Sequence variation in three mitochondrial DNA genes among isolates of Ascaridia galli originating from Guangdong, Hunan and Yunnan provinces, China

2012 ◽  
Vol 87 (3) ◽  
pp. 371-375 ◽  
Author(s):  
J.Y. Li ◽  
G.H. Liu ◽  
Y. Wang ◽  
H.Q. Song ◽  
R.Q. Lin ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Nadh Dehydrogenase ◽  
Sequence Variation ◽  
Phylogenetic Analyses ◽  
Ascaridia Galli ◽  
Sequence Variations ◽  
Geographical Regions ◽  
Statistical Support ◽  
Polymerase Chain ◽  
High Statistical Support

AbstractThe present study examined sequence variation in three mitochondrial DNA (mtDNA) genes, namely cytochrome c oxidase subunit 3 (cox3) and NADH dehydrogenase subunits 1 and 4 (nad1 and nad4), among Ascaridia galli isolates from different geographical localities in China. A portion of cox3 (pcox3), nad1 (pnad1) and nad4 (pnad4) genes were amplified by polymerase chain reaction (PCR) separately from adult A. galli individuals and the amplicons were subjected to sequencing from both directions. The length of the sequences of pcox3, pnad1 and pnad4 were 408 bp, 471 bp and 333 bp, respectively. The intraspecific sequence variations within A. galli were 0–1.7% for pcox3, 0–2.8% for pnad1 and 0–3.4% for pnad4. The A+T contents of the sequences were 67.16–67.65% (pcox3), 67.09–67.94% (pnad1) and 69.91–71.77% (pnad4). The interspecific sequence differences among members of the Ascaridida were significantly higher, being 13.2–30.9%, 12.8–29.0% and 15.1–34.1% for pcox3, pnad1 and pnad4, respectively. Phylogenetic analyses using combined sequences of pcox3, pnad1 and pnad4, with three different computational algorithms (Bayesian analysis, maximum likelihood and maximum parsimony), all revealed distinct groups with high statistical support. These findings demonstrated the existence of intraspecific variation in mitochondrial DNA (mtDNA) sequences among A. galli isolates from different geographical regions in China, and have implications for studying molecular epidemiology and population genetics of A. galli.

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.

scholarly journals Gene-based molecular characterization of cox1 and pnad5 in Hymenolepis nana isolated from naturally infected mice and rats in Saudi Arabia

2019 ◽  
Vol 39 (2) ◽  
Author(s):  
Dina M. Metwally ◽  
Huda A. Al-Enezy ◽  
Isra M. Al-Turaiki ◽  
Manal F. El-Khadragy ◽  
Hany M. Yehia ◽  
...  
Keyword(s):  
Saudi Arabia ◽  
Nadh Dehydrogenase ◽  
Present Species ◽  
Hymenolepis Nana ◽  
Geographical Regions ◽  
Close Relationship ◽  
Polymerase Chain ◽  
Genomic Similarity ◽  
Gc Contents

Abstract Mice and rats are animals commonly used in research and laboratory testing. Compared with other animal species, they harbor many more zoonotic agents. Hymenolepis nana (H. nana) is a common tapeworm that parasitizes both humans and rodents. Although this tapeworm is of socio-economic importance worldwide, information related to its mitochondrial genome is limited. The present study examined the sequence diversity of two mitochondrial (mt) genes, subunit I of cytochrome oxidase (cox1) and NADH dehydrogenase subunit 5 (pnad5), of H. nana in mice and rats from two geographical regions of Saudi Arabia (Makkah and Riyadh). Partial sequences of cox1 and pnad 5 from individual H. nana isolates were separately amplified using polymerase chain reaction (PCR) and sequenced. The GC contents of the sequences ranged between 31.6–33.5% and 27.2–28.6% for cox1 and pnad5, respectively. The genomic similarity among specimens determined via cox1 primer and pnad5 primer was 97.1% and 99.7%, respectively. Based on these primers, our data did not indicate any differences between H. nana from rat and mice isolates. Results demonstrated that the present species are deeply embedded in the genus Hymenolepis with close relationship to other Hymenolepis species, including H. nana as a putative sister taxon, and that the isolates cannot be categorized as belonging to two different groups with origins in Makkah and Riyadh.

