Taxonomy of Kudoa species (Myxosporea), using a small-subunit ribosomal DNA sequence

1997 ◽  
Vol 75 (12) ◽  
pp. 2112-2119 ◽  
Author(s):  
D. M. L. Hervio ◽  
J. Khattra ◽  
R. H. Devlin ◽  
M. L. Kent ◽  
J. Sakanari ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Coho Salmon ◽  
Geographic Location ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Polymerase Chain Reaction Test ◽  
Sequence Comparisons ◽  
Rdna Sequences ◽  
Commercial Species ◽  
Chain Reaction Test

Myxosporeans in the genus Kudoa infect the flesh of many marine fishes and often cause unsightly lesions and softening of the flesh texture. We are particularly interested in K. thyrsites because it is associated with soft flesh in the Atlantic salmon (Salmo solar), an important commercial species in Canada. Sequences of the small-subunit (SSU) rDNA (about 1600 base pairs) were obtained from K. miniauriculata, K. amanuensis, and K. poniformis. We aligned these sequences with one obtained from coho salmon (Oncorhynchus kisutch) and designed "Kudoa general" primers (KUD1f and KUD2r). These primers, in combination with other general primers, were then used to obtain the SSU rDNA sequence of K. thyrsites from two host species, Atlantic salmon and tubesnout (Aulorhynchus flavidus), from British Columbia, Canada. Sequence comparisons of these isolates indicated that Kudoa species cluster by geographic location rather than by morphology of spores. The three species from the eastern Pacific were approximately 97% identical, whereas K. amamiensis (from Japan) was about 91% identical with these species. Sequence comparisons of K. thyrsites from Atlantic salmon and tubesnout revealed a difference of only 0.07% between these isolates. Comparison of SSU rDNA sequences from the four Kudoa species and Henneguya salminicolo analyzed in this study with those from other available myxosporean genera (Myxidium and Myxoholus) showed that taxonomic divisions at the order and suborder levels were consistent with classical views of the taxonomy of the Myxosporea. Using specific regions of the SSU rDNA, we also developed a sensitive and specific polymerase chain reaction test for detection of K. thyrsites.

scholarly journals Quantitative Measure of Small-Subunit rRNA Gene Sequences of the Kingdom Korarchaeota

1998 ◽  
Vol 64 (12) ◽  
pp. 5064-5066 ◽  
Author(s):  
Clifford F. Brunk ◽  
Nicole Eis
Keyword(s):  
Internal Standard ◽  
Pcr Amplification ◽  
Quantitative Measure ◽  
Pcr Primers ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Rdna Sequence ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Rdna Sequences

ABSTRACT Comparative PCR amplification of small-subunit (SSU) rRNA gene (rDNA) sequences indicates substantial preferential PCR amplification of pJP27 sequences with korarchaeote-specific PCR primers. The coamplification of a modified SSU rDNA sequence can be used as an internal standard to determine the amount of a specific SSU rDNA sequence.

scholarly journals Ichthyobodo salmonis sp. n. (Ichthyobodonidae, Kinetoplastida), an euryhaline ectoparasite infecting Atlantic salmon (Salmo salar L.)

Parasitology ◽  
2011 ◽  
Vol 138 (9) ◽  
pp. 1164-1175 ◽  
Author(s):  
TROND E. ISAKSEN ◽  
EGIL KARLSBAKK ◽  
KUNINORI WATANABE ◽  
ARE NYLUND
Keyword(s):  
Atlantic Salmon ◽  
Salmo Salar ◽  
Phylogenetic Analyses ◽  
Light And Electron Microscopy ◽  
Morphological Characteristics ◽  
Sensu Stricto ◽  
Ssu Rdna ◽  
Morphological Description ◽  
Rdna Sequences ◽  
Attachment Region

SUMMARYPhylogenetic analyses of SSU rDNA sequences have previously revealed the existence of 2 Ichthyobodo species able to infect Atlantic salmon (Salmo salar L.). Ichthyobodo necator sensu stricto (s.s.) is assumed to be a freshwater parasite, while a genetically distinct but undescribed species, Ichthyobodo sp. II sensu Todal et al. (2004) have been detected on Atlantic salmon in both fresh- and seawater. In the present study a morphological description of Ichthyobodo sp. II from the gills of salmon reared in fresh-, brackish- and seawater is presented, using both light- and electron microscopy. Comparative morphometry show that Ichthyobodo sp. II from both freshwater and seawater displays a different cell shape, and is significantly smaller than I. necator s.s. Also, ultrastructural characteristics distinguish these two species, notably differences in the attachment region and the presence of spine-like surface projections in Ichthyobodo sp. II. Based on both unique SSU rDNA sequences and morphological characteristics, we conclude that Ichthyobodo sp. II. represents a novel species for which we propose the name Ichthyobodo salmonis sp. n.

