Sequence variability in four mitochondrial genes among Bunostomum trigonocephalum isolates from four provinces in China

2012 ◽  
Vol 87 (4) ◽  
pp. 416-421 ◽  
Author(s):  
C.R. Wang ◽  
J.F. Gao ◽  
Q.C. Chang ◽  
F.C. Zou ◽  
Q. Zhao ◽  
...  
Keyword(s):  
Direct Sequencing ◽  
Phylogenetic Analyses ◽  
Mitochondrial Genes ◽  
Sequence Variability ◽  
Specific Sequence ◽  
Sequence Variations ◽  
The Family ◽  
Specific Variation ◽  
Geographic Regions ◽  
Inference Methods

AbstractThe present study examined sequence variability in four mitochondrial genes, namely cytochrome c oxidase subunit (cox1), cytochrome b (cytb) and NADH dehydrogenase subunits 1 and 5 (nad1 and nad5), among Bunostomum trigonocephalum isolates from four different geographic regions in China. Ten B. trigonocephalum samples were collected from each of the four provinces (Heilongjiang, Jilin, Shaanxi and Yunnan), China. A part of the cox1 (pcox1), cytb (pcytb), nad1 and nad5 genes (pnad1 and pnad5) were amplified separately from individual hookworms by polymerase chain reaction (PCR) and were subjected to direct sequencing in order to define sequence variations and their phylogenetic relationships. The intra-specific sequence variations within B. trigonocephalum were 0–1.9% for pcox1, 0–2.0% for pcytb, 0–1.6% for pnad1 and 0–1.7% for pnad5. The A+T contents of the sequences were 69.6–70.4% (pcox1), 71.9–72.7 (pcytb), 70.4–71.1% (pnad1) and 72.0–72.6% (pnad5). However, the inter-specific sequence differences among members of the family Ancylostomatidae were significantly higher, being 12.1–14.2% for pcox1, 13.7–16.0 for cytb, 17.6–19.4 for nad1 and 16.0–21.6 for nad5. Phylogenetic analyses based on the combined partial sequences of cox1, cytb, nad1 and nad5 using three inference methods, namely Bayesian inference (Bayes), maximum likelihood (ML) and maximum parsimony (MP), revealed that all the B. trigonocephalum samples form monophyletic groups, but samples from the same geographical origin did not always cluster together, suggesting that there was no obvious geographical distinction within B. trigonocephalum based on sequences of the four mtDNA genes. These results demonstrated the existence of low-level intra-specific variation in mitochondrial DNA (mtDNA) sequences among B. trigonocephalum isolates from different geographic regions.

Genetic variation among Clonorchis sinensis isolates from different geographic regions in China revealed by sequence analyses of four mitochondrial genes

2011 ◽  
Vol 86 (4) ◽  
pp. 479-484 ◽  
Author(s):  
G.H. Liu ◽  
B. Li ◽  
J.Y. Li ◽  
H.Q. Song ◽  
R.Q. Lin ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Clonorchis Sinensis ◽  
Mtdna Sequences ◽  
Specific Sequence ◽  
Opisthorchis Felineus ◽  
Phylogenetic Studies ◽  
Sequence Variations ◽  
Specific Variation ◽  
Geographic Regions ◽  
Liver Flukes

AbstractThe present study examined sequence variation in four mitochondrial (mt) genes, namely cytochrome c oxidase subunits 1 (cox1) and 2 (cox2), and NADH dehydrogenase subunits 1 and 2 (nad1 and nad2) among Clonorchis sinensis isolates from different endemic regions in China, and their phylogenetic relationships with other zoonotic trematodes were reconstructed. A portion of the cox1 and cox2 genes (pcox1 and pcox2), and nad1 and nad2 genes (pnad1 and pnad2) were amplified separately from individual liver flukes by polymerase chain reaction (PCR) and the amplicons were subjected to sequencing from both directions. The intra-specific sequence variations within C. sinensis were 0–1.6% for pcox1, 0–1.4% for pcox2, 0–0.9% for pnad1 and 0–1.0% for pnad2. Phylogenetic analyses based on the combined sequences of pcox1, pcox2, pnad1 and pnad2 revealed that all the C. sinensis isolates grouped together and were closely related to Opisthorchis felineus. These findings revealed the existence of intra-specific variation in mitochondrial DNA (mtDNA) sequences among C. sinensis isolates from different geographic regions, and demonstrated that mtDNA sequences provide reliable genetic markers for phylogenetic studies of zoonotic trematodes.