Description of Xiphinema hangzhouense sp. n. (Nematoda: Longidoridae) from the rhizosphere of Magnolia grandiflora in Hangzhou, Zhejiang Province, China

Nematology ◽  
2018 ◽  
Vol 20 (1) ◽  
pp. 67-80 ◽  
Author(s):  
Ruihang Cai ◽  
Munawar Maria ◽  
Eda Marie Barsalote ◽  
Sergei A. Subbotin ◽  
Jingwu Zheng
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Total Body Length ◽  
28S Rrna ◽  
New Taxon ◽  
Magnolia Grandiflora ◽  
Statistical Support ◽  
Juvenile Stages ◽  
Total Body ◽  
High Statistical Support

Xiphinema hangzhouensesp. n. is described from the rhizosphere ofMagnolia grandiflorain Hangzhou, China. The new species is characterised by having a monodelphic reproductive system, slim body, total stylet = 186-192μm long and vulva located anteriorly at 27.6-31.2% of total body length. The new species has a gonad 400-450μm long with a simple uterus and no Z-organ. The female tail is elongated conoid with a rounded terminus. The species has four juvenile stages and no male was found. The polytomous identification codes ofX. hangzhouensesp. n. are A1, B4, C2, D23, E12, F2, G2, H2, I23, J2, K2, L1. The new species is morphologically similar toX. winotoi. Phylogenetic analyses of the 28S rRNA, ITS rRNA, 18S rRNA and partialCOIgene sequences ofX. hangzhouensesp. n. and some closely relatedXiphinemaspecies revealed that the new taxon clustered with high statistical support withX. radicicolaandX. setariae.

scholarly journals Sequence Variation inToxoplasma gondii rop17Gene among Strains from Different Hosts and Geographical Locations

2014 ◽  
Vol 2014 ◽  
pp. 1-4
Author(s):  
Nian-Zhang Zhang ◽  
Ying Xu ◽  
Si-Yang Huang ◽  
Dong-Hui Zhou ◽  
Rui-Ai Wang ◽  
...  
Keyword(s):  
Sequence Variation ◽  
High Ratio ◽  
Type I ◽  
Gene Sequences ◽  
Genetic Studies ◽  
Sequence Variations ◽  
Geographical Regions ◽  
Gene Data ◽  
Geographical Locations ◽  
Rhoptry Protein

Genetic diversity ofT. gondiiis a concern of many studies, due to the biological and epidemiological diversity of this parasite. The present study examined sequence variation in rhoptry protein 17 (ROP17) gene amongT. gondiiisolates from different hosts and geographical regions. Therop17gene was amplified and sequenced from 10T. gondiistrains, and phylogenetic relationship among theseT. gondiistrains was reconstructed using maximum parsimony (MP), neighbor-joining (NJ), and maximum likelihood (ML) analyses. The partialrop17gene sequences were 1375 bp in length and A+T contents varied from 49.45% to 50.11% among all examinedT. gondiistrains. Sequence analysis identified 33 variable nucleotide positions (2.1%), 16 of which were identified as transitions. Phylogeny reconstruction based onrop17gene data revealed two major clusters which could readily distinguish Type I and Type II strains. Analyses of sequence variations in nucleotides and amino acids among these strains revealed high ratio of nonsynonymous to synonymous polymorphisms (>1), indicating thatrop17shows signs of positive selection. This study demonstrated the existence of slightly high sequence variability in therop17gene sequences amongT. gondiistrains from different hosts and geographical regions, suggesting thatrop17gene may represent a new genetic marker for population genetic studies ofT. gondiiisolates.

