scholarly journals Molecular Identification and Phylogenetic Relationships of Threadfin Breams (Family: Nemipteridae) Using mtDNA Marker

2012 ◽  
Vol 4 (2) ◽  
pp. 13-18 ◽  
Author(s):  
Vaithilingam RAVITCHANDIRANE ◽  
Vaithianathan GEETHA ◽  
Vijayan RAMYA ◽  
Bilavendiran JANIFER ◽  
Muthusamy THANGARAJ ◽  
...  
Keyword(s):  
Fish Species ◽  
Phylogenetic Trees ◽  
Evolutionary Relationship ◽  
Coi Gene ◽  
Gene Sequences ◽  
Mtdna Coi ◽  
High Bootstrap ◽  
Commercially Important ◽  
Two Parameter ◽  
Mtdna Marker

Cytochrome c oxidase-1 gene sequences of mitochondrial genome were analyzed for species identification and phylogenetic relationship among the commercially important Nemipterus species. Sequence analysis of COI gene clearly indicated that all the nine fish species fell into distinct clads, which are genetically distant from each other and exhibited identical phylogenetic reservation. All the COI gene sequences provide sufficient phylogenetic information and evolutionary relationship to distinguish the nine Nemipterus species unambiguously. As per the neighbour-joining (NJ) and maximum likelihood (ML) trees, all the nine species are genetically distant from each other and exhibited identical phylogenetic reservation. Based on the NJ and ML phylogenetic trees N. mesoprion, N. zysron, N. hexodon, N. nematophorus, N. virgatus and N. bipunctatus were closely related with high bootstrap value (97). The overall mean Kimura two parameter (K2P) distances between the nine species was 0.109. The intra species K2P distance was high in N. japonicus (0.069) followed by N. peronii (0.050) and N. mesoprion (0.002). This study proves the use of mtDNA COI gene sequence based approach is an alternative tool for identifying fish species at a faster pace.

Phylogeny of Salmonoid Fishes (Salmonoidei) Based on mtDNA COI Gene Sequences (Barcoding)

2018 ◽  
Vol 11 (3) ◽  
pp. 271-285 ◽  
Author(s):  
V. S. Artamonova ◽  
O. V. Kolmakova ◽  
E. A. Kirillova ◽  
A. A. Makhrov
Keyword(s):  
Coi Gene ◽  
Gene Sequences ◽  
Mtdna Coi

scholarly journals Sequence analysis of mtDNA COI gene and molecular Phylogeny of Parasitic Unionicolid Mites (Acari: Unionicolidae: Unionicola) in China

2020 ◽  
Vol 185 ◽  
pp. 04024
Author(s):  
Jian Cheng ◽  
Xin Huang ◽  
Liangliang Huang ◽  
Chungen Wen
Keyword(s):  
Maximum Likelihood ◽  
Sequence Analysis ◽  
Nucleotide Sequence ◽  
Phylogenetic Trees ◽  
Coi Gene ◽  
Nucleotide Sequence Analysis ◽  
Gene Fragment ◽  
Neighbor Joining ◽  
Mtdna Coi ◽  
The Relationship

A nucleotide sequence analysis of cytochrome oxidase I (COI) gene fragment from parasitic unionicolid mites is performed in this paper. The aligned nucleotide fragment is 664bp (including gaps) in length, including 374 conserved sites, 284 variable sites, 73 conversion sites, 51 transpose sites. The conversion sites are much higher than the transpose sites with a conversion transpose ratio (si/sv) of 1.4. The percentages of A+T and G+C are 64.6% and 35.4% in the nucleotide sequence which indicates a strong AT bias. From the sequence analysis of COI gene, the relationship between Unionicola chelata and Unionicola arcuate are the farthest among all the parasitic unionicolid mites while the relationship between Unionicola ischyropalpus and U.arcuata are the closest. Using U.crassipes as an outgroup, the phylogenetic trees are reconstructed with maximum likelihood(ML) and neighbor-joining(NJ) inferences (PAUP4.0b10 tool), and the results show that U.arcuata is the more evoluted speciesand Unionicola agilex might be the first separated from ancestral species.

scholarly journals Molecular identification of seven species of the genus Stigmaeopsis (Acari: Tetranychidae) and preliminary attempts to establish their phylogenetic relationship

2017 ◽  
Vol 22 (1) ◽  
pp. 91 ◽  
Author(s):  
Hironori Sakamoto ◽  
Tomoko Matsuda ◽  
Reiko Suzuki ◽  
Yutaka Saito ◽  
Jian-Zhen Lin ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Trees ◽  
Molecular Level ◽  
Sibling Relationship ◽  
Coi Gene ◽  
Diagnostic Pcr ◽  
Mitochondrial Haplotypes ◽  
High Aggression ◽  
High Bootstrap ◽  
Rna Genes