Pinnule-less polyps: a new genus and new species of Indo-Pacific Clavulariidae and validation of the soft coral genus Acrossota and the family Acrossotidae (Coelenterata: Octocorallia)  

Zootaxa ◽  
2007 ◽  
Vol 1400 (1) ◽  
pp. 27 ◽  
Author(s):  
PHILP ALDERSLADE ◽  
CATHERINE S. McFADDEN
Keyword(s):  
New Genus ◽  
Soft Coral ◽  
Phylogenetic Analyses ◽  
Mitochondrial Genes ◽  
New Combination ◽  
New Genus And Species ◽  
Coral Genus ◽  
The Family ◽  
Lateral Margins ◽  
Number Of Authors

Clavularia amboinensis Burchardt, a species described as possessing simple, pinnule-less tentacles (a fact refuted by later authors) is confirmed to be as described and is transferred as a new combination to Acrossota Bourne — a genus dismissed until now by a number of authors. The species is compared to recently collected material with live photographs. A second new genus and species, Knopia octocontacanalis, is also described. This taxon resembles Acrossota in general form, but has tentacles where the pinnules appear as though they are fused side to side along the tentacles’ lateral margins. Preliminary phylogenetic analyses of two mitochondrial genes support placement of Knopia in Clavulariidae and retention of genus Acrossota in Bourne’s unrecognised family Acrossotidae.

Sequence variability in two mitochondrial DNA regions and internal transcribed spacer among three cestodes infecting animals and humans from China

2011 ◽  
Vol 86 (2) ◽  
pp. 245-251 ◽  
Author(s):  
R.S. Dai ◽  
G.H. Liu ◽  
H.Q. Song ◽  
R.Q. Lin ◽  
Z.G. Yuan ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
The Other ◽  
Sequence Variability ◽  
Taenia Hydatigena ◽  
Specific Sequence ◽  
5.8S Rdna ◽  
Rdna Sequences

AbstractSequence variability in two mitochondrial DNA (mtDNA) regions, namely cytochromecoxidase subunit 1 (cox1) and NADH dehydrogenase subunit 4 (nad4), and internal transcribed spacer (ITS) of rDNA among and within three cestodes,Spirometra erinaceieuropaei,Taenia multicepsandTaenia hydatigena, from different geographical origins in China was examined. A portion of thecox1 (pcox1),nad4 genes (pnad4) and the ITS (ITS1+5.8S rDNA+ITS2) were amplified separately from individual cestodes by polymerase chain reaction (PCR). Representative amplicons were subjected to sequencing in order to estimate sequence variability. While the intra-specific sequence variations within each of the tapeworm species were 0–0.7% for pcox1, 0–1.7% for pnad4 and 0.1–3.6% for ITS, the inter-specific sequence differences were significantly higher, being 12.1–17.6%, 18.7–26.2% and 31–75.5% for pcox1, pnad4 and ITS, respectively. Phylogenetic analyses based on the pcox1 sequence data revealed thatT. multicepsandT. hydatigenawere more closely related to the other members of theTaeniagenus, andS. erinaceieuropaeiwas more closely related to the other members of theSpirometragenus. These findings demonstrated clearly the usefulness of mtDNA and rDNA sequences for population genetic studies of these cestodes of socio-economic importance.

Sequence variability in three mitochondrial DNA regions of Spirometra erinaceieuropaei spargana of human and animal health significance

2011 ◽  
Vol 86 (3) ◽  
pp. 271-275 ◽  
Author(s):  
W. Liu ◽  
G.H. Liu ◽  
F. Li ◽  
D.S. He ◽  
T. Wang ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Nadh Dehydrogenase ◽  
Animal Health ◽  
Hunan Province ◽  
Sequence Variability ◽  
Specific Sequence ◽  
Sequence Variations ◽  
Geographical Regions ◽  
Health Significance ◽  
Polymerase Chain

