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.

Small subunit rDNA phylogeny shows the lichen families Caliciaceae and Physciaceae (Lecanorales, Ascomycotina) to form a monophyletic group

2000 ◽  
Vol 78 (2) ◽  
pp. 246-254 ◽  
Author(s):  
Mats Wedin ◽  
Heidi Döring ◽  
Anders Nordin ◽  
Leif Tibell
Keyword(s):  
Sister Group ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Surface Structures ◽  
Monophyletic Group ◽  
Spore Surface ◽  
Rdna Sequences ◽  
Small Subunit Rdna ◽  
Xanthoria Parietina ◽  
The Relationship

A phylogenetic analysis based on small subunit (SSU) rDNA sequences shows the lecanoralean lichen families Caliciaceae and Physciaceae form a well-supported monophyletic group within the order Lecanorales (Ascomycotina). Support for this relationship is present from anatomical data, in particular data from spore ontogeny, where close similarities between the pattern of development of spore surface structures in the two families are pointed out. The Caliciaceae-Physciaceae group is characterized by having thick-walled, pigmented spores, often with a distinctive ornamentation which is usually formed either from strongly melanized parts of the perispore, separated by nonmelanized, gelatinous parts that eventually dissolve, or by cracks in the perispore. The relationship to the Teloschistaceae, sometimes suggested as a possible sister-group to the Physciaceae, was not supported by jackknifing, but cannot be rejected with the present data. There is no support for the suggested order Teloschistales. A brief discussion of the evolution of the prototunicate ascus in the Lecanorales is given. New SSU rDNA sequences were produced from Buellia disciformis (Fr.) Mudd. and Physcia aipolia (Humb.) Fürnr. (Physciaceae), Cladonia sulphurina (Michx.) Fr. (Cladoniaceae), Cyphelium tigillare (Ach.) Ach. (Caliciaceae), and Caloplaca flavorubescens (Huds.) J.R. Laundon and Xanthoria parietina (L.) Th.Fr. (Teloschistaceae).Key words: 18S, fungi, lichens, molecular phylogeny, ribosomal DNA.

Molecular phylogeny of rhynchonellide articulate brachiopods (Brachiopoda, Rhynchonellida)

2013 ◽  
Vol 87 (2) ◽  
pp. 211-216 ◽  
Author(s):  
Bernard L. Cohen ◽  
Maria Aleksandra Bitner
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Phylogenetic Reconstruction ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Rdna Sequences ◽  
Relaxed Clock

We present here the first report based on phylogenetic analyses of small subunit (SSU/18S) and large subunit (LSU/28S) ribosomal DNA (rDNA) sequences from a wider-than-token sample of rhynchonellide articulate brachiopods, with data from 11 of ∼20 extant genera (12 species) belonging to all four extant superfamilies. Data exploration by network and saturation analyses shows that the molecular sequence data are free from major aberrations and are suitable for phylogenetic reconstruction despite the presence of large deletions in four SSU rDNA sequences. Although molecular sequence analyses cannot directly illuminate the systematics of fossils, the independent, genealogical evidence and phylogenetic inferences about extant forms that they make possible are highly relevant to paleontological systematics because they highlight the limitations of evolutionary inference from morphology. Parsimony, distance, maximum likelihood (no clock) and Bayesian (relaxed-clock) analyses all find a tree topology that disagrees strongly with the existing superfamily classification. All tested phylogenetic reconstructions agree that the taxa analyzed fall into three clades designated A1, A2, and B that reflect two major divergence events. The relaxed-clock analysis indicates that clades A and B diverged in the Paleozoic, while clades A1 and A2 reflect Permo-Triassic (and later) events. Morphological homoplasy and possible gene co-option are suggested as the main sources for the discord between the morpho-classification, the results of cladistic analyses of morphology, and the relationships reconstructed from molecular sequences. The origin, function and evolutionary implications of the deletion-bearing rhynchonellide SSU rDNA sequences are briefly discussed in relation to pseudogenes and concerted evolution in the rDNA genomic region.

scholarly journals Reconsideration of the ‘well-known’ hypotrichous ciliate Pleurotricha curdsi (Shi et al., 2002) Gupta et al., 2003 (Ciliophora, Sporadotrichida), with notes on its morphology, morphogenesis and molecular phylogeny

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3216-3225 ◽  
Author(s):  
Xiaoteng Lu ◽  
Chen Shao ◽  
Yuhe Yu ◽  
Alan Warren ◽  
Jie Huang
Keyword(s):  
Sequence Data ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Large Body ◽  
Small Subunit ◽  
Variable Number ◽  
Ssu Rdna ◽  
Intermediate Form ◽  
Rdna Sequence Data

The oxytrichid species Pleurotricha curdsi (Shi et al., 2002) Gupta et al., 2003, isolated from a tributary of the Yangtze River in the Mudong district of Chongqing, southern China, was reinvestigated with emphasis on its morphology, morphogenesis and small-subunit (SSU) rDNA-based phylogeny. Compared with three previously described populations, the Mudong population of P. curdsi is characterized by its large body size, 170–295 × 65–110 μm in vivo, and by having a variable number of right marginal rows, either two or three. Likewise, the number of right marginal rows anlagen (RMA) is also variable, i.e. usually two, but sometimes several small extra anlagen that give rise to the formation of the third row, are present to the left of the RMAs. We posit that the Mudong population is an intermediate form between the three previously described populations. Phylogenetic analyses based on the SSU rDNA sequence data show that all populations of P. curdsi cluster with the type species of the genus, Pleurotricha lanceolata, in a clade nested within the Oxytrichidae.

