Phylogenetic inference regarding Parergodrilidae and Hrabeiella periglandulata ('Polychaeta', Annelida) based on 18S rDNA, 28S rDNA and COI sequences

2004 ◽  
Vol 42 (4) ◽  
pp. 270-280 ◽  
Author(s):  
J. Jordens ◽  
T. Struck ◽  
G. Purschke
Keyword(s):  
18S Rdna ◽  
Phylogenetic Inference ◽  
28S Rdna ◽  
Coi Sequences

Morphological and molecular characterization of Paractinolaimus sahandi n. sp. (Nematoda: Actinolaimidae) from the Sahand Mountains in Iran

2010 ◽  
Vol 85 (3) ◽  
pp. 276-282 ◽  
Author(s):  
M. Pedram ◽  
G. Niknam ◽  
M.T. Vinciguerra ◽  
W. Ye ◽  
R.T. Robbins
Keyword(s):  
New Species ◽  
Molecular Characterization ◽  
Outer Layer ◽  
18S Rdna ◽  
Soil Samples ◽  
28S Rdna ◽  
First Report ◽  
Morphological And Molecular Characterization

AbstractParactinolaimus sahandi n. sp., found in wet soil samples collected from the rhizosphere of grasses of Sahand Mountains, Iran, is described. This new species is characterized by its long body (3.5–4.7 mm), high a value (74.5–88.5), anterior location of posterior subventral nuclei, occupying 62.5–68.0% of glandularium distance, the presence of 1–4 pre- and 1–3 post-vulval papillae and numerous tiny, not innervated papillae in front and behind the vulva in the outer layer of cuticle; common functional males in the population, with 62.5–81.3 μm long spicules and 15–17 ventromedian supplements. The new species, which is the only one in the genus showing the advulval cuticular tiny papillae and is unusually slender, is compared to four species of Paractinolaimus, namely P. macrolaimus, P. longidrilus, P. spanithelus and P. rafiqi. The ribosomal 18S rDNA (1246 bp sequenced) and 28S rDNA D2/D3 region (844 bp sequenced) of P. sahandi n. sp. were sequenced for molecular characterization. Sequences of the 18S and 28S D2/D3 of P. sahandi n. sp. have distinct differences from those of the only sequenced P. macrolaimus, with 6 bp differences in 18S and 38 bp differences and five gaps in 28S. This is the first report of the occurrence of members of Actinolaimidae in Iran.

Phylogenetics of the tribe Phalacropsyllini (Siphonaptera: Ctenophthalmidae: Neopsyllinae) based on molecular and morphological evidence

Zootaxa ◽  
2013 ◽  
Vol 3630 (2) ◽  
pp. 333-346 ◽  
Author(s):  
ROXANA ACOSTA ◽  
JUAN J. MORRONE
Keyword(s):  
Bayesian Inference ◽  
18S Rdna ◽  
Maximum Parsimony ◽  
Morphological Characters ◽  
28S Rdna ◽  
Morphological Evidence ◽  
Phylogenetic Classification ◽  
New Tribe ◽  
Molecular Characters

Six genera of the tribe Phalacropsyllini were analysed based on molecular (18S rDNA and 28S rDNA) and morphological characters, using maximum parsimony analyses and Bayesian inference. The results support the paraphyly of the tribe Phalacropsyllini, as shown in a previous study based only on molecular characters. Three main clades were identified: one includes the genera Neopsylla, Epitedia, Catallagia, and Delotelis; another includes Phalacropsylla and Strepsylla; and a third one includes only Meringis. In order to propose a phylogenetic classification we recognize three tribes, transferring Epitedia, Catallagia and Delotelis to Neopsyllini; keeping Phalacropsyllini only for Phalacropsylla and Strepsylla; and proposing the new tribe Meringini for Meringis.

scholarly journals Analysis of small and large subunit rDNA introns from several ectomycorrhizal fungi species

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0245714
Author(s):  
Li-hong Chen ◽  
Wei Yan ◽  
Ting Wang ◽  
Yu Wang ◽  
Jian Liu ◽  
...  
Keyword(s):  
18S Rdna ◽  
Large Subunit ◽  
Gc Content ◽  
Nucleotide Sequences ◽  
28S Rdna ◽  
Nuclear Ribosomal Dna ◽  
Rdna Site ◽  
Group I Introns ◽  
Intron Insertion ◽  
Group I

