scholarly journals Molecular evolutionary relationships of Vietnamese and global pulmonary Paragonimus species in the family paragonimidae and suborder xiphidiata (Platyhelminthes: Trematoda)

2021 ◽  
Vol 18 (4) ◽  
pp. 653-662
Author(s):  
Nguyen Thi Khue ◽  
Pham Thi Khanh Linh ◽  
Do Thi Roan ◽  
Doan Thi Thanh Huong ◽  
Pham Ngoc Doanh ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Analyses ◽  
The Philippines ◽  
28S Rdna ◽  
Evolutionary Relationships ◽  
Evolutionary Analysis ◽  
North West ◽  
Rdna Sequences ◽  
The Family ◽  
28S Rdna Sequences

Paragonimiasis, caused by Paragonimus species belonging to the family Paragonimidae of the suborder Xiphidiata (Platyhelminthes: Trematoda), often occurs in poor, upland, ethnic minorities, in Vietnam and the world. Asian Paragonimus species are distributed from Japan, South Korea, along with North and Southeast China, North-West and Central Vietnam, the Philippines, Thailand, Bangladesh, India, and Sri Lanka. There are various genetic variants, strains, and genotypes forming different complexes and evolutionary lineages. The 18S, 28S rDNA sequences and the intergenic transcribed spacer regions (ITS-1, ITS-2) of nuclear ribosomal transcription units are commonly used as molecular markers in genetic studies and phylogenetic analyses. We obtained a portion of 28S rDNA (domains D1–D3) of Paragonimus spp. including P. heterotremus (from Vietnam), P. ohirai (Japan), P. iloktsuenensis (Japan), and P. westermani (India and Vietnam) and conducted phylogenetic analysis for molecular evolutionary studies. The results showed that the family Paragonimidae formed the biggest cluster in a phylogenetic tree, which comprises of 46 sequences of 11 species belonging to 11 subgroups, among which the P. westermani complex of strains originating from China, Korea, Japan, India, Philippines, Malaysia, and Vietnam is present. P. westermani complex is arranged in a position of "sister" (sister group) with the subgroup P. siamensis. The P. heterotremus and P. ohirai complexes, and the P. miyazakii, P. harinasutai, P. mexicanus, P. kellicotti, and P. macrorchis complexes are clustered in a common population. P. westermani of Vietnam is in close proximity to the East Asian strains, as of which has been previously reported. P. ohirai and P. iloktsuenensis are considered “sibling” species, sharing the same clade. Phylogenetic analysis using the 28S rDNA sequences directly presented species position and their molecular evolutionary relationships in the families Paragonimidae, Troglotrematidae, Nanophyetidae, and Collyriclidae. Evolutionary analysis has also clarified a number of complex delineation problems and made a clear nomenclature for Paragonimus sp. of Vietnam, in particular, which has scientific grounds merited to recognize as that it is really the P. westermani species.

Phylogenetic relationships of the lower Cyclorrhapha (Diptera: Brachycera) based on 28S rDNA sequences

2002 ◽  
Vol 33 (4) ◽  
pp. 445-456 ◽  
Author(s):  
Brian M. Wiegmann ◽  
Kenneth P. Collins
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
28S Rdna ◽  
Morphological Data ◽  
Monophyletic Clade ◽  
Rdna Sequences ◽  
28S Rdna Sequences

AbstractCyclorrhaphan Diptera are an extremely successful clade of ecologically and phylogenenetically important flies. Despite their significance the relationships among lower cyclorrhaphans ('Aschiza') remain controversial in spite of several morphologically based phylogenetic analyses. We sequenced a 2.7-kb fragment of 28S rDNA for taxa representing all lower cyclorrhaphan families (except Ironomyiidae), four schizophoran families, and seven empidoid out-group taxa. Phylogenetic analysis of these data strongly supports a monophyletic Cyclorrhapha (including the enigmatic taxon Opetia nigra) that is divided into two clades - a well-supported Eumuscomorpha (Syrphidae + Pipunculidae + Schizophora), and a weakly-supported Platypezoidea (all non-Eumuscomorpha). Consequently, the former grouping known as Aschiza, which included syrphids and pipunculids, is not a valid monophyletic clade. Within Platypezoidea, most of our analyses place Lonchopteridae as sister group to Opetiidae, and strongly support the monophyly of Sciadoceridae + Phoridae. Among the Eumuscomorpha we do not recover the monophyly of Syrphoidea (Syrphidae + Pipunculidae). Instead, all analyses place Pipunculidae as the sister group to Schizophora. This novel finding has never been proposed based on morphological data and will require more data (both molecular and morphological) and taxa to confirm.

