Phylogenetic analysis of nuclear and mitochondrial rDNA sequences supports the view that loculoascomycetes (Ascomycota) are not monophyletic

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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Two Erysiphe species associated with recent outbreak of soybean powdery mildew: results of molecular phylogenetic analysis based on nuclear rDNA sequences

Mycoscience ◽

10.1007/s102670200049 ◽

2002 ◽

Vol 43 (4) ◽

pp. 333-341 ◽

Cited By ~ 20

Author(s):

Susumu Takamatsu ◽

Yusuke Taguchi ◽

Hyeon-Dong Shin ◽

Urailak Paksiri ◽

Saranya Limkaisang ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Powdery Mildew ◽

Molecular Phylogenetic Analysis ◽

Nuclear Rdna ◽

Rdna Sequences ◽

Recent Outbreak ◽

Molecular Phylogenetic

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Sequence characterization and phylogenetic analysis of the 5S ribosomal DNA in species of the family Batrachoididae

Genome ◽

10.1139/g10-048 ◽

2010 ◽

Vol 53 (9) ◽

pp. 723-730 ◽

Cited By ~ 15

Author(s):

María Úbeda-Manzanaro ◽

Manuel Alejandro Merlo ◽

José Luis Palazón ◽

Carmen Sarasquete ◽

Laureana Rebordinos

Keyword(s):

Phylogenetic Analysis ◽

Ribosomal Dna ◽

5S Rdna ◽

Purifying Selection ◽

The Other ◽

Fish Family ◽

Sequence Characterization ◽

Rdna Sequences ◽

The Family ◽

Clear Differentiation

5S ribosomal DNA (rDNA) sequences were analyzed in four species belonging to different genera of the fish family Batrachoididae. Several 5S rDNA variants differing in their non-transcribed spacers (NTSs) were found and were grouped into two main types. Two species showed both types of 5S rDNA, whereas the other two species showed only one type. One type of NTS of Amphichthys cryptocentrus showed a high polymorphism due to several deletions and insertions, and phylogenetic analysis showed a between-species clustering of this type of NTS in Amphichthys cryptocentrus. These results suggest a clear differentiation in the model of 5S rDNA evolution of these four species of Batrachoididae, which appear to have been subject to processes of concerted evolution and birth-and-death evolution with purifying selection.

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The 5S rRNA gene units in ancestral two-rowed barley (Hordeum spontaneum C. Koch) and bulbous barley (H. bulbosum L.): sequence analysis and phylogenetic relationships with the 5S rDNA units of cultivated barley (H. vulgare L.)

Genome ◽

10.1139/g96-019 ◽

1996 ◽

Vol 39 (1) ◽

pp. 140-149 ◽

Cited By ~ 36

Author(s):

Bernard R. Baum ◽

Douglas A. Johnson

Keyword(s):

Phylogenetic Analysis ◽

5S Rdna ◽

Hordeum Spontaneum ◽

Wild Relatives ◽

5S Rrna ◽

Rrna Genes ◽

Rrna Gene ◽

Sequence Comparisons ◽

Rdna Sequences ◽

Cultivated Barley

5S rRNA genes from several accessions of Hordeum spontaneum and Hordeum bulbosum, wild relatives of cultivated barley, Hordeum vulgare, have been amplified by the polymerase chain reaction, cloned, and sequenced. Evaluation of aligned sequences along with principal coordinate analysis demonstrates that the two classes of 5S rDNA sequences found in cultivated barley, and subclasses (groups) of these sequences, can also be found in its closest wild relatives. The two classes of units, formerly categorized as containing short or long 5S rDNA repeats, are distinguishable by the presence or absence of a TAG repeating unit. Sequence comparisons of individual clones (units) isolated from different species have allowed us to confirm that orthology exists for several groups. This demonstration of orthologous groups suggests that the 5S rDNA sequence may be useful for further phylogenetic analysis in the genus Hordeum and possibly in the Triticeae. Key words : 5S rDNA, barley, sequence diversity, phylogenetic analysis.