scholarly journals An SSU rDNA barcoding approach to the diversity of marine interstitial cercozoans, including descriptions of four novel genera and nine novel species

2010 ◽  
Vol 60 (8) ◽  
pp. 1962-1977 ◽  
Author(s):  
Chitchai Chantangsi ◽  
Brian S. Leander
Keyword(s):  
Novel Species ◽  
Phylogenetic Analyses ◽  
Environmental Dna ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Morphological Features ◽  
Molecular Signature ◽  
Nucleotide Sequence Analysis ◽  
Heterotrophic Flagellates ◽  
Rdna Sequences

Environmental DNA surveys have revealed a great deal of hidden diversity within the Cercozoa. An investigation into the biodiversity of heterotrophic flagellates in marine benthic habitats of British Columbia, Canada, demonstrated the presence of several undescribed taxa with morphological features that resemble the cercozoan genera Cryothecomonas and Protaspis. Nine novel species of marine interstitial cercozoans are described that are distributed into five genera, four of which are new. Phylogenetic analyses of small subunit rDNA sequences derived from two uncultured isolates of Protaspis obliqua and nine novel cercozoan species (within four novel genera) provided organismal anchors that helped establish the cellular identities of several different environmental sequence clades. These data, however, also showed that the rarity of distinctive morphological features in cryomonads, and other groups of cercozoans, makes the identification and systematics of the group very difficult. Therefore, a DNA barcoding approach was applied as a diagnostic tool for species delimitation that used a 618 bp region at the 5′ end of the SSU rDNA sequence. Nucleotide sequence analysis of this region showed high intergeneric sequence divergences of about 7 % and very low intraspecific sequence divergences of 0–0.5 %; phylogenetic analyses inferred from this barcoding region showed very similar tree topologies to those inferred from the full-length sequence of the gene. Overall, this study indicated that the 618 bp barcoding region of SSU rDNA sequences is a useful molecular signature for understanding the biodiversity and interrelationships of marine benthic cercozoans.

scholarly journals Taxonomy and SSU rDNA-Based Phylogeny of Two Heterotrich Ciliates (Ciliophora, Heterotrichea) Collected From Subtropical Wetlands of China, Including the Description of a New Species, Linostomella pseudovorticella n. sp.

2021 ◽  
Vol 12 ◽  
Author(s):  
Didi Jin ◽  
Xuetong Zhao ◽  
Tingting Ye ◽  
Jie Huang ◽  
Alan Warren ◽  
...  
Keyword(s):  
New Species ◽  
Food Web ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Microbial Food Web ◽  
Model Organisms ◽  
Rdna Sequences ◽  
The Family ◽  
A New Species

The Heterotrichea Stein, 1859 are a group of ciliated protists (single-celled eukaryotes) that occur in a wide variety of aquatic habitat where they play important roles in the flow of nutrients and energy within the microbial food web. Many species are model organisms for research in cytology and regenerative biology. In the present study, the morphology and phylogeny of two heterotrich ciliates, namely, Linostomella pseudovorticella n. sp. and Peritromus kahli Villeneuve-Brachon, 1940, collected from subtropical wetlands of China, were investigated using morphological and molecular methods. L. pseudovorticella n. sp. differs from its only known congener, Linostomella vorticella Ehrenberg, 1833 Aescht in Foissner et al., 1999, by having more ciliary rows (48–67, mean about 56 vs. 26–51, mean about 42) and its small-subunit (SSU) rDNA sequence, which shows a 15-bp divergence. Although P. kahli has been reported several times in recent decades, its infraciliature has yet to be described. A redescription and improved diagnosis of this species based on a combination of previous and present data are here supplied. Phylogenetic analyses based on SSU rDNA sequences revealed that the genus Linostomella is positioned within Condylostomatidae, and Peritromidae is sister to Climacostomidae with relatively low support, and the family Spirostomidae is the root branch of the class Heterotrichea.

