C Oxidase Subunit 1 Gene Research Articles

Morphological and molecular characters of Lemuru fish (Sardinella lemuru) from Tanjung Luar Waters, East Lombok

Lemuru fish from the Clupeidae family in various countries have many similarities that are difficult to distinguish between one species and another. This study aims to determine the morphological and molecular characteristics, genetic diversity, and kinship of lemuru fish in Tanjung Luar waters with lemuru fish species in countries. The molecular feature of lemuru fish used in this study was a marker for the cytochrome c oxidase subunit 1 (CO1) gene. The lemuru fish sample used in this study was lemuru caught in the waters of Tanjung Luar by small-scale fishermen. Lemuru fish sampling method using random, totaling 100 individuals. Firstly, the lemuru fish samples were grouped based on morphological characters. Next, segregation and augmentation of the CO1 gene DNA in five lemuru fish samples using a pair of primers. The amplification of DNA about 700 bp in size was sequenced. CO1 gene sequence data of lemuru samples were analyzed using MEGA 11 Software (Molecular Evolutionary Genetics Analysis) Version 11. The phylogenetic relationships obtained showed that the lemuru samples from Tanjung Luar waters, East Lombok, is in the same clade as Sardinella Jussieu from Malaysia and has a very close kinship relationship.

Mitochondrial phylogenetic and diversity analysis in Azi-Kheli buffalo.

The present study was conducted for the first time in Pakistan to investigate Cytochrome C Oxidase Subunit 1 (CO1) gene and full-length Displacement Loop (D-loop) region of mitochondrial DNA in Azi-Kheli buffalo breed native to northern hilly areas of Khyber Pakhtunkhwa Province of Pakistan. The present study was designed to investigate phylogeny and diversity in Azi-Kheli buffalo, through two mitochondrial DNA regions, i.e., Cytochrome C Oxidase Subunit-I (CO1) and Displacement Loop (D-loop) region. Thirty (30) blood samples were taken from Azi-Kheli pure breed animals from original breeding tract, i.e., Khwazakhela, Swat. Polymerase chain reactions using gene-specific primers were carried out for amplifying 709-bp region of CO1 gene and 1159-bp region of D-Loop for identification, phylogeny, and diversity in Azi-Kheli buffalo, respectively. The sequences of CO1 gene revealed four (04) haplotypes, whereas D-loop sequences revealed five (05) haplotypes. Mean interspecific diversity with related species was 2.56%, and mean intraspecific diversity within Azi-Kheli buffalo was 0.25%, estimated via Kimura-2 parameter. Phylogenetic tree (maximum likelihood) revealed clustering of Azi-Kheli haplotypes with river buffalo and is distinct from swamp buffalo and other related species of genus Bubalus. Mean haplotype and nucleotide diversity of D-loop were Hd = 0.9601 ± SD = 0.096 and π = 0.01208 ± SD = 0.00182, respectively. Phylogenetic tree (neighbor-joining) revealed two main clades, i.e., river buffalo and swamp buffalo clade. The haplotypes of Azi-Kheli clustered with haplotypes of different river buffalo breeds at different positions. The current study suggests that Azi-Kheli has common origin with other river buffalo breeds; hence, it is river buffalo which harbors high genetic diversity.

Utility of mitochondrial CO1 sequences for species discrimination of Spirotrichea ciliates (Protozoa, Ciliophora)

Ciliates are a diverse species group of the Protozoa, and nuclear and mitochondrial genes have been utilized to discover new species and discriminate closely related species. The mitochondrial cytochrome c oxidase subunit 1 (CO1) gene has been used to discriminate metazoan species and has also been applied for some groups in the phylum Ciliophora. However, it is difficult to produce a universal primer as a standard barcode, because unlike metazoans, mitochondrial DNA sequences of ciliates are long and highly variable. Therefore, to design the new primer set, we sequenced the mitochondrial genomes of two pseudokeronopsids in the class Spirotrichea using next-generation sequencing technology (HiSeq™ 2000). Based on putative CO1 gene fragments of the pseudokeronopsids, we designed the new primer set and successfully sequenced the CO1 of 69 populations representing 47 species (five orders, 14 families, and 27 genera). We found that CO1 showed higher resolution for separating congeneric species than did nuclear SSU rRNA gene sequences, and we identified some putative cryptic species.