scholarly journals Whole genome comparisons of Staphylococcus agnetis isolates from cattle and chickens

2020 ◽  
Author(s):  
Abdulkarim Shwani ◽  
Pamela R. F. Adkins ◽  
Nnamdi S. Ekesi ◽  
Adnan Alrubaye ◽  
Michael J. Calcutt ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Phylogenetic Trees ◽  
University Of Missouri ◽  
Commercial Broiler ◽  
Chicken Isolate ◽  
Broiler Farm ◽  
Molecular Relationships ◽  
The University ◽  
The Relationship ◽  
Genome Comparisons

AbstractS. agnetis has been previously associated with subclinical or clinically mild cases of mastitis in dairy cattle and is one of several Staphylococcal species that have been isolated from the bone and blood of lame broilers. We were the first to report that S. agnetis could be obtained frequently from bacterial chondronecrosis with osteomyelitis (BCO) lesions of lame broilers. Further, we showed that a particular isolate of S. agnetis, chicken isolate 908, can induce lameness in over 50% of exposed chickens, far exceeding normal BCO incidences in broiler operations. We have previously reported the assembly and annotation of the genome of isolate 908. To better understand the relationship between dairy cattle and broiler isolates, we assembled 11 additional genomes for S. agnetis isolates, including an additional chicken BCO strain, and ten isolates from milk, mammary gland secretions or udder skin, from the collection at the University of Missouri. To trace phylogenetic relationships, we constructed phylogenetic trees based on multi-locus sequence typing, and Genome-to-Genome Distance Comparisons. Chicken isolate 908 clustered with two of the cattle isolates along with three isolates from chickens in Denmark and an isolate of S. agnetis we isolated from a BCO lesion on a commercial broiler farm in Arkansas. We used a number of BLAST tools to compare the chicken isolates to those from cattle and identified 98 coding sequences distinguishing isolate 908 from the cattle isolates. None of the identified genes explain the differences in host or tissue tropism. These analyses are critical to understanding how Staphylococci colonize and infect different hosts and potentially how they can transition to alternative niches (bone vs dermis).ImportanceStaphylococcus agnetis has been recently recognized as associated with disease in dairy cattle and meat type chickens. The infections appear to be limited in cattle and systemic in broilers. This report details the molecular relationships between cattle and chicken isolates in order to understand how this recently recognized species infects different hosts with different disease manifestations. The data show the chicken and cattle isolates are very closely related but the chicken isolates all cluster together suggesting a single jump from cattle to chickens.

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 Redescription, Morphogenesis, and Molecular Phylogeny of Pseudosincirra longicirrata nov. comb., With Establishment of a New Genus Pseudosincirra nov. gen. (Ciliophora, Hypotrichia)

2021 ◽  
Vol 12 ◽  
Author(s):  
Qi Gao ◽  
Chen Shao ◽  
Qiuyue Tang ◽  
Jingbao Li
Keyword(s):  
Molecular Phylogeny ◽  
New Genus ◽  
Sequence Data ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Original Population ◽  
The Family ◽  
Rdna Sequence Data

The morphology and morphogenesis of Pseudosincirra longicirrata nov. gen. and nov. comb., isolated from southern China, were investigated with living observation and protargol staining. Our population is similar to the original population in living characteristics and ciliary patterns. The main determinable morphogenetic features of P. longicirrata nov. comb. are the presence of five frontoventral-transverse cirral anlagen (FVT-anlagen) and a dorsomarginal kinety anlage. According to the origin of FVT-anlagen IV and V in proter, it can be determined that P. longicirrata nov. comb. possesses two frontoventral rows and one right marginal row. Hence, a new genus, Pseudosincirra nov. gen., is proposed, and the diagnosis of P. longicirrata nov. comb. is improved. The new genus is diagnosed as follows: adoral zone of membranelles and undulating membranes is in a Gonostomum pattern; there are three enlarged frontal cirri, one buccal cirrus, and one parabuccal cirrus; postperistomial cirrus and transverse cirri are lacking; there are two more or less long frontoventral rows and one right and two or more left marginal rows; cirri within all rows very widely spaced; dorsal kinety pattern is of Urosomoida type, that is, three dorsal kineties and one dorsomarginal kinety; and caudal cirri are present. Phylogenetic analyses based on the small subunit ribosomal (SSU rDNA) sequence data indicate that P. longicirrata nov. comb. clusters with Deviata and Perisincirra. It is considered that Pseudosincirra nov. gen. and Perisincirra paucicirrata should be assigned to the family Deviatidae; fine cirri, and cirri within all rows being relatively widely spaced, should be considered as plesiomorphies of Deviatidae; and Deviatidae is closely related to Dorsomarginalia or Strongylidium–Hemiamphisiella–Pseudouroleptus.

