scholarly journals Molecular phylogeny of Toxoplasmatinae: comparison between inferences based on mitochondrial and apicoplast genetic sequences

2016 ◽  
Vol 25 (1) ◽  
pp. 82-89 ◽  
Author(s):  
Michelle Klein Sercundes ◽  
Samantha Yuri Oshiro Branco Valadas ◽  
Lara Borges Keid ◽  
Tricia Maria Ferreira Souza Oliveira ◽  
Helena Lage Ferreira ◽  
...  
Keyword(s):  
Neospora Caninum ◽  
Mitochondrial Gene ◽  
Mitochondrial Genes ◽  
Sarcocystis Neurona ◽  
Gene Coding ◽  
The Family ◽  
Caseinolytic Protease ◽  
Evolutionary Studies ◽  
Genetic Sequences ◽  
Sarcocystis Falcatula

Abstract Phylogenies within Toxoplasmatinae have been widely investigated with different molecular markers. Here, we studied molecular phylogenies of the Toxoplasmatinae subfamily based on apicoplast and mitochondrial genes. Partial sequences of apicoplast genes coding for caseinolytic protease (clpC) and beta subunit of RNA polymerase (rpoB), and mitochondrial gene coding for cytochrome B (cytB) were analyzed. Laboratory-adapted strains of the closely related parasites Sarcocystis falcatula and Sarcocystis neurona were investigated, along with Neospora caninum, Neospora hughesi, Toxoplasma gondii (strains RH, CTG and PTG), Besnoitia akodoni, Hammondia hammondiand two genetically divergent lineages of Hammondia heydorni. The molecular analysis based on organellar genes did not clearly differentiate between N. caninum and N. hughesi, but the two lineages of H. heydorni were confirmed. Slight differences between the strains of S. falcatula and S. neurona were encountered in all markers. In conclusion, congruent phylogenies were inferred from the three different genes and they might be used for screening undescribed sarcocystid parasites in order to ascertain their phylogenetic relationships with organisms of the family Sarcocystidae. The evolutionary studies based on organelar genes confirm that the genusHammondia is paraphyletic. The primers used for amplification of clpC and rpoB were able to amplify genetic sequences of organisms of the genus Sarcocystisand organisms of the subfamily Toxoplasmatinae as well.

scholarly journals Evidence for Unknown Sarcocystis-Like Infection in Stranded Striped Dolphins (Stenella coeruleoalba) from the Ligurian Sea, Italy

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1201
Author(s):  
Federica Giorda ◽  
Umberto Romani-Cremaschi ◽  
Antoinette E. Marsh ◽  
Carla Grattarola ◽  
Barbara Iulini ◽  
...  
Keyword(s):  
Neospora Caninum ◽  
Positive Staining ◽  
Ligurian Sea ◽  
Sarcocystis Neurona ◽  
Stenella Coeruleoalba ◽  
Polyclonal Antisera ◽  
Ligurian Coast ◽  
Sarcocystis Falcatula ◽  
The Brain ◽  
The Mediterranean Basin

Two striped dolphins (SD1, SD2), stranded along the Ligurian coast of Italy, were diagnosed with a nonsuppurative meningoencephalitis associated with previously undescribed protozoan tissue cysts. As tissue cysts were morphologically different from those of Toxoplasma gondii, additional histopathological, immunohistochemical, ultrastructural, and biomolecular investigations were performed, aiming to fully characterize the organism. Histopathology revealed the presence of large Sarcocystis-like tissue cysts, associated with limited inflammatory lesions in all CNS areas studied. IHC was inconclusive, as positive staining with polyclonal antisera did not preclude cross-reaction with other Sarcocystidae coccidia. Applied to each animal, 11 different PCR protocols precluded a neural infection by Sarcocystis neurona, Sarcocystis falcatula, Hammondia hammondi, and Neospora caninum. T. gondii coinfection was confirmed only in dolphin SD2. Sarcocystis sp. sequences, showing the highest homology to species infecting the Bovidae family, were amplified from SD1 myocardium and SD2 skeletal muscle. The present study represents the first report of Sarcocystis-like tissue cysts in the brain of stranded cetaceans along with the first description of Sarcocystis sp. infection in muscle tissue of dolphins from the Mediterranean basin.