First report of Tasmanian sheep strain (G2) genotype isolated from Iranian goat using the high resolution melting (HRM) analysis.

The present study was aimed to evaluate E. granulosus genotypes isolated from goats using HRM analysis in Isfahan province. Cystic echincoccosis, so-called hydatidosis, is widespread infection caused by the larval stage of Echinococcus granulosus. This is an important zoonotic disease worldwide, especially in the developing countries such as Iran. To date, molecular studies mainly based on the mitochondrial DNA sequences have identified distinct genotypes termed G1-G10 which can differ in some characteristics such as the growth and infectivity to different intermediate hosts or the survival rate in the definitive hosts that are important for the development of control strategies. From August to December 2014, 1341 goats were investigated and hydatid cysts were collected from the liver and lungs of 43 infected goats in Isfahan province abattoirs, Isfahan, Iran. Total genomic DNA was extracted from each sample, amplified for the presence of polymorphism of mitochondrial gene coding for cytochrome c oxidase subunit 1 (CO1), using high resolution melting curve (HRM) method. the results of HRM analysis using the sequence of CO1 gene for 43 Echinococcus granulosus isolates from goats showed 31, 2 and 10 isolates were identified as G1, G2, and G3 genotypes, respectively. G1 is the predominant genotype in the isolated goat samples in Isfahan province, and the presence of G2 strain was reported for the first time in goat in Iran.

Molecular characterization and detection of variants of Taenia multiceps in sheep in Turkey.

Taenia multiceps is a cestode (family Taeniidae) that in its adult stage lives in the small intestine of dogs and other canids. The metacestode, known as Coenurus cerebralis, is usually found in the central nervous system including brain and spinal card in sheep and other ruminants. The presence of cysts typically leads to neurological symptoms that in the majority of cases result in the death of the animal. Coenurosis could cause high losses in sheep farms because the disease commonly affects young animals. A total of 20 C. cerebralis isolates collected from naturally infected sheep in Mardin province of Turkey were characterized through the polymerase chain reaction and sequencing of a fragment of cytochrome c oxidase subunit 1 (CO1) gene. The results showed that the CO1 gene sequences were highly conserved in C. cerebralis isolates. Phylogenetic analysis based on partial CO1 gene sequences revealed that C. cerebralis isolates were composed of three different variants.

Molecular Study of the G1 Haplotypes of Echinococcus granulosus from Iran Based on Cytochrome C Oxidase (Subunit 1) Sequence.

In this study, we attempted to identify new Echinococcus granulosus isolates in the North West provinces of Iran based on the mitochondrial cytochrome c oxidase subunit 1 (CO1) sequence. Twenty-nine hydatid cysts from sheep and goats were collected. Genomic DNAs were extracted, and a partial sequence of the CO1 gene was amplified. Polymerase chain reaction products were cloned and sequenced with M13 primers in both directions. All Iranian isolates were located in G1 and G3 genotypes. For the first time, a new G1 haplotype in two Iranian isolates were identified. It seems that this new haplotype was transmitted from Jordan to Iran or vice versa.

Barcoding of fresh water fishes from Pakistan

DNA bar-coding is a taxonomic method that uses small genetic markers in organisms’ mitochondrial DNA (mt DNA) for identification of particular species. It uses sequence diversity in a 658-base pair fragment near the 5′ end of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene as a tool for species identification. DNA barcoding is more accurate and reliable method as compared with the morphological identification. It is equally useful in juveniles as well as adult stages of fishes. The present study was conducted to identify three farm fish species of Pakistan (Cyprinus carpio, Cirrhinus mrigala, and Ctenopharyngodon idella) genetically. All of them belonged to family cyprinidae. CO1 gene was amplified. PCR products were sequenced and analyzed by bioinformatic software. Conspecific, congenric, and confamilial k2P nucleotide divergence was estimated. From these findings, it was concluded that the gene sequence, CO1, may serve as milestone for the identification of related species at molecular level.