Marinophialophora garethjonesii gen. et sp. nov.: a new hyphomycete associated with Halocyphina from marine habitats in Thailand

Phytotaxa ◽  
2018 ◽  
Vol 345 (1) ◽  
pp. 1 ◽  
Author(s):  
JUNFU LI ◽  
RAJESH JEEWON ◽  
RUNGTIWA PHOOKAMSAK ◽  
DARBHE J. BHAT ◽  
AUSANA MAPOOK ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Dna Sequence Data ◽  
Marine Habitats ◽  
The Family ◽  
Statistical Support ◽  
Branched Chains ◽  
Mangrove Wood ◽  
High Statistical Support ◽  
Basidiomycete Fungus

Marinophialophora garethjonesii sp. nov., representing a novel genus Marinophialophora gen. nov., associated with the basidiomycete fungus, Halocyphina on mangrove wood from Phetchaburi, Thailand, is described and illustrated. Marinophialophora morphologically resembles Phialophora and Junctospora (Herpotrichiellaceae, Chaetothyriales) in having macronematous, unbranched or branched conidiophores, globose to subglobose, solitary, acrogenous, pale to subhyaline, aseptate, conidia in chains and phialidic conidiogenous cells. Marinophialophora mainly differs from other related genera due to its conidia borne in basipetally developing branched chains and septate conidiophores. Phylogenetic analyses of a combined ITS, LSU and SSU sequence data show that Marinophialophora garethjonesii constitutes an independent lineage with high statistical support basal to the genus Exophiala within the family Herpotrichiellaceae (Chaetothyriales). The new marine taxon is described herein with illustrations and relationships inferred from DNA sequence data.

Detection of cows' milk in goats' cheeses inferred from mitochondrial DNA polymorphism

2001 ◽  
Vol 68 (2) ◽  
pp. 229-235 ◽  
Author(s):  
CÉLIA MAUDET ◽  
PIERRE TABERLET
Keyword(s):  
Mitochondrial Dna ◽  
Dna Polymorphism ◽  
Simple Approach ◽  
Milk Analysis ◽  
Chain Reaction ◽  
Specific Primers ◽  
Mitochondrial Dna Polymorphism ◽  
Sequence Variations ◽  
Spin Column ◽  
Polymerase Chain

A new polymerase chain reaction (PCR)-based method was developed to detect cows' milk in goat cheese. This method is based on mitochondrial DNA (mtDNA) control region sequence variations. DNA extractions from 150 mg of cheese were carried out using a spin column-based method. Subsequent PCR amplifications of DNA were performed with cow specific primers, demonstrating the ability to detect cows' milk in a variety of cheeses. This simple approach provides high quality DNA, and is shown to be very sensitive, with a detection limit of less than 0·1% of cows' milk. Analysis of an agarose gel digital image allows a rough estimation of the percentage of cows' milk used in adulteration.

scholarly journals Additions to Phaeosphaeriaceae (Pleosporales): Elongaticollum gen. nov., Ophiosphaerella taiwanensis sp. nov., Phaeosphaeriopsis beaucarneae sp. nov. and a new host record of Neosetophoma poaceicola from Musaceae

MycoKeys ◽  
2020 ◽  
Vol 70 ◽  
pp. 59-88
Author(s):  
Danushka S. Tennakoon ◽  
Kasun M. Thambugala ◽  
Dhanushka N. Wanasinghe ◽  
Eleni Gentekaki ◽  
Itthayakorn Promputtha ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Host Record ◽  
Similar Species ◽  
New Host ◽  
New Host Record ◽  
The Family ◽  
Distinct Genus ◽  
Statistical Support ◽  
High Statistical Support

A novel ascomycetous genus, Elongaticollum, occurring on leaf litter of Hedychium coronarium (Zingiberaceae) in Taiwan, is described and illustrated. Elongaticollum is characterized by dark brown to black, superficial, obpyriform, pycnidial conidiomata with a distinct elongate neck, and oval to oblong, hyaline, aseptate conidia. Phylogenetic analyses (maximum likelihood, maximum parsimony and Bayesian) of combined ITS, LSU, SSU and tef1-α sequence data revealed Elongaticollum as a distinct genus within the family Phaeosphaeriaceae with high statistical support. In addition, Ophiosphaerella taiwanensis and Phaeosphaeriopsis beaucarneae are described as new species from dead leaves of Agave tequilana and Beaucarnea recurvata (Asparagaceae), respectively. Neosetophoma poaceicola is reported as a new host record from dead leaves of Musa acuminata (Musaceae). Newly described taxa are compared with other similar species and comprehensive descriptions and micrographs are provided.