The small (18S) and large (28S) nuclear ribosomal DNA (rDNA) introns have been researched and sequenced in a variety of ectomycorrhizal fungal taxa in this study, it is found that both 18S and 28S rDNA would contain introns and display some degree variation in size, nucleotide sequences and insertion positions within the same fungi species (Meliniomyces). Under investigations among the tested isolates, 18S rDNA has four sites for intron insertions, 28S rDNA has two sites for intron insertions. Both 18S and 28S rDNA introns among the tested isolates belong to group I introns with a set of secondary structure elements designated P1-P10 helics and loops. We found a 12 nt nucleotide sequences TACCACAGGGAT at site 2 in the 3’-end of 28S rDNA, site 2 introns just insert the upstream or the downstream of the12 nt nucleotide sequences. Afters sequence analysis of all 18S and 28S rDNA introns from tested isolates, three high conserved regions around 30 nt nucleotides (conserved 1, conserved 2, conserved 3) and identical nucleotides can be found. Conserved 1, conserved 2 and conserved 3 regions have high GC content, GC percentage is almost more than 60%. From our results, it seems that the more convenient host sites, intron sequences and secondary structures, or isolates for 18S and 28S rDNA intron insertion and deletion, the more popular they are. No matter 18S rDNA introns or 18S rDNA introns among tested isolates, complementary base pairing at the splicing sites in P1-IGS-P10 tertiary helix around 5’-end introns and exons were weak.

scholarly journals Morphological and molecular characterization of Sarcocystis wenzeli in chickens (Gallus gallus) in China

2020 ◽  
Author(s):  
Jing Pan ◽  
Chunli Ma ◽  
Zhumei Huang ◽  
Yulong Ye ◽  
Hongxia Zeng ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
18S Rdna ◽  
Sequence Similarity ◽  
Rpob Gene ◽  
28S Rdna ◽  
Ground Substance ◽  
Molecular Characteristics ◽  
Cox1 Gene ◽  
Intermediate Hosts ◽  
Sarcocystis Spp

Abstract Background: There has been considerable confusion concerning the number and classification of Sarcocystis spp. in chickens. Scarce nucleotide data of Sarcocystis spp. from chickens are provided in GenBank. The study aimed to investigate the morphological and molecular characteristics of Sarcocystis spp. found in chickens in China.Methods: Tissues from 33 chickens were collected in 2019. Sarcocysts were observed using light (LM) and transmission electron microscopy (TEM). Individual sarcocysts from different chickens were selected for DNA extraction, and five loci, 18S rDNA, 28S rDNA, ITS1 region, the mitochondrial cox1 gene and the apicoplastic rpoB gene, were amplified from each sarcocyst, sequenced and analyzed.Results: Only S. wenzeli was found in 14 of 33 (42.4%) chickens. Under LM, the sarcocysts were microscopic and exhibited palisade-like villar protrusions measuring 1.5–2.8 μm. Ultrastructurally, the sarcocyst wall contained numerous stubby hill-like villar protrusions. The protrusions included scattered microtubules, which extended from the tips of the protrusions into the ground substance. The five loci were successfully sequenced and the sequences deposited in GenBank. At 18S rDNA, ITS1 and cox1, the most similar sequences in GenBank were those of Sarcocystis sp. obtained from the brains of chickens, i.e. 99.9–100%, 98.1–98.5% and 99.3% identity, respectively. The five loci (18S rDNA, 28S rDNA, ITS1, cox1 and rpoB) showed different levels of interspecific sequence similarity with other closely related species of Sarcocystis (e.g. 99.8%, 99.0–99.2%, 89.3-89.7%, 98.5%, and 97.5%, respectively, with S. anasi). Phylogenetic analysis based on four of the loci (18S rDNA, cox1, rpoB and ITS1) revealed that S. wenzeli formed an independent clade with Sarcocystis spp. that utilize geese or ducks as intermediate hosts and canines as the known or presumed definitive host.Conclusions: To our knowledge, the sequences of 28S rDNA and rpoB reported here constitute the first records of genetic markers of Sarcocystis spp. in chickens. Based on molecular analysis, S. wenzeli might be responsible for the neurological disease in chickens, and ITS1 and rpoB are more suitable for discriminating it from closely related Sarcocystis spp. Phylogenetic analysis revealed that S. wenzeli presents a close relationship with Sarcocystis spp. in geese or ducks.