Zoonotic onchocerciasis in Hiroshima, Japan, and molecular analysis of a paraffin section of the agent for a reliable identification

Japan is a country of high specific diversity of Onchocerca with eight species, the adults of two not yet known. Onchocerca dewittei japonica, a common filarial parasite of wild boar, had been proved to be the agent of five zoonotic onchocerciasis in Kyushu island with morphological and molecular studies. The sixth case, at Hiroshima in the main island, was identified to the same Onchocerca species, based on adult characters observed on histological sections. To consolidate the identification, mitochondrial cytochrome c oxidase subunit 1 (CO1) gene analysis was attempted with the formalin-fixed, paraffin-embedded parasite specimen. The sequence (196 bp) of a CO1 gene fragment of the parasite successfully PCR-amplified agreed well with those of O. dewittei japonica registered in GenBank, confirming the morphological identification. Moreover a comparison with the CO1 gene sequences of six other Onchocerca species in GenBank excluded the possibility that Onchocerca sp. from wild boar and Onchocerca sp. type A from cattle in Japan, were the causative agents in this case. Mitochondrial DNA analysis proved to be a valuable tool to support the morphological method for the discrimination of zoonotic Onchocerca species in a histological specimen.

Molecular investigation of the Arabian horse breeds of racing, productivity and longevity

The Arabian; horse Equus caballus is belonging to family Equidae that all of its species are in danger of extinction. We sequenced 1059 nucleotides from three mitochondrial DNA protein coding genes for some breeds of the Arabian and English horses designated for race, productivity and longevity in order to investigate their genetic variation. The sequenced genes were NADH dehydrogenase subunit 2 (ND2), cyto-chrome C oxidase subunit 1 (CO1) and ATPase subunit 6 (ATP6). ATP6 discriminated among the different breeds where seven substitutions were recorded of which 2 were non-synonymous. The other loci recoded 8 synonymous substitutions of transitions most of which were among the breeds of longevity. The data of CO1 gene were used to construct the relationship of the Arabian horse to the thoroughbreds. Maximum-likelihood (ML) and Neighbor-joining (NJ) analytical methods were used. The two analytical methods showed clustering of the Arabian breeds in one group and the non-sister relationship within the thoroughbreds. One of the thoroughbreds clustered within the Arabian breeds suggesting the possibility of their out breeding. Increasing tendency in the variation of the studied genes was proportional to the utility of these genes in energy production within the mitochondria. The present study is therefore a preliminary step in the conservational efforts of the Arabian horse of equestrian..

Studying sources of incongruence in arthropod molecular phylogenies: Sea spiders (Pycnogonida) as a case study

In this report, we analyze the phylogeny of Pycnogonida using the three nuclear and three mitochondrial markers currently sequenced for studying inter- and intrafamilial relationships within Arthropoda: 18S and 28S rRNA genes, Histone H3, cytochrome c oxidase subunit 1 (CO1), 12S and 16S rRNA genes. We identify several problems in previous studies, due to the use of inappropriate sequences (taxonomic misidentification, DNA contamination, sequencing errors, missing data) or taxa (outgroup choice). Our analyses show that most markers are not powerful to study the phylogeny of sea spiders. The results suggest however a recent diversification of the group (Mesozoic rather than Paleozoic) and the early divergence of Austrodecidae, followed by Colossendeidae, Pycnogonidae and Rhynchothoracidae. Except Ammotheidae and Callipallenidae, all other families were recovered as monophyletic. Analyses of synonymous sites in CO1 sequences reveal an extreme heterogeneity of nucleotide composition within sea spiders, as six unrelated species show a reverse strand-specific bias. We therefore suggest that several independent reversals of asymmetric mutational constraints occurred during the evolution of Pycnogonida, as a consequence of genomic inversions involving either the control region or a fragment containing the CO1 gene. These hypotheses are supported by the comparison of two complete mitochondrial genomes of sea spiders ( Achelia bituberculata and Nymphon gracile) with that of Limulus.