AbstractSequence variability in three mitochondrial DNA (mtDNA) regions, namely cytochrome c oxidase subunit 3 (cox3), NADH dehydrogenase subunits 1 and 4 (nad1 and nad4) in Spirometra erinaceieuropaei spargana from different geographical regions in China was examined. A portion of each of the cox3 (pcox3), nad1 (pnad1) and nad4 genes (pnad4) were amplified separately from individual S. erinaceieuropaei spargana by polymerase chain reaction (PCR). Representative amplicons were subjected to sequencing in order to estimate sequence variability. The sequences of pcox3, pnad1 and pnad4 were 541, 607 and 847 bp in length, respectively. The A+T contents of the sequences were 68.39–68.76% (pcox3), 63.76–64.91% (pnad1) and 67.18–67.77% (pnad4), respectively, while the intra-specific sequence variations within each of the S. erinaceieuropaei spargana were 0–1.5% for pcox3, 0–2.8% for pnad1 and 0–2.7% for pnad4. Phylogenetic analysis using neighbour joining (NJ), maximum likelihood (ML) and maximum parsimony (MP) methods, indicated that all the spargana isolates in Hunan Province represented S. erinaceieuropaei. These findings demonstrated clearly the usefulness of the three mtDNA sequences for population genetics studies of S. erinaceieuropaei spargana of human and animal health significance.

Sequence variation in two mitochondrial DNA regions and internal transcribed spacer among isolates of the nematode Oesophagostomum asperum originating from goats in Hunan Province, China

2014 ◽  
Vol 90 (1) ◽  
pp. 1-6 ◽  
Author(s):  
F. Li ◽  
T. Hu ◽  
N.C. Duan ◽  
W.Y. Li ◽  
Q. Teng ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Its Rdna ◽  
Hunan Province ◽  
Nuclear Ribosomal Dna ◽  
Specific Sequence ◽  
5.8S Rdna ◽  
Rdna Sequences ◽  
Specific Variation

AbstractThe present study examined sequence variability in two mitochondrial DNA (mtDNA) regions, namely cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 1 (nad1), and internal transcribed spacer (ITS) of nuclear ribosomal DNA (rDNA) among Oesophagostomum asperum isolates from goats in Hunan Province, China. A portion of the cox1 (pcox1), nad1 (pnad1) genes and the ITS (ITS1+5.8S rDNA+ITS2) rDNA were amplified by polymerase chain reaction (PCR) separately from adult O. asperum individuals and the representative amplicons were subjected to sequencing from both directions. The lengths of pcox1, pnad1 and ITS rDNA were 366 bp, 681 bp and 785 bp, respectively. The A+T contents of gene sequences were 71.5–72% for pcox1, 73.7–74.2% for pnad1 and 58–58.8% for ITS rDNA. Intra-specific sequence variations within O. asperum were 0–1.6% for pcox1, 0–1.9% for pnad1 and 0–1.7% for ITS rDNA, while inter-specific sequence differences among members of the genus Oesophagostomum were significantly higher, being 11.1–12.5%, 13.3–17.7% and 8.5–18.6% for pcox1, pnad1 and ITS rDNA, respectively. Phylogenetic analyses using combined sequences of pcox1 and pnad1, with three different computational algorithms (Bayesian inference, maximum likelihood and maximum parsimony), revealed distinct groups with high statistical support. These findings demonstrated the existence of intra-specific variation in mtDNA and rDNA sequences among O. asperum isolates from goats in Hunan Province, China, and have implications for studying molecular epidemiology and population genetics of O. asperum.

Pinnule-less polyps: a new genus and new species of Indo-Pacific Clavulariidae and validation of the soft coral genus Acrossota and the family Acrossotidae (Coelenterata: Octocorallia)  

Zootaxa ◽  
2007 ◽  
Vol 1400 (1) ◽  
pp. 27-44 ◽  
Author(s):  
PHILP ALDERSLADE ◽  
CATHERINE S. McFADDEN
Keyword(s):  
New Genus ◽  
Soft Coral ◽  
Phylogenetic Analyses ◽  
Mitochondrial Genes ◽  
New Combination ◽  
New Genus And Species ◽  
Coral Genus ◽  
The Family ◽  
Lateral Margins ◽  
Number Of Authors

Clavularia amboinensis Burchardt, a species described as possessing simple, pinnule-less tentacles (a fact refuted by later authors) is confirmed to be as described and is transferred as a new combination to Acrossota Bourne — a genus dismissed until now by a number of authors. The species is compared to recently collected material with live photographs. A second new genus and species, Knopia octocontacanalis, is also described. This taxon resembles Acrossota in general form, but has tentacles where the pinnules appear as though they are fused side to side along the tentacles’ lateral margins. Preliminary phylogenetic analyses of two mitochondrial genes support placement of Knopia in Clavulariidae and retention of genus Acrossota in Bourne’s unrecognised family Acrossotidae.

