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 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.

Phylogeny of dracunculoid nematodes (Chromadorea: Rhabditida: Spirurina: Dracunculoidea) from some Eurasian freshwater fishes

Zootaxa ◽  
2020 ◽  
Vol 4858 (4) ◽  
pp. 521-541
Author(s):  
SERGEY G. SOKOLOV ◽  
ALEXANDER P. KALMYKOV ◽  
SVETLANA V. MALYSHEVA
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationship ◽  
Ribosomal Dna ◽  
Phylogenetic Relationships ◽  
Type Species ◽  
Freshwater Fishes ◽  
Ssu Rdna ◽  
Lsu Rdna ◽  
Rdna Sequences ◽  
The Family

Sets of small ribosomal DNA (SSU rDNA) and large ribosomal DNA (LSU rDNA) sequences were obtained for Philometroides moraveci Vismanis & Yunchis, 1994, Philometra kotlani (Molnár, 1969), Philometra rischta Skrjabin, 1923, Philometra cf. obturans (Prenant, 1886) (Philometridae), Sinoichthyonema amuri (Garkavi, 1972), Agrachanus scardinii (Molnár, 1966), Kalmanmolnaria intestinalis (Dogiel & Bychowsky, 1934) and Skrjabillanus tincae Shigin & Shigina, 1958 (Skrjabillanidae). Phylogenetic analysis of SSU rDNA data shows that dracunculoid nematodes are divided into two well-supported clades designated as Clade I and Clade II, respectively. Clade I includes the type species of the genus Philonema Kuitunen-Ekbaum, 1933, some species from the family Daniconematidae Moravec & Køie, 1987 and two subfamilies of skrjabillanids, Skrjabillaninae Shigin & Shigina, 1958 and Esocineminae Moravec, 2006. Clade II unites species from the families Dracunculidae Stiles, 1907, Micropleuridae Baylis & Daubney, 1926 and Philometridae Baylis & Daubney, 1926. Within the Philometridae, there are several well-supported groups of species, one of which unites freshwater Philometra spp. from the Palearctic cyprinids, identified as P. kotlani, P rischta, P. ovata (Zeder, 1803) and P. cyprinirutili (Creplin, 1825). However, the phylogenetic relationships of most philometrids are unresolved. An analysis of partial SSU and LSU rDNA sequences indicates that there is no direct phylogenetic relationship between Agrachanus Tikhomirova, 1971 (type species Skrjabillanus scardinii Molnár, 1966) and Skrjabillanus Shigin & Shigina, 1958 (type species Sk. tincae), which means that the genus Agrachanus can be resurrected. Our study confirms that Philonematinae Ivashkin, Sobolev & Khromova, 1971 should be elevated to the family rank. We formally establish the family Philonematidae Ivashkin, Sobolev & Khromova, 1971 stat. nov. We also suggest combining the superfamilies Dracunculoidea Stiles, 1907 and Camallanoidea Railliet & Henry, 1915 into the infraorder Camallanomorpha Roberts, Janovy & Nadler, 2013. 

A phylogenetic study of the Micarea prasina group shows that Micarea micrococca includes three distinct lineages

2009 ◽  
Vol 42 (1) ◽  
pp. 7-21 ◽  
Author(s):  
Paweł CZARNOTA ◽  
Beata GUZOW-KRZEMIŃSKA
Keyword(s):  
Maximum Likelihood ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Maximum Parsimony ◽  
Small Subunit ◽  
Sister Species ◽  
Phylogenetic Study ◽  
Rdna Sequences ◽  
Small Subunit Ribosomal Dna

AbstractThe phylogeny of the Micarea prasina group was investigated using mitochondrial small subunit ribosomal DNA sequences from 14 taxa representing this group, four other members of the genus Micarea, and Psilolechia lucida as an outgroup. A total of 31 new mtSSU rDNA sequences were generated, including 10 from the M. micrococca complex. Bayesian, maximum parsimony (MP) and maximum likelihood (ML) methods were used to analyse the data. The results show that M. micrococca is not monophyletic and forms three strongly supported lineages: 1) M. micrococca s. str., 2) M. byssacea (Th. Fr.) Czarnota, Guzow-Krzemińska & Coppins comb. nov., and 3) a putative taxon that requires further studies. Micarea viridileprosa is a sister species to M. micrococca s. str. and the recently described M. nowakii is a sister species to M. prasina s. str. The placement of M. tomentosa within the M. prasina group is confirmed. Micarea hedlundii appears to be more closely related to the M. micrococca complex than M. prasina s. str. Descriptions, illustrations, taxonomic remarks, distribution and habitat data for M. micrococca s. str. and M. byssacea are provided. A lectotype for Biatora byssacea Hampe non Zwackh and a neotype for Catillaria prasina β [var.] byssacea are selected.