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Luteoporia citriniporia sp. nov. (Polyporales, Basidiomycota), evidenced by morphological characters and phylogenetic analysis

Phytotaxa ◽

10.11646/phytotaxa.461.1.4 ◽

2020 ◽

Vol 461 (1) ◽

pp. 31-39

Author(s):

ZHAN-BO LIU ◽

YUAN YUAN

Keyword(s):

Phylogenetic Analysis ◽

New Species ◽

Growth Habit ◽

Strong Support ◽

Morphological Characters ◽

Lemon Yellow ◽

Molecular Evidence ◽

Rdna Sequences ◽

Monophyletic Lineage ◽

Molecular Characters

A new poroid wood-inhabiting fungus in the Polyporales, Luteoporia citriniporia sp. nov., is described from Sri Lanka based on morphological and molecular evidence. L. citriniporia is characterized by an annual growth habit; resupinate basidiocarps with lemon yellow pores when fresh becoming buff to clay pink upon drying, a distinct snow white and fimbriate sterile margin, tissues becoming pink in KOH, a monomitic hyphal system, generative hyphae thin- to distinctly thick-walled, usually encrusted with fine yellow crystals, and oblong-ellipsoid to subcylindrical basidiospores measuring 3.4–4.2 × 1.8–2.1 µm. The phylogenetic analysis based on ITS + nLSU rDNA sequences shows that the new species belongs to Luteoporia, forming a monophyletic lineage with strong support (100% BS, 100% BP, 1.00 BPP) and is closely related to L. albomarginata; the lineage groups with Crustodontia chrysocreas, Phlebiporia bubalina and Mycoacia uda. Both morphological and molecular characters confirm the placement of the new species in Luteoporia.

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

Zootaxa ◽

10.11646/zootaxa.4858.4.3 ◽

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.

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Distribution and Diversity of Archaea Corresponding to the Limnological Cycle of a Hypersaline Stratified Lake (Solar Lake, Sinai, Egypt)

Applied and Environmental Microbiology ◽

10.1128/aem.66.8.3269-3276.2000 ◽

2000 ◽

Vol 66 (8) ◽

pp. 3269-3276 ◽

Cited By ~ 73

Author(s):

Eddie Cytryn ◽

Dror Minz ◽

Ronald S. Oremland ◽

Yehuda Cohen

Keyword(s):

Phylogenetic Analysis ◽

Gel Electrophoresis ◽

Denaturing Gradient Gel Electrophoresis ◽

Archaeal Community ◽

Seasonal Distribution ◽

Stratified Lake ◽

Rdna Sequences ◽

16S Rdna Sequences ◽

Gradient Gel Electrophoresis ◽

Solar Lake

ABSTRACT The vertical and seasonal distribution and diversity of archaeal sequences was investigated in a hypersaline, stratified, monomictic lake, Solar Lake, Sinai, Egypt, during the limnological development of stratification and mixing. Archaeal sequences were studied via phylogenetic analysis of 16S rDNA sequences as well as denaturing gradient gel electrophoresis analysis. The 165 clones studied were grouped into four phylogenetically different clusters. Most of the clones isolated from both the aerobic epilimnion and the sulfide-rich hypolimnion were defined as cluster I, belonging to theHalobacteriaceae family. The three additional clusters were all isolated from the anaerobic hypolimnion. Cluster II is phylogenetically located between the generaMethanobacterium and Methanococcus. Clusters III and IV relate to two previously documented groups of uncultured euryarchaeota, remotely related to the genusThermoplasma. No crenarchaeota were found in the water column of the Solar Lake. The archaeal community in the Solar Lake under both stratified and mixed conditions was dominated by halobacteria in salinities higher than 10%. During stratification, additional clusters, some of which may possibly relate to uncultured halophilic methanogens, were found in the sulfide- and methane-rich hypolimnion.

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