Morphological reports on two species of Dexiotricha (Ciliophora, Scuticociliatia), with a note on the phylogenetic position of the genus

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 680-688 ◽  
Author(s):  
Xinpeng Fan ◽  
Saleh A. Al-Farraj ◽  
Feng Gao ◽  
Fukang Gu
Keyword(s):  
Phylogenetic Analyses ◽  
Eastern China ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Contractile Vacuole ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
North West ◽  
Rdna Sequences

Two Dexiotricha species (Dexiotricha elliptica nov. comb. and Dexiotricha cf. granulosa), respectively isolated from soil north-west of Riyadh, Saudi Arabia, and freshwater in Shanghai, eastern China, were investigated using standard methods. The species Loxocephalus ellipticus Kahl, 1931 is reclassified here in the genus Dexiotricha and was characterized mainly by constantly showing 16 somatic kineties, three post-oral kineties with the middle one shortened, a contractile vacuole located subcaudally with an excretory pore near the posterior end of somatic kinety 2 and single caudal cilia. A Dexiotricha granulosa-like organism having a subcaudally located contractile vacuole and fewer somatic kineties was designated D. cf. granulosa. The small-subunit rRNA gene (SSU rDNA) sequences of these two species were characterized and their phylogenetic positions based on SSU rDNA sequences were revealed by means of Bayesian inference and maximum-likelihood analysis. Phylogenetic analyses confirmed Dexiotricha as a monophyletic genus and supported its assignment to the order Loxocephalida. However, its family assignment remains unsupported.

Molecular characterisation of some species of Mylonchulus (Nematoda: Mononchida) from Japan and comments on the status of Paramylonchulus and Pakmylonchulus

Nematology ◽  
2009 ◽  
Vol 11 (3) ◽  
pp. 337-342 ◽  
Author(s):  
Masaaki Araki ◽  
Wasim Ahmad ◽  
Majid Olia ◽  
Nobuhiro Minaka
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Data ◽  
Preliminary Investigation ◽  
Sister Group ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Rdna Sequences ◽  
The Status ◽  
Molecular Relationships ◽  
The Relationship

AbstractComparative analyses of different regions of ribosomal DNA have become a popular tool in understanding the relationship among different species and genera and nematodes are no exception to this. In this study, molecular relationships were inferred from a nearly complete small subunit (SSU) of total 16 OTUs for five species of Mylonchulus, Paramylonchulus and Pakmylonchulus collected from various parts of Japan with two out-group taxa (Mononchus aquaticus and Clarkus papillatus) to examine the relationship among these species. Out of 1685 bp SSU rDNA sequences, phylogenetic trees using distance (NJ), parsimony and likelihood algorithms were performed. Obtained tree topologies were stable across algorithms and sequence data show that populations of the same species clustered together and four out of five species (M. brachyuris, M. hawaiiensis, M. oceanicus, M. sigmaturus) formed a monophyletic assemblage while M. mulveyi formed a sister group. Populations of species lacking subventral teeth but with a double gonad (M. oceanicus) stand with other Mylonchulus species, thereby confirming the synonymy of Pakmylonchulus, while populations with a narrow buccal cavity with few rows of denticles, no subventral teeth and a single prodelphic gonad (M. mulveyi = Paramylonchulus mulveyi) support to some extent the validity of the genus Paramylonchulus. Though a preliminary investigation, it is the first report on molecular relationships in Mylonchulus, probably a paraphyletic genus. Our results suggest that SSU rDNA sequence data are useful in understanding the relationship between genera and species.

X-cell parasites in the European dab Limanda limanda are related to other X-cell organisms: a discussion on the potential identity of this new group of parasites

Parasitology ◽  
2009 ◽  
Vol 136 (9) ◽  
pp. 967-980 ◽  
Author(s):  
M. A. FREEMAN
Keyword(s):  
Phylogenetic Analyses ◽  
Protozoan Parasite ◽  
Small Subunit ◽  
Systematic Position ◽  
Ssu Rdna ◽  
Rdna Sequences ◽  
Hybridization Probes ◽  
The Pacific ◽  
Gill Pathology ◽  
X Cells

