Molecular evidence confirms that Proctoeces humboldti and Proctoeces chilensis (Digenea: Fellodistomidae) are the same species

2010 ◽  
Vol 84 (4) ◽  
pp. 341-347 ◽  
Author(s):  
I.M. Valdivia ◽  
L. Cardenas ◽  
K. Gonzalez ◽  
D. Jofré ◽  
M. George-Nascimento ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genetic Information ◽  
Intestinal Parasite ◽  
Phylogenetic Analyses ◽  
Marine Organisms ◽  
Molecular Evidence ◽  
Rrna Gene ◽  
Taxonomic Identification ◽  
Ssu Rrna ◽  
Phylogenetic Studies

AbstractTwo species of Proctoeces Odhner, 1911 have been described in marine organisms from Chile: P. humboldti George-Nascimento & Quiroga (1983), parasitizing the gonads of keyhole limpets (Fissurella spp.), and P. chilensis Oliva (1984), an intestinal parasite of Sicyases sanguineus (Teleostei); both species were subsequently considered as P. lintoni Siddiqi & Cable (1960). To assist in the resolution of the taxonomic identification of Proctoeces species in marine organisms from Chile, phylogenetic studies using DNA sequences from the V4 region of the SSU rRNA gene were performed. Several specimens of P. lintoni were isolated from keyhole limpets (Fissurella spp.) and clingfish (S. sanguineus) from Bahia San Jorge (23°40′S) and Bahia Concepción (36°50′S). Phylogenetic analyses were conducted using three different approaches: a neighbour-joining (NJ), a maximum likelihood (ML) and Bayesian inference (BI). The phylogenetic analysis confirms that specimens of Proctoeces obtained from keyhole limpets and those specimens from the clingfish are in fact the same species. We prefer to consider our specimens as Proctoeces cf. lintoni, as the morphology of Proctoeces appears to be of doubtful value and genetic information about P. lintoni Siddiqi & Cable (1960) is not available. In addition, our results strongly suggest that there are at least three species in this genus.

Redescription and SSU rRNA gene-based phylogeny of an anaerobic ciliate, Plagiopyla ovata Kahl, 1931 (Ciliophora, Plagiopylea)

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Ran Li ◽  
Wenbao Zhuang ◽  
Congcong Wang ◽  
Hamed El-Serehy ◽  
Saleh A. Al-Farraj ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Gene Trees ◽  
Ssu Rrna Gene ◽  
Anaerobic Ciliate ◽  
Pr China

The morphology and molecular phylogeny of Plagiopyla ovata Kahl, 1931, a poorly known anaerobic ciliate, were investigated based on a population isolated from sand samples collected from the Yellow Sea coast at Qingdao, PR China. Details of the oral ciliature are documented for the first time to our knowledge and an improved species diagnosis is given. The small subunit ribosomal RNA (SSU rRNA) gene was newly sequenced and phylogenetic analyses revealed that P. ovata clusters within the monophyletic family Plagiopylidae. However, evolutionary relationships within both the family Plagiopylidae and the genus Plagiopyla remain obscure owing to undersampling, the lack of sequence data from known species and low nodal support or unstable topologies in gene trees. A key to the identification of the species of the genus Plagiopyla with validly published names is also supplied.

Chloroplast genomes of seven species of Coryloideae (Betulaceae): structures and comparative analysis

Genome ◽  
2020 ◽  
Vol 63 (7) ◽  
pp. 337-348
Author(s):  
Guanglong Hu ◽  
Lili Cheng ◽  
Wugang Huang ◽  
Qingchang Cao ◽  
Lei Zhou ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Genetic Information ◽  
Molecular Breeding ◽  
Genomic Sequence ◽  
Phylogenetic Analyses ◽  
Phylogenetic Studies ◽  
Chloroplast Genomes ◽  
Mutational Hotspots ◽  
The Family ◽  
Identification Of Species

