scholarly journals Molecular characterization of Fasciola isolates collected from sheep, goats and cattle in Kisumu, Baringo and Narok Counties, Kenya

2021 ◽  
Author(s):  
Cornelius Kibet Kipyegen ◽  
Charles I. Muleke ◽  
Elick O. Otachi
Keyword(s):  
Phylogenetic Analysis ◽  
Fasciola Hepatica ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Rdna Sequences ◽  
Close Relationship ◽  
Control Programmes ◽  
Veterinary Importance ◽  
Liver Flukes ◽  
And Control

Abstract Fasciolosis is a neglected trematode infection of public health and veterinary importance caused by Fasciola gigantica and Fasciola hepatica. Molecular analysis using the internal transcribed spacers’ ITS-1 and ITS-2 of nuclear ribosomal DNA is useful in distinguishing Fasciola species. This study aimed to characterize liver flukes from sheep, goats and cattle using these genetic markers. Fifty nine adult Fasciola specimens were collected from livers of naturally infected sheep, goats and cattle at selected abattoirs in Kisumu, Baringo and Narok Counties. Sequence comparison of ITS-1 and ITS-2 sequences of Fasciola isolates from this study and sequences in Genbank was carried out. A maximum likelihood tree was constructed for phylogenetic analysis. Analysis of ITS-1 and ITS-2 rDNA sequences revealed that F. hepatica and F. gigantica caused infection in both cattle and sheep and in goats only F. gigantica caused infection. The sequenced PCR amplicons showed a close relationship between Fasciola species in this study with Fasciola isolates from other regions in the world. Phylogenetic analysis showed that sequences of F. hepatica are similar to the sequence from Spain, China and Tunisia obtained from GenBank. The sequences of F. gigantica in this study have similarity to the sequence from Iran and Burkina Faso. Data from this study provides information that serves as basis for further studies on the distribution of F. gigantica and F. hepatica in other localities in Kenya, and is also important in designing epidemiological and control programmes for zoonotic fascioliasis.

Characterization of Oesophagostomum asperum and O. columbianum by internal transcribed spacers of nuclear ribosomal DNA

2012 ◽  
Vol 88 (1) ◽  
pp. 74-81 ◽  
Author(s):  
G.H. Zhao ◽  
B. Hu ◽  
J.K. Song ◽  
Y.Q. Jia ◽  
H.M. Li ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Population Biology ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Chain Reaction ◽  
Genetic Studies ◽  
Rdna Sequences ◽  
Polymerase Chain ◽  
And Control

AbstractIn the present study, the internal transcribed spacers (ITS) of ribosomal DNA (rDNA) of Oesophagostomum asperum and O. columbianum were amplified and sequenced. The ITS-1, 5.8S and ITS-2 rDNA sequences of O. asperum were 374 bp, 153 bp and 259 bp in length, respectively, and the corresponding sequences of O. columbianum were 259, 153 and 218 bp in length, respectively. Sequence differences in the ITS-1 and ITS-2 rDNA between the two Oesophagostomum species were 9.5–10.2% and 12.7–13.9%, respectively. Sequence differences in the ITS-1 and ITS-2 rDNA among members of the genus Oesophagostomum were 2.5–11.6% and 6.8–22.3%, respectively. Based on genetic markers in the ITS rDNA, an effective polymerase chain reaction (PCR) approach was developed to differentiate O. columbianum from O. asperum with a sensitivity of 0.2 ng/μl DNA. Since accurate characterization of parasites at different taxonomic levels is essential for population genetic studies and control of parasitosis, the present findings have important implications for studying epidemiology, taxonomy and population biology, as well as for the control of oesophagostomiasis.

Characterization of Trichuris trichiura from humans and T. suis from pigs in China using internal transcribed spacers of nuclear ribosomal DNA

2012 ◽  
Vol 88 (1) ◽  
pp. 64-68 ◽  
Author(s):  
G.H. Liu ◽  
W. Zhou ◽  
A.J. Nisbet ◽  
M.J. Xu ◽  
D.H. Zhou ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Sequence Variation ◽  
Animal Health ◽  
Trichuris Trichiura ◽  
Its Rdna ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Economic Losses ◽  
Molecular Characteristics ◽  
Rdna Sequences