scholarly journals First molecular description, phylogeny and genetic variation of Taenia hydatigena from Nigerian sheep and goats based on three mitochondrial genes

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
John A. Ohiolei ◽  
Joshua Luka ◽  
Guo-Qiang Zhu ◽  
Hong-Bin Yan ◽  
Li Li ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Variation ◽  
Dna Markers ◽  
Nadh Dehydrogenase ◽  
Mitochondrial Genes ◽  
Full Length ◽  
Nadh Dehydrogenase Subunit ◽  
Taenia Hydatigena ◽  
Sheep And Goats ◽  
Geographical Regions

Abstract Background Cysticercosis caused by the metacestode larval stage of Taenia hydatigena is a disease of veterinary and economic importance. A considerable level of genetic variation among isolates of different intermediate hosts and locations has been documented. Generally, data on the genetic population structure of T. hydatigena is scanty and lacking in Nigeria. Meanwhile, similar findings in other cestodes like Echinococcus spp. have been found to be of epidemiological importance. Our aim, therefore, was to characterize and compare the genetic diversity of T. hydatigena population in Nigeria based on three mitochondrial DNA markers as well as to assess the phylogenetic relationship with populations from other geographical regions. Methods In the present study, we described the genetic variation and diversity of T. hydatigena isolates from Nigerian sheep and goats using three full-length mitochondrial genes: the cytochrome c oxidase subunit 1 (cox1), NADH dehydrogenase subunit 1 (nad1), and NADH dehydrogenase subunit 5 (nad5). Results The median-joining network of concatenated cox1-nad1-nad5 sequences indicated that T. hydatigena metacestodes of sheep origin were genetically distinct from those obtained in goats and this was supported by high FST values of nad1, cox1, and concatenated cox1-nad1-nad5 sequences. Genetic variation was also found to be higher in isolates from goats than from sheep. Conclusions To the best of our knowledge, the present study described the genetic variation of T. hydatigena population for the first time in Nigeria using full-length mitochondrial genes and suggests the existence of host-specific variants. The population indices of the different DNA markers suggest that analysis of long mitochondrial DNA fragments may provide more information on the molecular ecology of T. hydatigena. We recommend that future studies employ long mitochondrial DNA sequence in order to provide reliable data that would explain the extent of genetic variation in different hosts/locations and the biological and epidemiological significance.

Scanning for nucleotide variations in mitochondrial DNA fragments of Schistosoma japonicum by single-strand conformation polymorphism

Parasitology ◽  
1999 ◽  
Vol 118 (1) ◽  
pp. 73-82 ◽  
Author(s):  
H. O. BØGH ◽  
X. Q. ZHU ◽  
B.-Z. QIAN ◽  
R. B. GASSER
Keyword(s):  
Mitochondrial Dna ◽  
Schistosoma Japonicum ◽  
Nadh Dehydrogenase ◽  
Visual Display ◽  
Single Strand Conformation Polymorphism ◽  
Single Strand ◽  
Republic Of China ◽  
Mutation Scanning ◽  
Polymerase Chain ◽  
Conformation Polymorphism

In this study, we employed a mutation scanning approach for the direct visual display of genetic variability in mitochondrial DNA (mtDNA) fragments within and among populations of Schistosoma japonicum from the People's Republic of China. Fragments of the NADH dehydrogenase 1 gene (ND1) and the cytochrome c oxidase subunit I (COI) were individually amplified from parasite DNA by polymerase chain reaction (PCR), denatured and subjected to single-strand conformation polymorphism (SSCP) analysis. Using ND1 and COI fragments, individuals representing different genotypes could be readily identified based on characteristic and reproducible SSCP profiles. The results demonstrated the usefulness of SSCP for the direct visual display of low-level sequence variation in mtDNA of S. japonicum prior to DNA sequence analysis. This approach has important implications for studying the genetic structure and biology of S. japonicum populations, and for analysing the inheritance of mitochondrial DNA.

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