Phylogenetic analysis of the superfamily Hemiuroidea (Platyhelminthes, Neodermata:Trematoda) based on partial 28S rDNA sequences

Parasitology ◽  
2018 ◽  
Vol 146 (5) ◽  
pp. 596-603 ◽  
Author(s):  
Sergey G. Sokolov ◽  
Dmitry M. Atopkin ◽  
Misako Urabe ◽  
Ilya I. Gordeev
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationship ◽  
Phylogenetic Relationships ◽  
Sister Group ◽  
28S Rdna ◽  
Monophyletic Group ◽  
Rdna Sequences ◽  
The Family ◽  
Statistical Support ◽  
28S Rdna Sequences

AbstractIn the present paper, the phylogenetic relationships between genera, subfamilies and families of the Hemiuroidea are explored. Twelve new sequences of 28 rDNA and data taken from GenBank (NSBI) on 43 species affiliated to 34 genera were included in the analysis. Most of the hemiuroidean trematodes form two highly supported clades (A and B), which are sister groups to each other.Hemipera manterijoined withGonocercaspp. with moderate statistical support. This clade is basal relative to the clades A and B. Сlade A is polytomic and contains representatives of the families Accacoeliidae, Syncoeliidae, Didymozoidae, Hirudinellidae and Sclerodistomidae, and derogenid subfamilies Derogeninae and Halipeginae. At the same time, the Syncoeliidae, Hirudinellidae and Accacoeliidae form a well-supported monophyletic group. The phylogenetic relationship between Derogeninae and Halipeginae is poorly resolved. Сlade B unites the isoparorchiid, bunocotylid, lecithasterid and hemiurid trematodes. Our data re-establishes the family Bunocotylidae, which consists of two subfamilies, Opisthadeninae and Bunocotylinae, and theMachidatrema chilostoma+Hysterolecithoides frontilatusgroup. The Bunocotylidae is the sister group to the Hemiuridae + Lecithasteridae group and the Isoparorchiidae is a basal relative to the representatives of these three hemiuroid families.

scholarly journals Phylogenetic analyses of ribosomal transcription units from Haplorchis taichui and H. pumilio species of Heterophyidae (Platyhelminthes: Opisthorchiata)

2021 ◽  
Vol 18 (4) ◽  
pp. 643-652
Author(s):  
Le Thi Viet Ha ◽  
Nguyen Thi Khue ◽  
Dong Van Quyen ◽  
Le Thanh Hoa
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Analyses ◽  
28S Rdna ◽  
Rrna Genes ◽  
28S Rrna ◽  
Coding Sequence ◽  
Rdna Sequences ◽  
The Family ◽  
28S Rdna Sequences ◽  
Haplorchis Taichui

Heterophyidiasis caused by minute intestinal flukes becomes of public concern in many countries worldwide. Haplorchis taichui and H. pumilio, belonging to the family Heterophyidae (Platyhelminthes: Trematoda) are two of many infecting humans and commonly found in Vietnam. Sequence study of these two small intestinal flukes is still very limited, hence we need more prospective markers for taxonomic identification and classification. This study provides complete coding sequence of the ribosomal transcription units (rTU) from H. taichui and H. pumilio (Vietnamese samples) and demonstrates the use of complete 28S rDNA sequences for phylogenetic analysis.The complete coding sequence of the rTU (from 5' 18S to 3' 28S), consisting of complete 18S, ITS-1, 5.8S, ITS2 and complete 28S rRNA genes and spacers, from H. taichui (7,268 bp) and H. pumilio (7,416 bp) from human hosts in Vietnam, were determined and annotated. The 18S and 5.8S genes of both species were of the same length (1,992 bp/18S, 160 bp/5.8S), but 28S genes differed (3,875 bp/H. taichui and 3,870 bp/H. pumilio). ITS-1 in H. taichui (797 bp) and ITS-2 in H. pumilio (280 bp) do not contain tandem repeat units (TRUs), while ITS-1 in H. pumilio (1,106 bp) contains 3 TRUs of 136 bp/each and 2 TRUs of 116 bp/each and ITS-2 in H. taichui (444 bp) contain 3 TRUs (83–85 bp/each). A phylogenetic tree inferred from the alignment of complete 28S rDNA sequences of 32 trematode strains/species, including 2 Vietnamese Haplorchis spp. and 24 species of 8 families in the suborders Xiphidiata (families Nanophyetidae, Paragonimidae, Collyriclidae), Opisthorchiata (Heterophyidae, Opisthorchiidae), and Echinostomata (Echinostomatidae, Fasciolidae).  and Schistosoma japonicum of the family Schistosomatidae is used as an outgroup. The topology of the phylogenetic tree clearly confirmed the status of the Vietnamese H. taichui and H. pumilio species. These species gathered in a group (in the family Heterophyidae) clearly identified in the position of "sister” group to those in the family Opisthorchiidae (suborder Opisthorchiata, superfamily Opisthorchioidea).

