Phylogenetic analysis of Rhizoclonium (Cladophoraceae, Cladophorales), and the description of Rhizoclonium subtile sp. nov. from China

Phytotaxa ◽  
2018 ◽  
Vol 383 (2) ◽  
pp. 147 ◽  
Author(s):  
ZHI-JUAN ZHAO ◽  
HUAN ZHU ◽  
GUO-XIANG LIU ◽  
ZHENG-YU HU
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Large Subunit ◽  
Nuclear Gene ◽  
Morphological Characters ◽  
Small Subunit ◽  
Molecular Evidence ◽  
Gene Markers ◽  
Long Time ◽  
Small Subunit Ribosomal Dna

The genus Rhizoclonium (Cladophoraceae, Cladophorales) accommodates uniserial, unbranched filamentous algae, closely related to Cladophora and Chaetomorpha. Its taxonomy has been problematic for a long time due to the lack of diagnostic morphological characters. To clarify the species diversity and taxonomic relationships of this genus, we collected and analyzed thirteen freshwater Rhizoclonium specimens from China. The morphological traits of these specimens were observed and described in detail. Three nuclear gene markers small subunit ribosomal DNA (SSU), large subunit ribosomal DNA (LSU) and internal transcribed spacer 2 (ITS2) sequences were analyzed to elucidate their phylogenetic relationships. The results revealed that there were at least fifteen molecular species assignable to Rhizoclonium and our thirteen specimens were distributed in four clades. On the basis of morphological and molecular evidence we propose the new species, R. subtile sp. nov.

scholarly journals First record of Nocturama (Batrachospermales, Rhodophyta) in South America, with the description of a new species N. novamundensis

Phytotaxa ◽  
2016 ◽  
Vol 278 (3) ◽  
pp. 273
Author(s):  
ORLANDO NECCHI JR ◽  
TIMOTHY J. ENTWISLE ◽  
CIRO C.Z. BRANCO ◽  
MONICA O. PAIANO
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Large Subunit ◽  
First Record ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Molecular Evidence ◽  
Southern Brazil ◽  
Small Subunit Ribosomal Dna ◽  
A New Species

Specimens from southeastern and southern Brazil previously identified as Sheathia arcuata (= Batrachospermum arcuatum) are shown to be members of the recently described genus Nocturama, previously known only from Australia and New Zealand. Morphological and molecular evidence support recognizing the Brazilian specimens as a new species, described here as Nocturama novamundensis, sp. nov. Comparison of DNA sequences of the plastid-encoded ribulose-1,5-bisphosphatecarboxylase–oxygenase large subunit (rbcL) and the nuclear small subunit ribosomal DNA (SSU rDNA) markers showed Nocturama as a well supported clade. The sequence divergences between the new and the type species were high (95-98bp, 7.4–7.6%) for rbcL and 19bp, 1.1% for SSU), and those within each species were extremely low (0-1 bp, 0-0.1%). The new species can be distinguished from N. antipodites in having curved primary fascicles composed of non-‘audouinelloid’ cells (compared to straight primary fascicles with audouinelloid—cylindrical—cells) and in being always dioecious (only rarely is N. antipodites dioecious).

Daedalea americana sp. nov. (Polyporales, Basidiomycota) evidenced by morphological characters and phylogenetic analysis

Phytotaxa ◽  
2015 ◽  
Vol 204 (4) ◽  
pp. 277 ◽  
Author(s):  
MEI LING HAN ◽  
JOSEF VLASÁK ◽  
BAO KAI CUI
Keyword(s):  
Phylogenetic Analysis ◽  
Central America ◽  
Ribosomal Rna ◽  
Internal Transcribed Spacer ◽  
Large Subunit ◽  
Morphological Characters ◽  
Molecular Evidence ◽  
Pore Surface ◽  
Its Regions ◽  
Brown Band

A new polypore, Daedalea americana, collected from North and Central America, is described and illustrated based on morphological characters and molecular evidence. It is characterized by annual and pileate basidiocarps, grayish brown with brown to cinnamon brown band and concentrically zonate pileal surface when fresh, cream to clay-pink pore surface, circular to angular pores (4–5 per mm) and ellipsoid basidiospores measured as 4.0–5.1 × 2.1–3.0 µm. Phylogenetic analysis based on the internal transcribed spacer (ITS) regions and nuclear large subunit (nLSU) ribosomal RNA gene regions support D. americana as a distinctive species belonging to Daedalea.

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.