scholarly journals A Robust Species Tree for the Alphaproteobacteria

2007 ◽  
Vol 189 (13) ◽  
pp. 4578-4586 ◽  
Author(s):  
Kelly P. Williams ◽  
Bruno W. Sobral ◽  
Allan W. Dickerman
Keyword(s):  
Mitochondrial Genes ◽  
Species Tree ◽  
The Other ◽  
Protein Families ◽  
Branching Order ◽  
Expanded Group ◽  
Eukaryotic Nucleus ◽  
The Family ◽  
Evolutionary Studies

ABSTRACT The branching order and coherence of the alphaproteobacterial orders have not been well established, and not all studies have agreed that mitochondria arose from within the Rickettsiales. A species tree for 72 alphaproteobacteria was produced from a concatenation of alignments for 104 well-behaved protein families. Coherence was upheld for four of the five orders with current standing that were represented here by more than one species. However, the family Hyphomonadaceae was split from the other Rhodobacterales, forming an expanded group with Caulobacterales that also included Parvularcula. The three earliest-branching alphaproteobacterial orders were the Rickettsiales, followed by the Rhodospirillales and then the Sphingomonadales. The principal uncertainty is whether the expanded Caulobacterales group is more closely associated with the Rhodobacterales or the Rhizobiales. The mitochondrial branch was placed within the Rickettsiales as a sister to the combined Anaplasmataceae and Rickettsiaceae, all subtended by the Pelagibacter branch. Pelagibacter genes will serve as useful additions to the bacterial outgroup in future evolutionary studies of mitochondrial genes, including those that have transferred to the eukaryotic nucleus.

scholarly journals The 256 kb mitochondrial genome of Clavaria fumosa is the largest among phylum Basidiomycota and is rich in introns and intronic ORFs

IMA Fungus ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Xu Wang ◽  
Yajie Wang ◽  
Wen Yao ◽  
Jinwen Shen ◽  
Mingyue Chen ◽  
...  
Keyword(s):  
Large Scale ◽  
Mitochondrial Gene ◽  
Mitochondrial Genes ◽  
Gene Arrangement ◽  
Repeat Sequences ◽  
Gene Sets ◽  
The Family ◽  
Intergenic Regions ◽  
Complete Mitogenome ◽  
Gain Loss

AbstractIn the present study, the complete mitogenome of Clavaria fumosa, was sequenced, assembled, and compared. The complete mitogenome of C. fumosa is 256,807 bp in length and is the largest mitogenomes among all Basidiomycota mitogenomes reported. Comparative mitogenomic analysis indicated that the C. fumosa mitogenome contained the most introns and intronic ORFs among all fungal mitogenomes. Large intergenic regions, intronic regions, accumulation of repeat sequences and plasmid-derived genes together promoted the size expansion of the C. fumosa mitogenome. In addition, the rps3 gene was found subjected to positive selection between some Agaricales species. We found frequent intron gain/loss events in Agaricales mitogenomes, and four novel intron classes were detected in the C. fumosa mitogenome. Large-scale gene rearrangements were found occurred in Agaricales species and the C. fumosa mitogenome had a unique gene arrangement which differed from other Agaricales species. Phylogenetic analysis for 76 Basidiomycetes based on combined mitochondrial gene sets indicated that mitochondrial genes could be used as effective molecular markers for reconstructing evolution of Basidiomycota. The study served as the first report on the mitogenomes of the family Clavariaceae, which will promote the understanding of the genetics, evolution and taxonomy of C. fumosa and related species.

Species delimitation in the leaf beetle genus Macroplea (Coleoptera, Chrysomelidae) based on mitochondrial DNA, and phylogeographic considerations

2006 ◽  
Vol 37 (4) ◽  
pp. 467-479 ◽  
Author(s):  
Gregor Kölsch ◽  
Bo Vest Pedersen ◽  
Olof Biström
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Dna ◽  
Species Delimitation ◽  
Mitochondrial Gene ◽  
Leaf Beetle ◽  
Genetic Distances ◽  
Amino Acid Substitutions ◽  
Species Status ◽  
Leaf Beetles ◽  
Gene Coding