scholarly journals Internal phylogeny of the Chilopoda (Myriapoda, Arthropoda) using complete 18S rDNA and partial 28S rDNA sequences

1999 ◽  
Vol 354 (1380) ◽  
pp. 215-222 ◽  
Author(s):  
Gonzalo Giribet ◽  
Salvador Carranza ◽  
Marta Riutort ◽  
Jaume Baguñà ◽  
Carles Ribera
Keyword(s):  
18S Rdna ◽  
Gene Sequence ◽  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Strong Support ◽  
28S Rdna ◽  
Rdna Sequences ◽  
Mode Of Life ◽  
Branch Support ◽  
28S Rdna Sequences

The internal phylogeny of the ‘myriapod’ class Chilopoda is evaluated for 12 species belonging to the five extant centipede orders, using 18S rDNA complete gene sequence and 28S rDNA partial gene sequence data. Equally and differentially weighted parsimony, neighbour–joining and maximum–likelihood were used for phylogenetic reconstruction, and bootstrapping and branch support analyses were performed to evaluate tree topology stability. The results show that the Chilopoda constitute a monophyletic group that is divided into two lines, Notostigmophora (= Scutigeromorpha) and Pleurostigmophora, as found in previous morphological analyses. The Notostigmophora are markedly modified for their epigenic mode of life. The first offshoot of the Pleurostigmophora are the Lithobiomorpha, followed by the Craterostigmomorpha and by the Epimorpha s. str. (= Scolopendromorpha + Geophilomorpha), although strong support for the monophyly of the Epimorpha s. lat. (= Craterostigmomorpha + Epimorpha s. str.) is only found in the differentially weighted parsimony analysis.

Characterization of the complete nuclear ribosomal DNA sequences of Eurytrema pancreaticum

2017 ◽  
Vol 92 (4) ◽  
pp. 484-490 ◽  
Author(s):  
X. Su ◽  
Y. Zhang ◽  
X. Zheng ◽  
X.X. Wang ◽  
Y. Li ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
18S Rdna ◽  
Internal Transcribed Spacer ◽  
28S Rdna ◽  
Nuclear Ribosomal Dna ◽  
Economic Losses ◽  
Length Variation ◽  
5.8S Rdna ◽  
Rdna Sequences

AbstractEurytrema pancreaticum is one of the most common trematodes of cattle and sheep, and also infects humans occasionally, causing great economic losses and medical costs. In this study, the sequences of the complete nuclear ribosomal DNA (rDNA) repeat units of five E. pancreaticum individuals were determined for the first time. They were 8306–8310 bp in length, including the small subunit (18S) rDNA, internal transcribed spacer 1 (ITS1), 5.8S rDNA, internal transcribed spacer 2 (ITS2), large subunit (28S) rDNA and intergenic spacer (IGS). There were no length variations in any of the investigated 18S (1996 bp), ITS1 (1103 bp), 5.8S (160 bp), ITS2 (231 bp) or 28S (3669 bp) rDNA sequences, whereas the IGS rDNA sequences of E. pancreaticum had a 4-bp length variation, ranging from 1147 to 1151 bp. The intraspecific variations within E. pancreaticum were 0–0.2% for 18S rDNA, 0–0.5% for ITS1, 0% for 5.8S rDNA and ITS2, 0–0.2% for 28S rDNA and 2.9–20.2% for IGS. There were nine types of repeat sequences in ITS1, two types in 28S rDNA, but none in IGS. A phylogenetic analysis based on the 18S rDNA sequences classified E. pancreaticum in the family Dicrocoeliidae of Plagiorchiata, closely related to the suborder Opisthorchiata. These results provide useful information for the further study of Dicrocoeliidae trematodes.

scholarly journals First detection of Eimeria species in Myanmar domestic goats with both microscopic and molecular methods

Parasite ◽  
2020 ◽  
Vol 27 ◽  
pp. 38
Author(s):  
Saw Bawm ◽  
Tay Zar Bhone Win ◽  
Shwe Yee Win ◽  
Lat Lat Htun ◽  
Ryo Nakao ◽  
...  
Keyword(s):  
18S Rdna ◽  
Eimeria Species ◽  
Morphological Characters ◽  
Farm Animals ◽  
Detection Rates ◽  
Rdna Sequences ◽  
Faecal Samples ◽  
18S Rdna Sequences ◽  
Flotation Method ◽  
Coi Sequences