Rigidotubus tephroleucus gen. et sp. nov. (Cystostereaceae, Agaricales) evidenced by morphological characters and phylogenetic analyses

Phytotaxa ◽  
2018 ◽  
Vol 333 (2) ◽  
pp. 259 ◽  
Author(s):  
JIE SONG ◽  
JIA-HUI XING ◽  
XING JI ◽  
YI-FEI SUN ◽  
BAO-KAI CUI ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Morphological Characters ◽  
Molecular Evidence ◽  
Pore Surface ◽  
Ribosomal Rna Gene ◽  
Cotton Blue ◽  
Fungal Genus

A new poroid wood-inhabiting fungal genus, Rigidotubus, is proposed to accommodate  R. tephroleucus sp. nov. based on morphological characters and molecular evidence. The genus is characterized by tough and poroid basidiomata, white to grayish white pore surface, white sterile margin, a monomitic hyphal system with clamped generative hyphae, ovoid to ellipsoid basidiospores negative in Melzer’s reagent and Cotton Blue. The phylogenetic analyses inferred from the internal transcribed spacer (ITS) and nuclear large subunit (28S) ribosomal RNA gene regions confirmed that Rigidotubus belongs to Cystostereaceae in Agaricales. A key to the accepted genera of Cystostereaceae is provided.

scholarly journals Small Subunit Ribosomal DNA-Based Phylogenetic Analysis of Foliar Nematodes (Aphelenchoides spp.) and Their Quantitative Detection in Complex DNA Backgrounds

2012 ◽  
Vol 102 (12) ◽  
pp. 1153-1160 ◽  
Author(s):  
Katarzyna Rybarczyk-Mydłowska ◽  
Paul Mooyman ◽  
Hanny van Megen ◽  
Sven van den Elsen ◽  
Mariëtte Vervoort ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Developmental Stages ◽  
Nematode Species ◽  
Morphological Characters ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Rapid Screening ◽  
Quantitative Detection ◽  
Small Subunit Ribosomal Dna ◽  
Plant Parasitic

Foliar nematodes, plant-parasitic representatives of the genus Aphelenchoides, constitute a minority in a group dominated by fungivorous species. Distinction between (mostly harmless) fungal feeding Aphelenchoides species and high impact plant parasites such as A. besseyi, A. fragariae, A. ritzemabosi, and A. subtenuis is severely hampered by the scarcity of informative morphological characters, some of which are only observable in specific developmental stages. Poor description of a number of non-plant-parasitic Aphelenchoides species further complicates identification. Based on (nearly) full-length small subunit ribosomal DNA (SSU rDNA) sequences (≈1,700 bp), a phylogenetic tree was generated, and the four target species appeared as distinct, well-supported groups. Notably, this genus does not constitute a monophyletic group: A. besseyi and A. ritzemabosi cluster together and they are phylogenetically isolated from A. fragariae, A. subtenuis, and most other fungivorous species. A phylum-wide SSU rDNA framework was used to identify species-specific DNA motifs. For the molecular detection of four plant-parasitic Aphelenchoides species, polymerase chain reaction primers were developed with high, identical annealing temperatures (63°C). Within the molecular framework presented here, these primers can be used for the rapid screening of plant material and soil for the presence of one or multiple foliar nematode species.

Systematic status of Campydora Cobb, 1920 (Nematoda: Campydorina)

Nematology ◽  
2003 ◽  
Vol 5 (5) ◽  
pp. 699-711 ◽  
Author(s):  
Peter Mullin ◽  
Timothy Harris ◽  
Thomas Powers
Keyword(s):  
Maximum Likelihood ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Maximum Parsimony ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Systematic Position ◽  
Nominal Species ◽  
Competing Hypotheses ◽  
Small Subunit Ribosomal Dna

AbstractThe systematic position of Campydora Cobb, 1920, which possesses many unique morphological features, especially in pharyngeal structure and stomatal armature, has long been a matter of uncertainty with the 'position of the Campydorinae' (containing only Campydora) being questionable. A review of the morphology of C. demonstrans, the only nominal species of Campydora concluded that the species warranted placement as the sole member of a monotypic suborder, Campydorina, in the order Dorylaimida. Others placed Campydorina in the order Enoplida. We conducted phylogenetic analyses, using 18s small subunit ribosomal DNA sequences generated from a number of taxa in the subclasses Enoplia and Dorylaimia, to evaluate these competing hypotheses. Although precise taxonomic placement of the genus Campydora and the identity of its closest living relatives is in need of further investigation, our analyses, under maximum parsimony, distance, and maximum likelihood criteria, unambiguously indicate that Campydora shares a common, more recent, ancestry with genera such as Alaimus, Pontonema, Tripyla and Ironus (Enoplida), rather than with any members of Dorylaimida, Mononchida or Triplonchida.

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