scholarly journals A Phylogenetic and Taxonomic Study on Xylodon (Hymenochaetales): Focusing on Three New Xylodon Species from Southern China

2021 ◽  
Vol 8 (1) ◽  
pp. 35
Author(s):  
Meng-Han Qu ◽  
Dong-Qiong Wang ◽  
Chang-Lin Zhao
Keyword(s):  
New Species ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Fungal Species ◽  
Molecular Evidence ◽  
Taxonomic Study ◽  
The Family ◽  
Three New Species ◽  
Inference Methods ◽  
High Support

Three wood-inhabiting fungal species, Xylodon laceratus, X. montanus, and X. tropicus spp. nov., were collected from southern China, here proposed as new taxa based on a combination of morphological features and molecular evidence. Xylodon laceratus is characterized by the resupinate basidiomata with grandinioid hymenophore having cracked hymenial surface, and ellipsoid basidiospores; X. montanus is characterized by the annual basidiomata having the hard, brittle hymenophore with cream hymenial surface, and ellipsoid to broadly ellipsoid basidiospores (3.9–5.3 × 3.2–4.3 µm); and X. tropicus is characterized by its grandinioid hymenophore with buff to a pale brown hymenial surface and subglobose basidiospores measuring 2–4.8 × 1.6–4 µm. Sequences of ITS and nLSU rRNA markers of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony, and Bayesian inference methods. The ITS+nLSU analysis of the order Hymenochaetales indicated that the three new species clustered into the family Schizoporaceae, located in genus Xylodon; based on further analysis of ITS dataset, X. laceratus was a sister to X. heterocystidiatus; X. montanus closely grouped with X. subclavatus and X. xinpingensis with high support; while X. tropicus was retrieved as a sister to X. hastifer.

Molecular phylogeny and biogeography of the temperate Gondwanan family Triaenonychidae (Opiliones : Laniatores) reveals pre-Gondwanan regionalisation, common vicariance, and rare dispersal

2020 ◽  
Author(s):  
Caitlin M. Baker ◽  
Kate Sheridan ◽  
Shahan Derkarabetian ◽  
Abel Pérez-González ◽  
Sebastian Vélez ◽  
...  
Keyword(s):  
New Caledonia ◽  
Phylogenetic Analyses ◽  
Large Family ◽  
Taxonomic Revision ◽  
Sister Group ◽  
Divergence Times ◽  
Water Dispersal ◽  
The Family ◽  
Inference Methods ◽  
Transoceanic Dispersal

Triaenonychidae Sørensen in L. Koch, 1886 is a large family of Opiliones with ~480 described species broadly distributed across temperate forests in the Southern Hemisphere. However, it remains poorly understood taxonomically, as no comprehensive phylogenetic work has ever been undertaken. In this study we capitalise on samples largely collected by us during the last two decades and use Sanger DNA-sequencing techniques to produce a large phylogenetic tree with 300 triaenonychid terminals representing nearly 50% of triaenonychid genera and including representatives from all the major geographic areas from which they are known. Phylogenetic analyses using maximum likelihood and Bayesian inference methods recover the family as diphyletic, placing Lomanella Pocock, 1903 as the sister group to the New Zealand endemic family Synthetonychiidae Forster, 1954. With the exception of the Laurasian representatives of the family, all landmasses contain non-monophyletic assemblages of taxa. To determine whether this non-monophyly was the result of Gondwanan vicariance, ancient cladogenesis due to habitat regionalisation, or more recent over-water dispersal, we inferred divergence times. We found that most divergence times between landmasses predate Gondwanan breakup, though there has been at least one instance of transoceanic dispersal – to New Caledonia. In all, we identify multiple places in the phylogeny where taxonomic revision is needed, and transfer Lomanella outside of Triaenonychidae in order to maintain monophyly of the family.

scholarly journals Mitochondrial Genome Structures and Phylogenetic Analyses of Two Tropical Characidae Fishes