Genetic evidence for the presence of two species ofOnchocercafrom the wild boar in Japan

In order to clarify the genetic differences between Onchocerca dewittei japonica, the causative agent of zoonotic onchocerciasis in Japan and a related undescribed Onchocerca sp., both parasitizing wild boar (Sus scrofa) of which the infective larval stages are indistinguishable from each other, we compared the sequences of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene region from four infective larvae (recovered from experimentally infected black flies), one microfilaria, and one adult of O. dewittei japonica, and from one infective larva (recovered from an experimentally infected black fly), one microfilaria, and a pool of several microfilariae of O. sp. The length of the CO1 gene region was 649 bp for all samples but there was a difference of 8.8 to 9.4% in the sequences between the two species although there were intraspecific variations of 0 to 0.5%. The CO1 sequences of O. sp. did not correspond to any of those deposited in the databases. Our study provides evidence that O. dewittei japonica and O. sp. are genetically different from each other.

Mitochondrial cytochrome c oxidase subunit 1 gene and nuclear rDNA regions of Enterobius vermicularis parasitic in captive chimpanzees with special reference to its relationship with pinworms in humans

Sequences of mitochondrial cytochrome c oxidase subunit 1 (CO1) gene, nuclear internal transcribed spacer 2 (ITS2) region of ribosomal DNA (rDNA), and 5S rDNA of Enterobius vermicularis from captive chimpanzees in five zoos/institutions in Japan were analyzed and compared with those of pinworm eggs from humans in Japan. Three major types of variants appearing in both CO1 and ITS2 sequences, but showing no apparent connection, were observed among materials collected from the chimpanzees. Each one of them was also observed in pinworms in humans. Sequences of 5S rDNA were identical in the materials from chimpanzees and humans. Phylogenetic analysis of CO1 gene revealed three clusters with high bootstrap value, suggesting considerable divergence, presumably correlated with human evolution, has occurred in the human pinworms. The synonymy of E. gregorii with E. vermicularis is supported by the molecular evidence.

Systematic screening of nuclear encoded proteins involved in the splicing metabolism of group II introns in yeast mitochondria

Studies of yeast, algae and plants have provided genetic and biochemical evidence that the splicing reaction of organellar localized group II introns either depends on proteins encoded by the introns themselves (‘maturases’) or encoded by other genes of the host organisms. However, only a few of those proteins have been identified to date and characterized in more detail. In order to find new nuclear encoded proteins that assist group II splicing, we screened a complete knockout library of Saccharomyces cerevisiae strain BY4741 consisting of 4878 viable haploid clones. The strain contains a rho + mitochondrial genome with a set of 13 introns including the three group II introns (aI1, aI2, aI5γ) in the gene encoding cytochrome- c-oxidase subunit 1 ( COX1) and the single group II intron (bI1) in the gene encoding cytochrome b ( CYTB). In our screen and initial molecular analysis, we focus on intron aI5γ, the last intron in the COX1 gene.

Phylogenetic relationships of three hymenolepidid species inferred from nuclear ribosomal and mitochondrial DNA sequences.

Three hymenolepidid tapeworms, Hymenolepis diminuta, H. nana and H. microstoma, are commonly maintained in laboratory rodents and used in many experimental model systems of tapeworm infections. We examined partial sequences from the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene and nuclear ribosomal internal transcribed spacer 2 (ITS2) sequences to infer phylogenetic relationships of the 3 hymenolepidid species. Parts of the CO1 gene and ITS2 were amplified by PCR and sequenced directly. The CO1 gene sequence obtained was the same in length (391 bp) among all specimens. In the case of ITS2, however, several insertions and deletions were detected (671-741 bp) not only among species but also between an American isolate and a Japanese isolate of H. diminuta. Percentage nucleotide differences between H. diminuta and H. microstoma, or H. diminuta and H. nana were 16.6-18.2% for the CO1 gene and 21.3-22.9% for ITS2. The differences in both sequences between H. microstoma and H. nana were about 14%. Phylogenetic trees inferred from both of the nucleotide sequences showed similar topology, and suggest that H. diminuta may have diverged from the common ancestral line the earliest, and that H. nana is closer to H. microstoma than to H. diminuta.