The genus Stigmaeopsis (family Tetranychidae) has 11 species including the serious bamboo pest, S. nanjingensis. All Stigmaeopsis species are difficult to identify by their morphology, and the diagnostic character (the length of dorsal setae) can be used only to identify fresh specimens. To identify these species at the molecular level, we sequenced the cytochrome c oxidase subunit I (COI) gene of mitochondrial DNA and two nuclear ribosomal RNA genes (18S and 28S) of 20 strains of seven species of Stigmaeopsis [S. celarius, S. longus, S. miscanthi (both low- and high-aggression phenotypes), S. nanjingensis, S. tenuinidus, S. saharai and S. takahashii]. In maximum likelihood (ML) phylogenetic trees of both COI and combined 18S-28S genes, all but one Stigmaeopsis species could be identified as a monophyletic clade with high bootstrap values. The present results strongly suggested that the exceptional species, S. miscanthi, consists of three biologically different entities based on two phylogenetic trees. Though the phylogenetic trees did not comprehensively solve the phylogeny of Stigmaeopsis, a phylogenetic tree based on the combined nuclear genes showed a sibling relationship between two sub-social Stigmaeopsis species, S. miscanthi and S. longus. In addition, diagnostic PCR detected Wolbachia or Cardinium, which frequently affect mitochondrial haplotypes, in S. longus and S. nanjingensis. In the COI tree, S. longus was separated into two groups which were more consistent with their bacterial infection status than with their geographical distribution. 

Four new species of Splendid Ghost Moths (Lepidoptera: Hepialidae: Aenetus) from Australia and Papua New Guinea

Zootaxa ◽  
2020 ◽  
Vol 4809 (3) ◽  
pp. 449-474
Author(s):  
ETHAN P. BEAVER ◽  
MICHAEL D. MOORE ◽  
JOHN R. GREHAN ◽  
ALEJANDRO VELASCO-CASTRILLÓN ◽  
MARK I. STEVENS
Keyword(s):  
New Species ◽  
Papua New Guinea ◽  
Western Australia ◽  
New Caledonia ◽  
New Guinea ◽  
Northern Territory ◽  
Coi Gene ◽  
Similar Species ◽  
Gene Sequences ◽  
Mtdna Coi

Four new Aenetus Herrich-Schäffer species are described from northern Australasia; Aenetus simonseni sp. nov. from the top-end of the Northern Territory, Australia, A. maiasinus sp. nov. from the Kimberley region of Western Australia, A. trigonogrammus sp. nov. from south-eastern Queensland, Australia, and A. albadamanteum sp. nov. from eastern Papua New Guinea. Aenetus simonseni sp. nov. and A. maiasinus sp. nov. appear to belong to the tegulatus-group of species (sensu Grehan et al. 2018), A. trigonogrammus sp. nov. is part of the splendens-group of species (sensu Simonsen 2018), while A. albadamanteum sp. nov. shares morphological similarities with A. hampsoni (Joicey & Noakes, 1914), A. crameri Viette, 1956, and A. toxopeusi Viette, 1956, from New Guinea, and A. cohici Viette, 1961 from New Caledonia. The four new species are illustrated and compared with superficially similar species in morphology and, for two species, molecular (mtDNA COI gene) sequences. 

scholarly journals New Hosts ofSimplicimonas similisandTrichomitus batrachorumIdentified by 18S Ribosomal RNA Gene Sequences

2013 ◽  
Vol 2013 ◽  
pp. 1-5 ◽  
Author(s):  
Kris Genelyn B. Dimasuay ◽  
Orlie John Y. Lavilla ◽  
Windell L. Rivera
Keyword(s):  
Phylogenetic Trees ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Bootstrap Support ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Pathogenic Potential ◽  
Gene Sequence Analysis ◽  
High Bootstrap ◽  
Recent Classification

Trichomonads are obligate anaerobes generally found in the digestive and genitourinary tract of domestic animals. In this study, four trichomonad isolates were obtained from carabao, dog, and pig hosts using rectal swab. Genomic DNA was extracted using Chelex method and the 18S rRNA gene was successfully amplified through novel sets of primers and undergone DNA sequencing. Aligned isolate sequences together with retrieved 18S rRNA gene sequences of known trichomonads were utilized to generate phylogenetic trees using maximum likelihood and neighbor-joining analyses. Two isolates from carabao were identified asSimplicimonas similiswhile each isolate from dog and pig was identified asPentatrichomonas hominisandTrichomitus batrachorum, respectively. This is the first report ofS. similisin carabao and the identification ofT. batrachorumin pig using 18S rRNA gene sequence analysis. The generated phylogenetic tree yielded three distinct groups mostly with relatively moderate to high bootstrap support and in agreement with the most recent classification. Pathogenic potential of the trichomonads in these hosts still needs further investigation.

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