2021 ◽  
Vol 12 ◽  
Author(s):  
Cheng-He Sun ◽  
Hong-Yi Liu ◽  
Nan Xu ◽  
Xiao-Li Zhang ◽  
Qun Zhang ◽  
...  
Keyword(s):  
Fish Species ◽  
Stop Codon ◽  
Phylogenetic Analyses ◽  
Tropical Fish ◽  
Start Codon ◽  
Protein Coding ◽  
The Family ◽  
Phylogeny And Evolution ◽  
Inference Methods ◽  
Hemigrammus Erythrozonus

The Characidae family contains the largest number of tropical fish species. Morphological similarities make species identification difficult within this family. Here, the complete mitogenomes of two Characidae fish were determined and comparatively analyzed with those of nine other Characidae fish species. The two newly sequenced complete mitogenomes are circular DNA molecules with sizes of 16,701 bp (Hyphessobrycon amandae; MT484069) and 16,710 bp (Hemigrammus erythrozonus; MT484070); both have a highly conserved structure typical of Characidae, with the start codon ATN (ATG/ATT) and stop codon TAR (TAA/TAG) or an incomplete T−−/TA−. Most protein-coding genes of the 11 Characidae mitogenomes showed significant codon usage bias, and the protein-coding gene cox1 was found to be a comparatively slow-evolving gene. Phylogenetic analyses via the maximum likelihood and Bayesian inference methods confirmed that H. amandae and H. erythrozonus belong to the family Characidae. In all Characidae species studied, one genus was well supported; whereas other two genera showed marked differentiation. These findings provide a phylogenetic basis for improved classification of the family Characidae. Determining the mitogenomes of H. erythrozonus and H. amandae improves our understanding of the phylogeny and evolution of fish species.

scholarly journals Towards a Natural Classification of Hyphodontia Sensu Lato and the Trait Evolution of Basidiocarps within Hymenochaetales (Basidiomycota)

2021 ◽  
Vol 7 (6) ◽  
pp. 478
Author(s):  
Xue-Wei Wang ◽  
Tom W. May ◽  
Shi-Liang Liu ◽  
Li-Wei Zhou
Keyword(s):  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Ancestral State ◽  
Trait Evolution ◽  
Natural Classification ◽  
Multiple Loci ◽  
The Family ◽  
Phylogenetic Perspective ◽  
Taxonomic Framework ◽  
First Time

Hyphodontia sensu lato, belonging to Hymenochaetales, accommodates corticioid wood-inhabiting basidiomycetous fungi with resupinate basidiocarps and diverse hymenophoral characters. Species diversity of Hyphodontia sensu lato has been extensively explored worldwide, but in previous studies the six accepted genera in Hyphodontia sensu lato, viz. Fasciodontia, Hastodontia, Hyphodontia, Kneiffiella, Lyomyces and Xylodon were not all strongly supported from a phylogenetic perspective. Moreover, the relationships among these six genera in Hyphodontia sensu lato and other lineages within Hymenochaetales are not clear. In this study, we performed comprehensive phylogenetic analyses on the basis of multiple loci. For the first time, the independence of each of the six genera receives strong phylogenetic support. The six genera are separated in four clades within Hymenochaetales: Fasciodontia, Lyomyces and Xylodon are accepted as members of a previously known family Schizoporaceae, Kneiffiella and Hyphodontia are, respectively, placed in two monotypic families, viz. a previous name Chaetoporellaceae and a newly introduced name Hyphodontiaceae, and Hastodontia is considered to be a genus with an uncertain taxonomic position at the family rank within Hymenochaetales. The three families emerged between 61.51 and 195.87 million years ago. Compared to other families in the Hymenochaetales, these ages are more or less similar to those of Coltriciaceae, Hymenochaetaceae and Oxyporaceae, but much older than those of the two families Neoantrodiellaceae and Nigrofomitaceae. In regard to species, two, one, three and 10 species are newly described from Hyphodontia, Kneiffiella, Lyomyces and Xylodon, respectively. The taxonomic status of additional 30 species names from these four genera is briefly discussed; an epitype is designated for X. australis. The resupinate habit and poroid hymenophoral configuration were evaluated as the ancestral state of basidiocarps within Hymenochaetales. The resupinate habit mainly remains, while the hymenophoral configuration mainly evolves to the grandinioid-odontioid state and also back to the poroid state at the family level. Generally, a taxonomic framework for Hymenochaetales with an emphasis on members belonging to Hyphodontia sensu lato is constructed, and trait evolution of basidiocarps within Hymenochaetales is revealed accordingly.

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