Coryloideae is a subfamily in the family Betulaceae consisting of four extant genera: Carpinus, Corylus, Ostrya, and Ostryopsis. We sequenced the plastomes of six species of Corylus and one species of Ostryopsis for comparative and phylogenetic analyses. The plastomes are 159–160 kb long and possess typical quadripartite cp architecture. The plastomes show moderate divergence and conserved arrangement. Five mutational hotspots were identified by comparing the plastomes of seven species of Coryloideae: trnG-atpA, trnF-ndhJ, accD-psaI, ndhF-ccsA, and ycf1. We assembled the most complete phylogenomic tree for the family Betulaceae using 68 plastomes. Our cp genomic sequence phylogenetic analyses placed Carpinus, Ostrya, and Ostryopsis in a clade together and left Corylus in a separate clade. Within the genus Corylus, these analyses indicate the existence of five subclades reflecting the phylogeographical relationships among the species. The data offer significant genetic information for the identification of species of the Coryloideae, taxonomic and phylogenetic studies, and molecular breeding.

scholarly journals The phylogenetic conundrum of Lutzia (Diptera: Culicidae: Culicini): a cautionary account of conflict and support

2015 ◽  
Vol 46 (3) ◽  
pp. 269-290 ◽  
Author(s):  
Ian J. Kitching ◽  
C. Lorna Culverwell ◽  
Ralph E. Harbach
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Set ◽  
Generic Status ◽  
Strong Signal ◽  
Phylogenetic Studies ◽  
Data Support

Lutzia Theobald was reduced to a subgenus of Culex in 1932 and was treated as such until it was restored to its original generic status in 2003, based mainly on modifications of the larvae for predation. Previous phylogenetic studies based on morphological and molecular data have provided conflicting support for the generic status of Lutzia: analyses of morphological data support the generic status whereas analyses based on DNA sequences do not. Our previous phylogenetic analyses of Culicini (based on 169 morphological characters and 86 species representing the four genera and 26 subgenera of Culicini, most informal group taxa of subgenus Culex and five outgroup species from other tribes) seemed to indicate a conflict between adult and larval morphological data. Hence, we conducted a series of comparative and data exclusion analyses to determine whether the alternative positions of Lutzia are due to conflicting signal or to a lack of strong signal. We found that separate and combined analyses of adult and larval data support different patterns of relationships between Lutzia and other Culicini. However, the majority of conflicting clades are poorly supported and once these are removed from consideration, most of the topological disparity disappears, along with much of the resolution, suggesting that morphology alone does not have sufficiently strong signal to resolve the position of Lutzia. We critically examine the results of other phylogenetic studies of culicinine relationships and conclude that no morphological or molecular data set analysed in any study conducted to date has adequate signal to place Lutzia unequivocally with regard to other taxa in Culicini. Phylogenetic relationships observed thus far suggest that Lutzia is placed within Culex but further data and extended taxon sampling are required to confirm its position relative to Culex.

The morphology and phylogeny of two euplotid ciliates, Diophrys blakeneyensis spec. nov. and Diophrys oligothrix Borror, 1965 (Protozoa, Ciliophora, Euplotida)

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2757-2773 ◽  
Author(s):  
Xiaozhong Hu ◽  
Jie Huang ◽  
Alan Warren
Keyword(s):  
Salt Marshes ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Cladistic Analysis ◽  
Bootstrap Support ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Rrna Gene Sequence ◽  
Ssu Rrna Gene ◽  
Ssu Rrna Gene Sequence