Generic classification of some more hyphomycetes with solitary conidia borne on phialides

1998 ◽  
Vol 76 (9) ◽  
pp. 1570-1583 ◽  
Author(s):  
W Gams ◽  
K O'Donnell ◽  
H -J Schroers ◽  
M Christensen
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Elongation Factor ◽  
28S Rdna ◽  
New Combination ◽  
Rdna Sequences ◽  
28S Rdna Sequences ◽  
Three New Species ◽  
Morphological Species

Unlike most phialide-producing fungi that liberate a multiplicity of conidia from each conidiogenous cell, only single conidia are formed on phialide-like conidiogenous cells in Aphanocladium, Verticimonosporium, and some species of Sibirina. A group of isolates obtained from soil of native Artemisia tridentata (sagebrush) grassland in Wyoming and from desert soil in Iraq is compared with these genera and classified as a fourth genus, Stanjemonium, honouring Stanley J. Hughes. Phylogenetic analyses of partial nuclear small- (18S) and large-subunit (28S) rDNA sequences indicate that Stanjemonium spp. form a monophyletic group with Emericellopsis. Sequences from the nuclear 18S and 28S rDNA were too conserved to resolve morphological species of Stanjemonium; however, phylogenetic analysis of b-tubulin and translation elongation factor 1a gene exons and introns resolved all species distinguished morphologically. Numerous conidiogenous cells or denticles are scattered along the cells of aerial hyphae in Aphanocladium and Stanjemonium spp., very rapidly collapsing into denticles in the former, somewhat more persistent and leaving broad scars in the latter. In Cladobotryum-Sibirina and Verticimonosporium spp., conidiogenous cells are discrete in terminal and intercalary whorls; phialides of the latter taxon are particularly swollen. The taxonomy of Aphanocladium is not yet resolved. Two species are recognized in Verticimonosporium. Three new species of Stanjemonium are described, and one new combination from Aphanocladium is proposed, along with one new species of Cladobotryum.Key words: Aphanocladium, Cladobotryum, conidiogenesis, hyphomycetes, molecular phylogeny, phialide, Stanjemonium, systematics, Verticimonosporium.

Macrostomum shenda and M. spiriger, two new brackish-water species of Macrostomum (Platyhelminthes: Macrostomorpha) from China

Zootaxa ◽  
2019 ◽  
Vol 4603 (1) ◽  
pp. 105
Author(s):  
FAN XIN ◽  
SI-YU ZHANG ◽  
YONG-SHI SHI ◽  
LEI WANG ◽  
YU ZHANG ◽  
...  
Keyword(s):  
Brackish Water ◽  
Phylogenetic Analyses ◽  
28S Rdna ◽  
Body Region ◽  
Rdna Sequences ◽  
Molecular Phylogenetic ◽  
28S Rdna Sequences ◽  
Pore Opening ◽  
Brackish Water Species ◽  
Water Species

In this study, two new brackish-water species of Macrostomum (M. shenda n. sp. and M. spiriger n. sp.) collected from Shenzhen, China, were described based on morphological, histological, and molecular phylogenetic analyses. Macrostomum shenda n. sp. differs from its congeners in the oblique and non-thickening distal opening of its narrow funnel-shaped stylet. In addition, its sperm have neither bristles nor brush, and are surrounded by an undulating membrane in the mid-body region. In M. spiriger n. sp., the stylet is spirally twisted. Its reproductive apparatus has a seminal bursal pore opening exteriorly. Results of the 18S and 28S rDNA phylogenetic analyses also support the establishments of these two new species. Moreover, the 18S and 28S rDNA sequences of some species within Macrostomum in previous studies have been revised to avoid ambiguity, while Macrostomum dongyuanensis Wang & Sun, 2015 was re-identified as a new record of M. quiritium Kolasa, 1973 from China.

scholarly journals Mexicana rubra sp. nov. and Encotyllabe cf. spari Yamaguti, 1934 (Monogenea) of Orthopristis ruber (Cuvier, 1830) from the Brazilian Coast off Rio de Janeiro

2017 ◽  
Vol 54 (4) ◽  
pp. 336-347
Author(s):  
A. C. A. Camargo ◽  
J. L. Luque ◽  
C. P. Santos
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Rio De Janeiro ◽  
Genetic Data ◽  
28S Rdna ◽  
Brazilian Coast ◽  
Diagnostic Features ◽  
Rdna Sequences ◽  
28S Rdna Sequences ◽  
Partial 18S

Summary Mexicana rubra sp. nov. and Encotyllabe cf. spari are described from the gills of the marine fish Orthopristis ruber (Haemulidae) caught off Rio de Janeiro, Brazil. Morphological, ultrastructural and genetic data are provided. The main diagnostic features of this new species of ectoparasite are a posteriorly bipartite testis, a ventral bar with three deep bowed projections and a dorsal bar with two deep, conspicuous, antero-lateral indentations. Genetic data on Mexicana rubra sp. nov. are based on the ITS1, 5.8S and partial 18S and 28S rDNA. This is the sixth known species of Mexicana Caballero & Bravo-Hollis, 1959, a key to which is also presented. Encotyllabe cf. spari Yamaguti, 1934 is described from the same host, with new ultrastructural data and new partial 18S and 28S rDNA sequences. A phylogenetic analysis based on partial 18S and 28S sequences is undertaken for both species.