AbstractThe genus Macroplea Samouelle, 1819 is a group of highly specialized aquatic leaf beetles occurring in the Palaearctic. Since the members of this genus are morphologically very similar, we addressed the question of species identification and delimitation by analysing the second half of the mitochondrial gene coding for the cytochrome oxidase I (COI) subunit. Species limits are inferred from the multimodal frequency distribution of genetic distances between specimens: low genetic distances within a species are clearly set apart from distances between species. The species status of the hitherto controversial species M. japana (Jacoby, 1885) is confirmed. The pattern of nucleotide and amino acid substitutions is discussed in the light of functional domains of the COI molecule. Although the data are preliminary, the results provide new data on the distribution of the species. Together with the phylogenetic analysis they allow for a discussion of the phylogeography of the genus.

scholarly journals A new species of Ituglanis (Siluriformes: Trichomycteridae) from the rio Uruguai basin, southern Brazil

2017 ◽  
Vol 15 (3) ◽  
Author(s):  
Juliano Ferrer ◽  
Laura M. Donin
Keyword(s):  
New Species ◽  
Outer Layer ◽  
Mitochondrial Gene ◽  
Color Pattern ◽  
The Body ◽  
Southern Brazil ◽  
Unique Color ◽  
Pampa Biome ◽  
Genetic Sequences ◽  
A New Species

ABSTRACT A new species of Ituglanis associated to the grasslands of the Pampa biome is described from the rio Uruguai basin, southern Brazil. The new species is distinguished from its congeners by the low number of ribs and by a unique color pattern composed of an outer layer with scattered round black blotches equivalent in size to the eye circumference over a reddish brown background on the lateral surface of the body. We provide the genetic sequences of the mitochondrial gene Cytochrome c Oxydase subunit I (COI) for three of the paratypes and discuss aspects about the recent discovery of the new species.

scholarly journals The first representatives of the millipede family Glomeridellidae (Diplopoda, Glomerida) recorded from China and Indochina

ZooKeys ◽  
2020 ◽  
Vol 954 ◽  
pp. 1-15
Author(s):  
Weixin Liu ◽  
Sergei Golovatch
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Dna Barcoding ◽  
Southern China ◽  
Mitochondrial Gene ◽  
Guizhou Province ◽  
The Family ◽  
Structural Details ◽  
Molecular Phylogenetic ◽  
A New Species

A new species of glomeridellid millipede is described from Guizhou Province, southern China: Tonkinomeris huzhengkunisp. nov. This new epigean species differs very clearly in many structural details, being sufficiently distinct morphologically and disjunct geographically from T. napoensis Nguyen, Sierwald & Marek, 2019, the type and sole species of Tonkinomeris Nguyen, Sierwald & Marek, 2019, which was described recently from northern Vietnam. The genus Tonkinomeris is formally relegated from Glomeridae and assigned to the family Glomeridellidae, which has hitherto been considered strictly Euro-Mediterranean in distribution and is thus new to the diplopod faunas of China and Indochina. Tonkinomeris is re-diagnosed and shown to have perhaps the basalmost position in the family Glomeridellidae. Its relationships are discussed, both morphological and zoogeographical, within and outside the Glomeridellidae, which can now be considered as relict and basically Oriental in origin. Because of the still highly limited array of DNA-barcoding sequences of the COI mitochondrial gene available in the GenBank, the first molecular phylogenetic analysis of Glomerida attempted here shows our phylogram to be too deficient to consider meaningful.

Transcriptional analysis of the Saccharomyces cerevisiae mitochondrial var1 gene: anomalous hybridization of RNA from AT-rich regions

1983 ◽  
Vol 3 (9) ◽  
pp. 1615-1624
Author(s):  
H P Zassenhaus ◽  
F Farrelly ◽  
M E Hudspeth ◽  
L I Grossman ◽  
R A Butow
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mitochondrial Genes ◽  
Transcriptional Analysis ◽  
Asymmetric Distribution ◽  
Direct Function ◽  
Important Conclusion ◽  
The Family ◽  
Var1 Gene ◽  
Flanking Sequences ◽  
Transcription Map