The morphology, infraciliature and molecular phylogeny of two marine ciliated protozoans, Diophrys blakeneyensis spec. nov. and Diophrys oligothrix Borror, 1965, isolated from British salt marshes, were investigated using microscopic observations of live and protargol-impregnated specimens, and by small subunit (SSU) rRNA gene sequence analysis. Diophrys blakeneyensis spec. nov. is characterized as follows: cell oval to rectangular in outline; size variable, approximately 60–180 × 30–80 µm in vivo; adoral zone comprising about 45 membranelles; usually five frontal, two ventral, five transverse, two left marginal and three caudal cirri; five dorsal kineties with more than 10 dikinetids each; 7–23 spherical to ellipsoid macronuclear nodules in a ring-like pattern; marine biotope. The population of Diophrys oligothrix described here corresponds well with previous populations in terms of its general morphology and ciliary pattern, in particular the continuous ciliary rows on the dorsal side with loosely arranged cilia. The main differences between the present and previously reported populations are the broader buccal field and greater number of dorsal kineties in the present population, both of which are regarded as population-dependent features. Phylogenetic analyses based on SSU rRNA gene sequence data demonstrate that Diophrys blakeneyensis is most closely related to Diophrys oligothrix, and both organisms cluster with two congeners with high bootstrap support within a larger group that contain the core species of the Diophrys-complex. Cladistic analysis based on morphological and morphogenetic data broadly agree with the SSU rRNA gene sequence phylogeny. Both analyses suggest that the genus Diophrys may be polyphyletic.

Redescriptions of three trachelocercid ciliates (Protista, Ciliophora, Karyorelictea), with notes on their phylogeny based on small subunit rRNA gene sequences

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3506-3514 ◽  
Author(s):  
Ying Yan ◽  
Yuan Xu ◽  
Zhenzhen Yi ◽  
Alan Warren
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Small Subunit Rrna ◽  
Small Subunit Rrna Gene ◽  
Ssu Rrna Gene Sequence ◽  
First Time

Three trachelocercid ciliates, Kovalevaia sulcata (Kovaleva, 1966) Foissner, 1997, Trachelocerca sagitta (Müller, 1786) Ehrenberg, 1840 and Trachelocerca ditis (Wright, 1982) Foissner, 1996, isolated from two coastal habitats at Qingdao, China, were investigated using live observation and silver impregnation methods. Data on their infraciliature and morphology are supplied. The small subunit rRNA (SSU rRNA) genes of K. sulcata and Trachelocerca sagitta were sequenced for the first time. Phylogenetic analyses based on SSU rRNA gene sequence data indicate that both organisms, and the previously sequenced Trachelocerca ditis, are located within the trachelocercid assemblage and that K. sulcata is sister to an unidentified taxon forming a clade that is basal to the core trachelocercids.

scholarly journals First description of male Philometra thaiensis Moravec, Fiala et Dyková, 2004 (Nematoda: Philometridae) from the body cavity of the eyespot pufferfish Tetraodon biocellatus Tirant, and evolutionary relationships of this species with other dracunculoids as inferred from SSU rRNA gene sequences

2014 ◽  
Vol 51 (3) ◽  
pp. 236-245 ◽  
Author(s):  
K. Quiazon ◽  
T. Yoshinaga ◽  
H. Doi ◽  
J. Araki ◽  
K. Ogawa
Keyword(s):  
18S Rrna ◽  
Molecular Data ◽  
Small Subunit ◽  
Body Cavity ◽  
The Body ◽  
Evolutionary Relationships ◽  
Rrna Gene ◽  
Taxonomic Identification ◽  
Ssu Rrna ◽  
First Time

Abstract Finding male philometrid nematodes is essential for taxonomic identification among congeneric species. In this study, male Philometra thaiensis Moravec, Fiala et Dyková, 2004 were collected and described for the first time, from the body cavity of the freshwater fish (eyespot pufferfish) Tetraodon biocellatus Tirant (Tetraodontiformes, Tetraodontidae), and conspecific females were redescribed based on the additional morphological biometrics examined. Molecular examination was carried out on the small subunit 18S rRNA, revealing the evolutionary relationships of P. thaiensis and reported philometrid species (Philometra and Philometroides) from Japan with other dracunculoids deposited in the GenBank. Based on the molecular data, there are some genera (Philometra, Philometroides, Clavinema, and Margolisianum [genus inquirendum]) requiring further morphological re-evaluation that should be supported with molecular data.