The aberrant millipede genus Pteridoiulus and its position in a revised molecular phylogeny of the family Julidae (Diplopoda : Julida)

2013 ◽  
Vol 27 (5) ◽  
pp. 515 ◽  
Author(s):  
Henrik Enghoff ◽  
Gitte Petersen ◽  
Ole Seberg
Keyword(s):  
16S Rdna ◽  
Eastern Alps ◽  
28S Rdna ◽  
28S Rrna ◽  
Rdna Sequences ◽  
16S Gene ◽  
The Family ◽  
Species Pairs ◽  
Gap Opening ◽  
28S Rdna Sequences

A phylogenetic analysis of 62 species (32 genera) of the Palaearctic millipede family Julidae, including the aberrant alpine genus Pteridoiulus Verhoeff, 1913, was made based on partial sequences of the mitochondrial 16S rRNA (16S) gene and the nuclear 28S rRNA (28S) gene, respectively. The two datasets (16S rDNA and 28S rDNA) were analysed in combination but treated as different partitions using direct optimisation as implemented in POY. The 16S rDNA and the 28S rDNA sequences vary from 410 to 449 bp and from 467 to 525 bp in length, respectively. All searches were performed under six different gap opening costs, an extension gap cost of 1, and a substitution cost of 2. Based on previous investigations the optimal gap opening cost was set to 4, and the robustness of different gap opening costs ranging from 1 to 6 investigated. Additionally, the two data partitions were aligned individually using MAFTT and run in TNT both with gaps treated as a fifth state, and as missing, and finally the alignments were used as input in a maximum likelihood (ML) analysis. The order Julida and the family Julidae were recovered as monophyletic under all weight sets in POY, as well as in the TNT and ML analyses. Likewise, in all analyses Pteridoiulus was found to be sister to another monotypic alpine genus, Heteroiulus Verhoeff, 1897. The Pteridoiulus + Heteroiulus clade is robust to parameter changes but lacks morphological support. The distribution pattern of the clade, Pteridoiulus in the eastern Alps (mainly Austria), Heteroiulus in the southern Alps (Italy) seems unique, since similar patterns all involve very similar, closely related species pairs.

Phylogenetic analysis of the Monocotylidae (Monogenea) inferred from 28S rDNA sequences

2001 ◽  
Vol 31 (13) ◽  
pp. 1537-1547 ◽  
Author(s):  
Leslie A. Chisholm ◽  
Jess A.T. Morgan ◽  
Rob D. Adlard ◽  
Ian D. Whittington
Keyword(s):  
Phylogenetic Analysis ◽  
28S Rdna ◽  
Rdna Sequences ◽  
28S Rdna Sequences

scholarly journals Erysiphe deutziicola sp. nov. (Erysiphaceae, Ascomycota), a powdery mildew species found on Deutzia parviflora (Hydrangeaceae) with unusual appendages

MycoKeys ◽  
2019 ◽  
Vol 51 ◽  
pp. 97-106
Author(s):  
Peng-Lei Qiu ◽  
Uwe Braun ◽  
Yu Li ◽  
Shu-Yan Liu
Keyword(s):  
New Species ◽  
Powdery Mildew ◽  
Microscopic Examination ◽  
Phylogenetic Analyses ◽  
28S Rdna ◽  
Bootstrap Support ◽  
Rdna Sequences ◽  
28S Rdna Sequences ◽  
Beijing China ◽  
Ornamental Shrub

A powdery mildew (Erysiphales) has recently been collected on leaves of an ornamental shrub Deutziaparviflora in Baihua Mountain, Beijing, China. Microscopic examination of the chasmothecia suggested a species belonging to Erysiphesect.Erysiphe, above all due to mycelioid chasmothecial appendages, although circinate apices of the appendages were rather in favour of Erysiphesect.Uncinula, which is a fairly rare combination of appendage characteristics in Erysiphe. Phylogenetic analyses of ITS and 28S rDNA sequences demonstrated that the two examined powdery mildew collections on D.parviflora clustered together as an independent lineage within Erysiphe with 100% bootstrap support, representing a species of its own, which is phylogenetically allied to, but clearly distinct from Erysiphedeutziae and, in addition, morphologically quite different from all known Erysiphe species on hosts belonging to the Hydrangeaceae. The new species on D.parviflora is described as Erysiphedeutziicola.

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