SUMMARYUnusual tumour-like pathologies caused by mysterious cells termed ‘X-cells’ have been reported from numerous fish groups worldwide. After nearly 100 years of research, the tumour-like growths have recently been shown to be caused by a protozoan parasite. In the present study, histopathology and small subunit ribosomal DNA (SSU rDNA) sequences are used to assess whether the X-cell parasite infecting Atlantic dab Limanda limanda L. is distinct from the X-cell parasite infecting Japanese flounder and goby, and to determine their systematic position within the protists. SSU rDNA from Scottish dab was 89·3% and 86·7% similar to Japanese X-cell sequences from flounder and goby respectively, indicating that the parasite infecting dab in the Atlantic is distinct from the Pacific species. Histological studies revealed significant gill pathology and demonstrated the precise location of the parasites within the gill tissues using specific in situ hybridization probes. Phylogenetic analyses showed that the X-cell parasites from Scotland and Japan form a monophyletic group within the Myzozoa, and are basal alveolates. However, ultrastructure of X-cells from dab fails to confirm this systematic placement.

Molecular identification of the strongyloid nematode Oesophagostomum aculeatum in the Asian wild elephant Elephas maximus

2015 ◽  
Vol 90 (4) ◽  
pp. 434-440 ◽  
Author(s):  
O. Phuphisut ◽  
W. Maipanich ◽  
S. Pubampen ◽  
M. Yindee ◽  
N. Kosoltanapiwat ◽  
...  
Keyword(s):  
Domestic Animal ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Elephas Maximus ◽  
Rdna Sequences ◽  
Helminth Infections ◽  
Faecal Samples ◽  
High Prevalence ◽  
Global Concern ◽  
Strongyloid Nematode

AbstractThe transmission of zoonoses by wildlife, including elephants, is a growing global concern. In this study, we screened for helminth infections among Asian wild elephants (Elephas maximus) of the Salakpra Wildlife Sanctuary, Kanchanaburi, Thailand. Elephant faecal samples (45) were collected from the sanctuary grounds during January through November 2013 and assayed individually using the tetranucleotide microsatellite technique. Microscopic examination indicated a high prevalence of strongylids (93.0%) and low prevalences of trichurids (2.3%) and ascarids (2.3%). To identify the strongylid species, small subunit (SSU) rDNA sequences were amplified from copro-DNA and compared with sequences in GenBank. The generated SSU-rDNA sequences comprised five distinct haplotypes that were closely related to Oesophagostomum aculeatum. A phylogenetic analysis that incorporated related nematodes yielded a tree separated into two main clades, one containing our samples and human and domestic animal hookworms and the other consisting of Strongyloides. The present results indicate that O. aculeatum in local elephants is a potential source of helminthiasis in human and domestic animals in this wild-elephant irrupted area.

scholarly journals Small Subunit rDNA-Based Phylogeny of the Tylenchida Sheds Light on Relationships Among Some High-Impact Plant-Parasitic Nematodes and the Evolution of Plant Feeding

2009 ◽  
Vol 99 (3) ◽  
pp. 227-235 ◽  
Author(s):  
M. Holterman ◽  
G. Karssen ◽  
S. van den Elsen ◽  
H. van Megen ◽  
J. Bakker ◽  
...  
Keyword(s):  
Dna Barcode ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Parasitic Nematodes ◽  
Species Variation ◽  
Good Resolution ◽  
Ancestral State ◽  
Root Knot Nematodes ◽  
Plant Feeding ◽  
Rdna Sequences

Cyst (Heteroderidae), root knot (Meloidogyne spp.), and lesion (Pratylenchus spp.) nematodes all belong to a single nematode order, Tylenchida. However, the relationships between and within these economically highly relevant groups, and their relatedness to other parasitic Tylenchida is unclear. We constructed a phylogeny of 116 Tylenchida taxa based on full length small subunit ribosomal DNA (small subunit [SSU] rDNA) sequences. Ancestral state reconstruction points at a gradual development of simple to more complex forms of plant parasitism. Good resolution was observed in distal clades that include cyst, root knot, and lesion nematodes, and monophyly of most families was confirmed. Our data suggest that root knot nematodes have evolved from an ancestral member of the genus Pratylenchus, but it remains unclear which species is closest to this branching point. Contrary to the notoriously polyphagous distal representatives, basal members of the genus Meloidogyne (and probably, their common ancestor) have narrow host ranges. Our analysis also shows that mitotic parthenogeny has arisen at least two times independently among root knot nematodes. In many cases resolution till species was observed, suggesting that SSU rDNA sequences have a potential for DNA barcode-based species identification with, due to the overall conserved nature of this gene, limited intra-species variation.

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