scholarly journals Morphology, ontogenetic features and SSU rRNA gene-based phylogeny of a soil ciliate, Bistichella cystiformans spec. nov. (Protista, Ciliophora, Stichotrichia)

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4049-4060 ◽  
Author(s):  
Yangbo Fan ◽  
Xiaozhong Hu ◽  
Feng Gao ◽  
Saleh A. Al-Farraj ◽  
Khaled A. S. Al-Rasheid
Keyword(s):  
Novel Species ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Final Conclusion ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
The Novel ◽  
Ssu Rrna Gene ◽  
To Come ◽  
Mode 3

The morphology, ontogeny and SSU rRNA gene-based phylogeny of Bistichella cystiformans spec. nov., isolated from the slightly saline soil of a mangrove wetland in Zhanjiang, southern China, were investigated. The novel species was characterized by having five to eight buccal cirri arranged in a row, three to five transverse cirri, four macronuclear nodules aligned, and 17–32 and 20–34 cirri in frontoventral rows V and VI, respectively, both extending to the transverse cirri. The main ontogenetic features of the novel species were as follows: (1) the parental adoral zone of the membranelles is completely inherited by the proter; (2) the frontoventral and transverse cirri are formed in a six-anlagen mode; (3) basically, the frontal-ventral-transverse cirral anlagen II–V generate one transverse cirrus each at their posterior ends, while anlage VI provides no transverse cirrus; (4) both marginal rows and dorsal kineties develop intrakinetally, no dorsal kinety fragment is formed; and (5) the macronuclear nodules fuse into a single mass at the middle stage. Phylogenetic analyses based on the SSU rRNA gene showed that the novel species groups with the clade containing Bistichella variabilis, Parabistichella variabilis, Uroleptoides magnigranulosus and two species of the genus Orthoamphisiella. Given present knowledge, it was considered to be still too early to come to a final conclusion regarding the familial classification of the genus Bistichella; further investigations of key taxa with additional molecular markers are required.

scholarly journals A rare case of equine Haemotropic Mycoplasma infection in Nigeria

2021 ◽  
Vol 41 (3) ◽  
pp. 274-286
Author(s):  
A.N Happi ◽  
P.E Oluniyi
Keyword(s):  
16S Rrna ◽  
Bacterial Infections ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Clinical Findings ◽  
Epidemiological Surveillance ◽  
Response To Treatment ◽  
Molecular Evidence ◽  
Rrna Gene ◽  
16S Rrna Sequence

Equine haemotropic mycoplasmosis (EHM) is a condition rarely reported worldwide. A horse presented with unspecific clinical findings and non-response to treatment to the common and endemic haemoparasitic and bacterial infections, warranted a thorough molecular investigation of suspected haemoparasitic infection given the fluctuating parasitaemia and the low sensitivity and specificity of Light Microscopy (LM) detection of haemoparasitic infections. Blood collected from an adult horse, domiciled at the University of Ibadan Veterinary Teaching Hospital, Ibadan, Nigeria was screened by LM and PCR techniques for haemo-parasites. The 16S rRNA gene of pan-Hemoplasma spp was targeted amplified and sequenced using Sanger automatic sequencing techniques. This case shows the very first molecular evidence of EHM in Africa and Nigeria, and the third case in the World. Microscopic examination of the horse’s blood smear presented with signs of lethargy, inactivity, anorexia and moderate emaciation, showed numerous coccoid-shaped epierythrocytic parasites. Subsequent 16S rRNA sequence data and phylogenetic analyses confirmed the presence of a haemotropic mycoplasma (‘Candidatus M. haemocervae’–like) in the horse. The hemoplasma sequence obtained falls in the same clade with some Candidatus Mycoplasma haemocervae sequences with which it shared more than 98.7% homology. This finding suggests that horses in this geographical region may also be suffering from EHM and calls for the need of epidemiological surveillance of equine hemoplasmosis with emphasis on their clinical, economic, performance and zoonotic implications in the sub-region. Keywords: Nigeria, Horse, Haemotropic mycoplasma, ‘Candidatus M. haemocervae’–like