On the phylogeny of Ophiostoma, Ceratocystis s.s., and Microascus, and relationships within Ophiostoma based on partial ribosomal DNA sequences

1993 ◽  
Vol 71 (9) ◽  
pp. 1249-1265 ◽  
Author(s):  
G. Hausner ◽  
J. Reid ◽  
G. R. Klassen
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Large Subunit ◽  
Small Subunit ◽  
Data Set ◽  
Rdna Sequences ◽  
Morphological Criteria ◽  
Small Subunit Rdna ◽  
Rdna Sequence Data ◽  
Large Subunit Rdna

Phylogenetic analysis of partial rDNA sequences suggests that Ophiostoma should remain the sole genus of the Ophiostomataceae, and this should be the sole family within the Ophiostomatales, whereas Ceratocystis s.s. would be best disposed within the Microascales. Although morphological criteria suggest that the genus Ophiostoma is heterogeneous, analysis of partial small subunit rDNA sequence data shows that Ophiostoma (excluding O. roraimense) represents a monophyletic taxon. Analysis of a partial large subunit rDNA data set, which included sequences from 55 species assignable to Ophiostoma, failed to support the strict subdivision of the genus based on either ascospore characters or the nature of the anamorph. Key words: Ceratocystis, Microascus, Ophiostoma, partial rDNA sequences, phylogeny.

Systematic position of Dinidoridae within the superfamily Pentatomoidea (Hemiptera: Heteroptera) revealed by the Bayesian phylogenetic analysis of the mitochondrial 12S and 16S rDNA sequences

Zootaxa ◽  
2012 ◽  
Vol 3423 (1) ◽  
pp. 61 ◽  
Author(s):  
JERZY A. LIS ◽  
PAWEŁ LIS ◽  
DARIUSZ J. ZIAJA ◽  
ANNA KOCOREK
Keyword(s):  
16S Rdna ◽  
Phylogenetic Trees ◽  
Taxonomic Status ◽  
Sister Group ◽  
Systematic Position ◽  
Bayesian Phylogenetic Analysis ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Molecular Affinity ◽  
The Moment

Mitochondrial 12S and 16S rDNA sequences of five species of Dinidoridae Stål, 1868, a largely Paleotropical family, and 16 other shield bugs (Pentatomoidea) were studied. This was the first molecular examination of the systematic position of this family within the superfamily Pentatomoidea using more than a single dinidorid species. Phylogenetic trees obtained from the Bayesian inference of 12S and 16S sequences of these mitochondrial DNA, identified Dinidoridae as the monophylum and a sister group to the Tessaratomidae. Moreover, results of the study suggested a close molecular affinity of the genus Eumenotes to representatives of the subfamily Dinidorinae, which contradicts all previous morphological analyses that placed it within the subfamily Megymeninae. We suggest restoring taxonomic status of the tribe Eumenotini and removing it from the synonymy of Megymenini, leaving the genus with no subfamilial assignment for the moment.

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 The molecular phylogenetic status of <i>Elphidium williamsoni</i> (Haynes, 1973) as inferred from partial 18S-rDNA sequences

2001 ◽  
Vol 20 (2) ◽  
pp. 183-183 ◽  
Author(s):  
Martin R. Langer
Keyword(s):  
North Sea ◽  
Sequence Data ◽  
Taxonomic Status ◽  
Molecular Data ◽  
Small Subunit ◽  
The North ◽  
Rdna Sequences ◽  
Molecular Phylogenetic ◽  
The North Sea ◽  
Muddy Sediments

Abstract. Comparative studies on DNA nucleotide sequences have revolutionized our understanding of the phylogenetic relationships of many organisms and have become an important tool in evolutionary, ecological and palaeobiological inquiry. We have analysed partial small-subunit 18S sequences (srDNA) of Elphidium williamsoni (Haynes, 1973), a common intertidal benthic foraminiferid from the North Sea. The molecular phylogenetic analysis of the ribosomal rDNA sequence data indicate that E. williamsoni constitutes a well-defined genetic entity that is closely related to Elphidium aculeatum.Elphidium williamsoni is a prominent and frequently encountered foraminiferid in the North Sea and other tidal flats. It was originally described by Williamson (1858) as Polystomella umbilicata and subsequently renamed by Haynes (1973). Because of its phenotypic similarities with other elphidiids, this species has been frequently confused with, for example E. excavatum or Cribrononion alvarezianum (see Haynes for discussion). The molecular data provided here, and their direct comparison to other benthic foraminifera including one elphidiid, may therefore provide additional insight into the taxonomic status and the validity of this species.Individuals of the foraminiferid Elphidium williamsoni were collected in October 1997 from the intertidal mud flats of the Crildumersiel at the outer Jade Bay near Wilhelmshaven, North Sea (see Langer et al., 1989 for details). The mud flats are characterized by fine-grained, muddy sediments containing high contents of organic material. In the laboratory, specimens were transferred into petri dishes, examined and cleaned under a stereo microscope. Living specimens of E. williamsoni were picked out separately and placed into clean glass dishes containing filtered. . .

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