AbstractTrichuris trichiura and Trichuris suis parasitize (at the adult stage) the caeca of humans and pigs, respectively, causing trichuriasis. Despite these parasites being of human and animal health significance, causing considerable socio-economic losses globally, little is known of the molecular characteristics of T. trichiura and T. suis from China. In the present study, the entire first and second internal transcribed spacer (ITS-1 and ITS-2) regions of nuclear ribosomal DNA (rDNA) of T. trichiura and T. suis from China were amplified by polymerase chain reaction (PCR), the representative amplicons were cloned and sequenced, and sequence variation in the ITS rDNA was examined. The ITS rDNA sequences for the T. trichiura and T. suis samples were 1222–1267 bp and 1339–1353 bp in length, respectively. Sequence analysis revealed that the ITS-1, 5.8S and ITS-2 rDNAs of both whipworms were 600–627 bp and 655–661 bp, 154 bp, and 468–486 bp and 530–538 bp in size, respectively. Sequence variation in ITS rDNA within and among T. trichiura and T. suis was examined. Excluding nucleotide variations in the simple sequence repeats, the intra-species sequence variation in the ITS-1 was 0.2–1.7% within T. trichiura, and 0–1.5% within T. suis. For ITS-2 rDNA, the intra-species sequence variation was 0–1.3% within T. trichiura and 0.2–1.7% within T. suis. The inter-species sequence differences between the two whipworms were 60.7–65.3% for ITS-1 and 59.3–61.5% for ITS-2. These results demonstrated that the ITS rDNA sequences provide additional genetic markers for the characterization and differentiation of the two whipworms. These data should be useful for studying the epidemiology and population genetics of T. trichiura and T. suis, as well as for the diagnosis of trichuriasis in humans and pigs.

scholarly journals Phylogenetic Analysis and Molecular Diversity of Capsicum Based on rDNA-ITS Region

Horticulturae ◽  
2020 ◽  
Vol 6 (4) ◽  
pp. 87
Author(s):  
Kumpei Shiragaki ◽  
Shuji Yokoi ◽  
Takahiro Tezuka
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Wild Species ◽  
Morphological Characteristics ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Rdna Its ◽  
Rdna Its Region ◽  
Genus Capsicum

The genus Capsicum is comprised of 5 domesticated and more than 30 wild species. The region of nuclear ribosomal DNA internal transcribed spacers (rDNA-ITS) has widely been used for species identification, but has rarely been used in Capsicum. In this study, the evaluation of genetic diversity and a phylogenetic analysis were conducted using rDNA-ITS of 28 Capsicum accessions, including five domesticated and two wild species. We surveyed six conventional keys of domesticated species and another five traits in Capsicum accessions. Specific morphological characteristics were found in C. annuum, C. baccatum, and C.pubescens. Three subclones of each accession were sequenced, and rDNA-ITS polymorphisms were detected in all accessions excluding C. annuum, suggesting that incomplete concerted evolution occurred in rDNA-ITS of Capsicum. The genetic diversity was evaluated using nucleotide polymorphism and diversity. C. annuum had the lowest genetic diversity of all species in this study. The phylogenetic tree formed a species-specific clade for C. annuum, C. baccatum, and C. pubescens. The C. chinense clade existed in the C. frutescens clade, implying that it was a cultivated variant of C. frutescens. C. chacoense likely belonged to the C. baccatum complex according to its morphologic and genetic features. This study indicated that the rDNA-ITS region can be used for simple identification of domesticated Capsicum species.

Characterization ofDicrocoelium dendriticumisolates from small ruminants in Shaanxi Province, north-western China, using internal transcribed spacers of nuclear ribosomal DNA

2013 ◽  
Vol 89 (1) ◽  
pp. 124-129 ◽  
Author(s):  
Q.Q. Bian ◽  
G.H. Zhao ◽  
Y.Q. Jia ◽  
Y.Q. Fang ◽  
W.Y. Cheng ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Small Ruminants ◽  
Internal Transcribed Spacers ◽  
Shaanxi Province ◽  
Western China ◽  
Nuclear Ribosomal Dna ◽  
Specific Sequence ◽  
Sheep And Goats ◽  
Rdna Sequences ◽  
Geographical Regions

AbstractThe genetic variations in internal transcribed spacers (ITS) spanning ITS-1, 5.8S and ITS-2 rDNA ofDicrocoelium dendriticum, isolated from sheep and goats in four geographical regions in Shaanxi province, were examined. The lengths of ITS-1, 5.8S and ITS-2 rDNA sequences forD. dendriticumwere 749 bp, 161 bp and 234 bp, respectively. Intra-specific sequence variations ofD. dendriticumwere 0–0.5% for ITS-1 and 0–1.3% for ITS-2 rDNA, while the inter-specific variations among species in genusDicrocoeliumin ITS-2 rDNA were 3.4–12.3%. Phylogenetic analysis based on sequences of ITS-2 rDNA showed that allD. dendriticumisolates in the present study were grouped with referenceD. dendriticumisolates from sheep and goats, andD. dendriticumisolates from cattle and Japanese serow were clustered in a sister clade. However, the phylogenetic tree could not reveal geographically genetic relationships ofD. dendriticumisolates in different origins and hosts. These findings provided basic information for further study of molecular epidemiology and control ofD. dendriticuminfection in Shaanxi province as well as in the world.

A framework for a phylogenetic classification in the genus Cortinarius (Basidiomycota, Agaricales) derived from morphological and molecular data

2005 ◽  
Vol 83 (11) ◽  
pp. 1457-1477 ◽  
Author(s):  
Sigisfredo Garnica ◽  
Michael Weiß ◽  
Bernhard Oertel ◽  
Franz Oberwinkler
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Data ◽  
Internal Transcribed Spacers ◽  
Molecular Phylogenetic Analysis ◽  
Nuclear Rdna ◽  
Ecological Data ◽  
Natural Classification ◽  
Geographical Patterns ◽  
Rdna Sequences ◽  
Molecular Phylogenetic

Phylogenetic relationships in the genus Cortinarius with emphasis on European species were studied by integrating a molecular phylogenetic analysis of nuclear rDNA sequences with morphological, chemical, and ecological data. Internal transcribed spacers (ITS1 and ITS2, including 5.8S) and the D1–D2 regions of nuclear rDNA of 262 Cortinarius species including most of the recognised subgenera from Europe, South America, Australia, Tasmania, New Zealand, and Asia were sequenced and analysed by maximum likelihood and neighbour joining. Our morphological and molecular analyses showed considerable disagreement with earlier morphology-based hypotheses concerning the infrageneric delimitations in Cortinarius. We propose a new base for a more natural classification system in Cortinarius involving the taxonomic rearrangement of the species into the following major lineages that we informally designate as “clades” at this time: (1) phlegmacioid species are included in Alluti, Amarescentes, Arguti, Calochroi, Caerulescentes, Percomes, Phlegmacioides, Phlegmacium, Purpurascentes, Scauri, and Vulpini; (2) the Heterocliti clade includes species of the subgenera Leprocybe and Cystogenes ; (3) most of the Myxacium species are included in the Delibuti and Myxacium clades; (4) part of Rozites are included in the Rozites clade; (5) the north-hemispheric species of subgenus Dermocybe are included in the Dermocybe clade and part of the south-hemispheric species in the Splendidi clade; (6) part of Sericeocybe are integrated in the Anomali and Telamonia clades; (7) members of subgenus Cortinarius are assigned to the Cortinarius clade; (8) telamonioid taxa are included in the Obtusi, Renidentes, and Telamonia clades. Several Cortinarius species with peculiar patterns of morphology and basidiome coloration had isolated positions in the sequence analysis, and the evolutionary relationships among the major lineages remained unresolved. Our results suggest the convergent evolution of certain morphological traits across phylogenetically divergent lineages in Cortinarius. However, combinations of features such as pileipellis anatomy, spore shape, veil coloration, basidiome pigments, and stipe shape appear useful to circumscribe clades. Our molecular phylogenetic analysis allows insights in global geographical patterns of species distribution within the major lineages in the genus Cortinarius. The clade structure proposed here could be used as backbone for further more detailed systematic studies.

Spissiomyces endophytica (Dothideomycetes, Ascomycota), a new endophytic fungus from Thailand

Phytotaxa ◽  
2018 ◽  
Vol 333 (2) ◽  
pp. 219 ◽  
Author(s):  
NAKARIN SUWANNARACH ◽  
JATURONG KUMLA ◽  
SAISAMORN LUMYONG
Keyword(s):  
Phylogenetic Analysis ◽  
Large Subunit ◽  
Small Subunit ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Full Description ◽  
Morphological Investigation ◽  
Lampang Province ◽  
A New Species ◽  
Β Tubulin

A new species of endophytic fungi, described herein as Spissiomyces endophytica, was isolated from tubers of Balanophora fungosa in Lampang Province, Thailand. A morphological investigation revealed that this species was distinguished from the previously described Spissiomyces species by its lager conidial size. Phylogenetic analysis was performed using combined sequence datasets of the small subunit (SSU), large subunit (LSU) and internal transcribed spacers (ITS) of the nuclear ribosomal DNA (rDNA), a part of the RNA polymerase (RPB2) and β-tubulin (TUB) genes, in order to support the morphological results. A full description, illustrations, phylogenetic tree and key to the species are provided.

A morphological and molecular phylogenetic analysis of relationships between genera of the nematode sub-family Cloacininae (Stossich) (Strongyloidea: Chabertiidae) parasitic in kangaroos, wallabies and rat-kangaroos (Marsupialia: Macropodoidea) 

Zootaxa ◽  
2020 ◽  
Vol 4851 (2) ◽  
pp. 271-288
Author(s):  
I. BEVERIDGE ◽  
A. JABBAR ◽  
A. KOEHLER ◽  
T. SUKEE
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Dna ◽  
Morphological Characteristics ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Molecular Phylogenetic Analysis ◽  
Molecular Phylogenetic ◽  
Phenetic Classification

A phylogenetic analysis of the genera of the strongyloid sub-family Cloacininae from macropodoid marsupials in Australasia was undertaken based on morphological characteristics and analysis of concatenated sequences (ITS+) of the first (ITS-1) and second (ITS-2) internal transcribed spacers of nuclear ribosomal DNA. Neither approach provided a robust phylogeny, but similarities between the two methods in terms of generic groupings suggested that substantial revision is needed of the current phenetic classification, with some of the key morphological characteristics currently used to define genera and tribes proving to be homoplasious. 

scholarly journals Identification and molecular phylogeny of agriculturally important spider mites (Acari: Tetranychidae) based on mitochondrial and nuclear ribosomal DNA sequences, with an emphasis on Tetranychus

Zootaxa ◽  
2010 ◽  
Vol 2647 (1) ◽  
pp. 1 ◽  
Author(s):  
GUO-QING LI ◽  
XIAO-FENG XUE ◽  
KAI-JUN ZHANG ◽  
XIAO-YUE HONG
Keyword(s):  
Ribosomal Rna ◽  
Dna Sequences ◽  
Genetic Distances ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Agricultural Pests ◽  
Geographical Differences ◽  
Important Species ◽  
Rdna Sequences ◽  
Identification Of Species

Tetranychid mites are serious agricultural pests. Identification of species in the Tetranychidae is hampered by their close morphological similarities, especially for species within the genus Tetranychus. In this study, we examined the relationships of nine agriculturally important species in the Tetranychidae from China based on mitochondrial (cytochrome c oxidase subunit 1) and nuclear (internal transcribed spacer 1 and 2 of ribosomal RNA gene) sequences. The results confirm the monophyly of the morphologically defined Tetranychus, Panonychus, Amphitetranychus and Petrobia. However the position of Amphitetranychus viennensis within the Tetranychidae needs to be confirmed. The genetic distances between Tetranychus truncatus, T. turkestani and T. urticae that their taxonomy needs revision. In particular, both cytochrome oxidase 1 and the internal transcribed spacers 1 and 2 of rDNA sequences showed large geographical differences within T. cinnabarinus, suggesting the existence of cryptic species within this species.

scholarly journals Molecular and Morphological Characterization ofFasciolaspp. Isolated from Different Host Species in a Newly Emerging Focus of Human Fascioliasis in Iran

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Reza Shafiei ◽  
Bahador Sarkari ◽  
Seyed Mahmuod Sadjjadi ◽  
Gholam Reza Mowlavi ◽  
Abdolali Moshfe
Keyword(s):  
Fasciola Hepatica ◽  
Morphological Diversity ◽  
Morphological Characterization ◽  
Image Analysis System ◽  
Human Fascioliasis ◽  
Rflp Profile ◽  
Analysis System ◽  
Liver Flukes ◽  
Southwest Of Iran ◽  
And Control

The current study aimed to find out the morphometric and genotypic divergences of the flukes isolated from different hosts in a newly emerging focus of human fascioliasis in Iran. AdultFasciolaspp. were collected from 34 cattle, 13 sheep, and 11 goats from Kohgiluyeh and Boyer-Ahmad province, southwest of Iran. Genomic DNA was extracted from the flukes and PCR-RFLP was used to characterize the isolates. The ITS1, ITS2, and mitochondrial genes (mtDNA) of NDI and COI from individual liver flukes were amplified and the amplicons were sequenced. Genetic variation within and between the species was evaluated by comparing the sequences. Moreover, morphometric characteristics of flukes were measured through a computer image analysis system. Based on RFLP profile, from the total of 58 isolates, 41 isolates (from cattle, sheep, and goat) were identified asFasciola hepatica, while 17 isolates from cattle were identified asFasciola gigantica. Comparison of the ITS1 and ITS2 sequences showed six and seven single-base substitutions, resulting in segregation of the specimens into two different genotypes. The sequences of COI markers showed seven DNA polymorphic sites forF. hepaticaand 35 DNA polymorphic sites forF. gigantica. Morphological diversity of the two species was observed in linear, ratios, and areas measurements. The findings have implications for studying the population genetics, epidemiology, and control of the disease.

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