A family of mitochondrial RNAs hybridizes specifically to the var1 region on Saccharomyces cerevisiae mitochondrial DNA (Farrelly et al., J. Biol. Chem. 257:6581-6587, 1982). We constructed a fine-structure transcription map of this region by hybridizing DNA probes containing different portions of the var1 region and some flanking sequences to mitochondrial RNAs isolated from var1-containing petites. We also report the nucleotide sequence of more than 1.2 kilobases of DNA flanking the var1 gene. Our primary findings are: (i) The family of RNAs we detect with homology to var1 DNA is colinear with the var1 gene. Their direction of transcription is olil to cap, as it is for most other mitochondrial genes. (ii) Extensive hybridization anomalies are present, most likely due to the high A-T (A-U) content of the hybridizing species and to the asymmetric distribution of their G-C residues. An important conclusion is that failure to detect transcripts from A-T-rich regions of the yeast mitochondrial genome by standard blot transfer hybridizations cannot be interpreted to mean that such sequences, which are commonly supposed to be spacer DNA, are noncoding or lack direct function in the expression of mitochondrial genes.

scholarly journals PCR-based detection of cow’s milk in goat and sheep cheeses marketed in the Czech Republic

2011 ◽  
Vol 24 (No. 3) ◽  
pp. 127-132 ◽  
Author(s):  
E. Mašková ◽  
I. Paulíčková
Keyword(s):  
Mitochondrial Gene ◽  
Retail Trade ◽  
Animal Origin ◽  
The Czech Republic ◽  
Goat Cheese ◽  
Gene Coding ◽  
Reverse Primer ◽  
Pcr Method ◽  
Italian Origin ◽  
Species Specific

A method based on the polymerase chain reaction (PCR) principle was validated for detecting cow’s milk in goat and sheep cheeses. DNA was isolated from the cheeses using the isolation kit Invisorb Spin Food I by Invitek Co., designed for the samples of animal origin. The PCR method applied utilizes the sequence of the mitochondrial gene coding cytochrome b which is specific for mammals. It uses the common forward primer and the reverse primer species-specific. After electrophoresis, cow DNA was characterised by the fragment of the size of 274 bp, goat DNA by the fragment of 157 bp, and sheep DNA by the fragment of 331 bp. The detection limit of the PCR method described (1%) was determined with model samples made from pure goat cheese with a defined addition of cheese made from cow’s milk. The method validated was applied in the analysis of 17 goat cheeses and 7 sheep cheeses obtained from retail trade. Products of Czech, Slovak, French, Dutch, and Italian origin were examined. The presence of undeclared cow’s milk was detected in three kinds of goat cheese and in one of sheep cheese.  

scholarly journals Genetic evidence that different functional domains of the PET54 gene product facilitate expression of the mitochondrial genes COX1 and COX3 in Saccharomyces cerevisiae.

1991 ◽  
Vol 11 (5) ◽  
pp. 2399-2405 ◽  
Author(s):  
M L Valencik ◽  
J E McEwen
Keyword(s):  
Gene Expression ◽  
Gene Product ◽  
Rna Splicing ◽  
Rna Secondary Structure ◽  
Mitochondrial Gene ◽  
Mrna Translation ◽  
Mitochondrial Genes ◽  
Mitochondrial Gene Expression ◽  
Single Mechanism ◽  
Insertion Mutations

Expression of the yeast mitochondrial genes COX1 and COX3, which encode subunits I and III of cytochrome oxidase, respectively, is controlled by a common nuclear-encoded trans-acting factor. This protein, encoded by the PET54 gene, controls expression of COX1 at the level of RNA splicing and COX3 at the level of mRNA translation. While the steps of COX1 and COX3 gene expression affected by the PET54 gene product are different, it is possible that the PET54 protein is monofunctional and affects expression of each gene by a single mechanism, such as modulation of RNA secondary structure. The goal of this study was to address whether the PET54 protein is monofunctional or multifunctional with respect to its role in COX1 and COX3 gene expression. Ten insertion mutations, which each resulted in the in-frame addition of four amino acids within the PET54 polypeptide, were generated, and the resulting mutants were characterized for respiration phenotype and mitochondrial gene expression. Five of the ten mutants were respiration deficient. Two of these five mutants were defective in expression of COX3 but not in expression of COX1, while two other mutants had the opposite phenotype (primarily defective in expression of COX1). The fifth mutant was equally defective in expression of both genes. These results demonstrate that the two functions of PET54 are genetically separable and support the idea that the PET54 protein is multifunctional.

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