Small-subunit rDNA sequences from representatives of selected families of the Gigartinales and Rhodymeniales (Rhodophyta). 3. Delineating the Gigartinales sensu stricto

2004 ◽  
Vol 82 (1) ◽  
pp. 43-74 ◽  
Author(s):  
Gary W Saunders ◽  
Anthony Chiovitti ◽  
Gerald T Kraft
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Family Relationships ◽  
Small Subunit ◽  
Sensu Stricto ◽  
Rdna Sequences ◽  
Small Subunit Rdna ◽  
First Time ◽  
Small Subunit Ribosomal Dna ◽  
Ordinal Level

Nuclear small-subunit ribosomal DNA sequences were determined for 65 members of the Gigartinales and related orders. With representatives of 15 families of the Gigartinales sensu Kraft and Robins included for the first time, our alignment now includes members of all but two of the ca. 40 families. Our data continue to support ordinal status for the Plocamiales, to which we provisionally transfer the Pseudoanemoniaceae and Sarcodiaceae. The Halymeniales is retained at the ordinal level and consists of the Halymeniaceae (including the Corynomorphaceae), Sebdeniaceae, and Tsengiaceae. In the Halymeniaceae, Grateloupia intestinalis is only distantly related to the type species, Grateloupia filicina, but is closely affiliated with the genus Polyopes. The Nemastomatales is composed of the Nemastomataceae and Schizymeniaceae. The Acrosymphytaceae (now including Schimmelmannia, formerly of the Gloiosiphoniaceae) and the Calosipho niaceae (represented by Schmitzia) have unresolved affinities and are considered as incertae sedis among lineage 4 orders. We consider the Gigartinales sensu stricto to include 29 families, although many contain only one or a few genera and mergers will probably result following further investigation. Although the small-subunit ribosomal DNA was generally too conservative to resolve family relationships within the Gigartinales sensu stricto, a few key conclusions are supported. The Hypneaceae, questionably distinct from the Cystocloniaceae on anatomical grounds, is now subsumed into the latter family. As recently suggested, the Wurdemanniaceae should be incorporated into the Solieriaceae, but the latter should not be merged with the Areschougiaceae. The Corynocystaceae Kraft, fam. nov., is described and added to the Gigartinales sensu stricto.Key words: Corynocystaceae, Cryptonemiales, Florideophyceae, Gigartinales, Rhodymeniales, systematics.

Phylogenetic Relationships among Eight Eimeria Species Infecting Domestic Fowl Inferred Using Complete Small Subunit Ribosomal DNA Sequences

1997 ◽  
Vol 83 (2) ◽  
pp. 262 ◽  
Author(s):  
John R. Barta ◽  
Donald S. Martin ◽  
Paul A. Liberator ◽  
Michael Dashkevicz ◽  
Jennifer W. Anderson ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Domestic Fowl ◽  
Eimeria Species ◽  
Small Subunit ◽  
Small Subunit Ribosomal Dna

scholarly journals DNA Sequence Duplication in Rhodobacter sphaeroides 2.4.1: Evidence of an Ancient Partnership between Chromosomes I and II

2004 ◽  
Vol 186 (7) ◽  
pp. 2019-2027 ◽  
Author(s):  
Madhusudan Choudhary ◽  
Yun-Xin Fu ◽  
Chris Mackenzie ◽  
Samuel Kaplan
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequence ◽  
Rhodobacter Sphaeroides ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Sequence Similarity ◽  
Gene Duplications ◽  
Chromosomal Dna ◽  
History Of ◽  
Complex Genome

ABSTRACT The complex genome of Rhodobacter sphaeroides 2.4.1, composed of chromosomes I (CI) and II (CII), has been sequenced and assembled. We present data demonstrating that the R. sphaeroides genome possesses an extensive amount of exact DNA sequence duplication, 111 kb or ∼2.7% of the total chromosomal DNA. The chromosomal DNA sequence duplications were aligned to each other by using MUMmer. Frequency and size distribution analyses of the exact DNA duplications revealed that the interchromosomal duplications occurred prior to the intrachromosomal duplications. Most of the DNA sequence duplications in the R. sphaeroides genome occurred early in species history, whereas more recent sequence duplications are rarely found. To uncover the history of gene duplications in the R. sphaeroides genome, 44 gene duplications were sampled and then analyzed for DNA sequence similarity against orthologous DNA sequences. Phylogenetic analysis revealed that ∼80% of the total gene duplications examined displayed type A phylogenetic relationships; i.e., one copy of each member of a duplicate pair was more similar to its orthologue, found in a species closely related to R. sphaeroides, than to its duplicate, counterpart allele. The data reported here demonstrate that a massive level of gene duplications occurred prior to the origin of the R. sphaeroides 2.4.1 lineage. These findings lead to the conclusion that there is an ancient partnership between CI and CII of R. sphaeroides 2.4.1.

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