scholarly journals Cytochrome Oxidase C Subunit I (COI) for Identification and Genetic Variation of Loaches (Nemacheilus fasciatus)

2020 ◽  
Vol 7 (3) ◽  
pp. 142-153
Author(s):  
Amalia Ayuk Riyadini ◽  
Maheno Sri Widodo ◽  
Mohamad Fadjar
Keyword(s):  
Cytochrome Oxidase ◽  
Haplotype Diversity ◽  
Coi Gene ◽  
Research Needs ◽  
Morphological Similarity ◽  
Cytochrome Oxidase Subunit ◽  
River Waters ◽  
Outgroup Species ◽  
C Subunit ◽  
Larger Sample

Nemacheilus fasciatus is an Indonesian freshwater fish species that can be found in river waters on Java. This fish has a morphological similarity between species. This study aims to identify species of samples found and know their genetic kinship. This study used the Cytochrome Oxidase subunit I (COI) gene as a molecular marker, and then the results were analyzed using MEGA X software. The genetic structure and phylogeny of N. fasciatus sequences were combined with outgroup species from GenBank and analyzed using Maximum Likehood (ML), Pairwise Genetic Distance and Bootstrapping Phylogeny Model of Kimura 2 Parameters. The results showed that the primary pairs of LCO1490 and HCO2198 used to amplify the sample N. fasciatus with COI as a marker. The nucleotide frequencies of these loaches are A=26.5%, T=23.8%, C=19.9% and G=29.9%. The estimated Transition/Transversion bias (R) is 0.60. The number of haplotype diversity (Hd) was 0.972, and nucleotide (Pi) diversity was 0.05115. The kinship of N. fasciatus compared to the outgroup is closer to N. pallidus than N. chrysolaimos. Research needs to be conducted with a larger sample size for the genetic diversity of N. fasciatus in Indonesia.

First record of body colour polymorphism in giant African snail Achatina fulica (Bowdich, 1822) - a comparative study using mitochondrial cytochrome oxidase subunit I (COI) gene

ENTOMON ◽  
2019 ◽  
Vol 44 (2) ◽  
pp. 155-160
Author(s):  
Keerthy Vijayan ◽  
R. Sugantha Sakthivel ