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.

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.

Description of the pseudocryptic species Conticribra weissflogiopsis sp. nov. (Thalassiosirales, Bacillariophyta) isolated from brackish waters in Korea, based on its cingulum structure and molecular analysis

Phytotaxa ◽  
2014 ◽  
Vol 191 (1) ◽  
pp. 115 ◽  
Author(s):  
JOON SANG PARK ◽  
JIN HWAN LEE
Keyword(s):  
Morphological Evolution ◽  
Morphological Characters ◽  
Molecular Data ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Diatom Species ◽  
Brackish Waters ◽  
Valve Structure ◽  
Small Subunit Ribosomal Dna ◽  
Pseudocryptic Species

We describe the new fultoportulate diatom species, Conticribra weissflogiopsis, isolated from brackish waters in Korea, based on morphological characters and molecular data. The new species is characterized by having areolae venation with internal (semi-) continuous cribra, a flat valve face, a single marginal rimoportula replacing a marginal fultoportula, a subcentral ring of the valve face fultoportulae, and a dextral pattern of cingulum structure. The overall valve structure of C. weissflogiopsis resembles that of C. weissflogii; however, the cingulum structure differs between the two species—C. weissflogiopsis has a dextral offset of band opening in the cingulum, whereas C. weissflogii has a sinistral offset. Phylogenetic analysis of the nuclear small subunit ribosomal DNA (SSU rDNA) revealed that C. weissflogiopsis is located in the Conticribra clade. Further, the pairwise genetic distance based on the SSU rDNA and the internal transcribed spacer 2 (ITS2) indicated that C. weissflogiopsis is a distinct Conticribra species. On the basis of the morphology and molecular phylogeny, we expand the hypothesis regarding the morphological evolution of Conticribra 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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