scholarly journals ULASAN Kajian Filogenetika Molekuler dan Peranannya dalam Menyediakan Informasi Dasar untuk Meningkatkan Kualitas Sumber Genetik Anggrek

2016 ◽  
Vol 4 (1) ◽  
pp. 35 ◽  
Author(s):  
Topik Hidayat ◽  
Adi Pancoro
Keyword(s):  
Dna Sequences ◽  
Molecular Phylogenetics ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Biochemical Properties ◽  
Intergeneric Hybrids ◽  
Basic Knowledge ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
Ornamental Crops

<p>Early information<br />resulted from molecular phylogenetic studies of many important<br />ornamental crops is often less attention to many<br />growers and farmers. Phylogenetics is one of the most preferable<br />method in systematics to reconstruct evolutionary<br />relationships of groups of biological organisms in order to<br />understand their biodiversities. This has been revolutionized<br />by DNA sequences data. In this method, a group of organisms<br />that shares many identical characteristics are considered<br />to be closely related; deriving from a common<br />ancestor and is assumed to have similar genetic patterns<br />and biochemical properties. By these basic principles,<br />molecular phylogenetics plays important roles in revealing a<br />basic knowledge on pattern of relationships to which<br />genetic resources can be improved. Over the past decade,<br />botanists have done several thousand phylogenetic analyses<br />based on molecular data of economically and horticulturally<br />important crops. Orchids are the best example for this.<br />There is no doubt that most orchid plants had played roles in<br />horticulture and hybridization. At present, many infrageneric<br />and intergeneric hybrids are available commercially. Successful<br />hybridization can be achieved if two or more individual<br />plants understudy are closely related in respect to their<br />genetics and evolution.</p>

scholarly journals Four new species in the Tremella fibulifera complex (Tremellales, Basidiomycota)

MycoKeys ◽  
2021 ◽  
Vol 82 ◽  
pp. 33-56
Author(s):  
Long-Fei Fan ◽  
Renato Lúcio Mendes Alvarenga ◽  
Tatiana Baptista Gibertoni ◽  
Fang Wu ◽  
Yu-Cheng Dai
Keyword(s):  
New Species ◽  
Rna Polymerase Ii ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Elongation Factor ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Small Subunit ◽  
Molecular Evidence ◽  
Rrna Gene

Samples of species close to Tremella fibulifera from China and Brazil are studied, and T. fibulifera is confirmed as a species complex including nine species. Five known species (T. cheejenii, T. fibulifera s.s., T. “neofibulifera”, T. lloydiae-candidae and T. olens) and four new species (T. australe, T. guangxiensis, T. latispora and T. subfibulifera) in the complex are recognized based on morphological characteristics, molecular evidence, and geographic distribution. Sequences of eight species of the complex were included in the phylogenetic analyses because T. olens lacks molecular data. The phylogenetic analyses were performed by a combined sequence dataset of the internal transcribed spacer (ITS) and the partial nuclear large subunit rDNA (nLSU), and a combined sequence dataset of the ITS, partial nLSU, the small subunit mitochondrial rRNA gene (mtSSU), the translation elongation factor 1-α (TEF1), the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2). The eight species formed eight independent lineages with robust support in phylogenies based on both datasets. Illustrated description of the six species including Tremella fibulifera s.s., T. “neofibulifera” and four new species, and discussions with their related species, are provided. A table of the comparison of the important characteristics of nine species in the T. fibulifera complex and a key to the whitish species in Tremella s.s. are provided.

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