Pacific echinoids. As the first step, we are establishing methods to infer their phylogenetic relationships using molecular data; we developed effective methods to obtain complete mitochondrial DNA sequences, and determined their effectiveness in phylogenetic analysis. We have also been gathering data concerning the ecology and systematics of Japanese extant echinoids, which arguably has among the highest genus-level diversities in the West Pacific or perhaps even in the world. We have collected 58 species from middle and southern Japan representing 48 genera. In the next year, we will collect sea urchins from northern Japan, and within 2 years we will finish collecting data on ecology and systematics of Japanese echinoids, and provide a set of standardized data that will be useful for many researchers studying western Pacific echinoids. At that time, we will start comparative analyses of echinoid faunas distributed in the western Pacific.

On the subdivision of Ceratocystis s.l., based on partial ribosomal DNA sequences

1993 ◽  
Vol 71 (1) ◽  
pp. 52-63 ◽  
Author(s):  
G. Hausner ◽  
J. Reid ◽  
G. R. Klassen
Keyword(s):  
Key Words ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Cell Walls ◽  
Large Subunit ◽  
Rdna Sequences

Analyses of partial rDNA sequences from both the small and large subunit genes of species of Ceratocystis s.l. support the contention that species that lack Chalara anamorphs, are resistant to cycloheximide, and have rhamnose in their cell walls should be assigned to Ophiostoma, whereas only species with Chalara anamorphs should be accommodated in Ceratocystis s.s. The data also show that Ceratocystiopsis is polyphyletic, and Sphaeronaemella fimicola appears to have little relation to either Ceratocystis or Ophiostoma. Key words: Ceratocystis, Ophiostoma, phylogeny, partial rDNA sequences.

Combined phylogenetic analysis of ribosomal ITS1 sequences and new chromosome data supports three subgroups of Dolly Varden char (Salvelinus malma)

1999 ◽  
Vol 56 (8) ◽  
pp. 1504-1511 ◽  
Author(s):  
Ruth B Phillips ◽  
Linda I Gudex ◽  
Kathleen M Westrich ◽  
Alfred DeCicco
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Lake Trout ◽  
Salvelinus Alpinus ◽  
Dolly Varden ◽  
Salvelinus Malma ◽  
Dolly Varden Char ◽  
The North ◽  
Rdna Sequences ◽  
Kamchatka River

A phylogenetic analysis of the subspecies of Salvelinus malma (Dolly Varden char) was done using DNA sequences from the first internal transcribed spacer (ITS1) of the ribosomal DNA (rDNA). Sequences were obtained from the northern S. malma malma from the Noatak River, Alaska, and the Kamchatka River, Russia; from the southern North American form S. malma lordi from the Fox River, Kenai peninsula, and Auke Bay near Juneau, Alaska; and from the southern Asian form S. malma krascheninnikovi from Belaya River in Sakhalin Island, Russia. These sequences were combined with others from Salvelinus alpinus (Arctic char) from several locations in the North Pacific and Europe and analyzed using maximum parsimony and neighbor joining algorithms with Salvelinus namaycush (lake trout) as an outgroup. The resulting trees had two well-supported groups: S. m. malma and S. m. krascheninnikovi in one group and S. m. lordi and various populations of S. alpinus in the other. Salvelinus m. malma and S. m. krascheninnikovi were sister taxa, and S. m. lordi was most closely related to S. alpinus from Northwest Territories (S. a. erythrinus). New chromosome data from S. m. malma from northwestern Alaska supported the three named subspecies because S. m. malma from both Alaska and Russia have 2n = 78 compared with 2n = 82 for the two southern forms and the location of the nuclear organizer regions (NORs) was different in each of the three subspecies.

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