Coccidiosis is of great economic importance in many farm animals. This study involved analysis of 280 faecal samples collected from 12 traditional goat farms from Nay Pyi Taw area, Myanmar. Faecal samples were examined by the flotation method and concentrated oocysts were identified on the basis of morphological characters. Of 280 faecal samples examined, 168 (60.0%) were positive for Eimeria oocysts. Three different Eimeria species were identified and their positive detection rates in the herd were: E. arloingi (25.4%), followed by E. hirci (20.7%) and E. christenseni (13.9%). Identifications were confirmed by 18S rDNA and COI sequences. 18S rDNA sequences showed 100% homology with, respectively, E. christenseni reported from Australia, E. arloingi reported from Australia and Iran, and E. hirci from Australia. COI sequences of E. christenseni, E. hirci, and E. arloingi, respectively, exhibited 98.9%, 98.4%, and 98.5% similarities with those reported from Australia. This is the first report of Eimeria infection in Myanmar goats.

The phylogenetic relationships between Amphinomidae, Archinomidae and Euphrosinidae (Amphinomida: Aciculata: Polychaeta), inferred from molecular data

2008 ◽  
Vol 88 (3) ◽  
pp. 509-513 ◽  
Author(s):  
Helena Wiklund ◽  
Arne Nygren ◽  
Fredrik Pleijel ◽  
Per Sundberg
Keyword(s):  
Maximum Likelihood ◽  
Hydrothermal Vent ◽  
Phylogenetic Relationships ◽  
18S Rdna ◽  
Single Species ◽  
Molecular Data ◽  
Junior Synonym ◽  
28S Rdna ◽  
Bayesian Analyses ◽  
The Family

Amphinomida is an ‘isolated’ clade within the polychaete group Aciculata and traditionally includes the families Amphinomidae, Archinomidae and Euphrosinidae. Archinomidae were erected for a single species, the hydrothermal vent polychaete Archinome rosacea. Originally, A. rosacea was assigned to Euphrosinidae although it shares more morphological similarities with Amphinomidae. In this study we assess the position of Archinome, Euphrosinidae and Amphinomidae by using molecular data from nuclear 18S rDNA and 28S rDNA. Parsimony, maximum likelihood and Bayesian analyses are performed on the nucleotide datasets covering in total 19 terminals from Amphinomidae, Euphrosinidae, Archinomidae and outgroups. Our results conclusively show that Euphrosinidae and Amphinomidae are sister taxa and that Archinome is sister to Chloeia within Amphinomidae. Based on these results the family name Archinomidae is treated as a junior synonym of Amphinomidae.

Molecular identification of two morphologically similar Eulecanium species: E. giganteum and E. kuwanai (Hemiptera: Coccidae)

2015 ◽  
Vol 148 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Jun Deng ◽  
Hai-Bin Li ◽  
Xu-Bo Wang ◽  
Fang Yu ◽  
Yan-Zhou Zhang ◽  
...  
Keyword(s):  
Host Plants ◽  
Ornamental Plants ◽  
Fruit Trees ◽  
28S Rdna ◽  
Similar Species ◽  
Cytochrome C Oxidase I ◽  
Match Analysis ◽  
Accurate Identification ◽  
Close Match ◽  
Coi Sequences

AbstractMost species of the genus Eulecanium Cockerell (Hemiptera: Coccidae) are important economic pests for ornamental plants and fruit trees. Two morphologically similar species, Eulecanium giganteum Shinji and E. kuwanai Kanda, are distributed mainly in China and are quite difficult to identify because of the paucity of distinguishing characteristics, which can only be observed in slide-mounted young, adult females. Furthermore, we demonstrate here that the species occur in sympatry and on many of the same host plants. Mitochondrial cytochrome c oxidase I (COI) and the D2–D3 expansion segments of 28S rDNA were used for accurate identification of these two Eulecanium species from 19 different locations in China. The average K2P distances of COI sequences were 0.47% in E. kuwanai and 0.32% in E. giganteum, and the interspecific divergences varied from 7.23% to 8.34%. Neighbour-joining (NJ) trees of COI and 28S rDNA revealed two distinct non-overlapping clusters, respectively. Meanwhile, “best close match” analysis also showed that 100% of individuals were classified successfully using COI and 28 S sequences. Differentiating between E. giganteum and E. kuwanai is challenging when using ecological and morphological traits. In contrast, identification using DNA diagnostics appears to be very effective, especially when slide-mounted specimens are difficult to obtain.

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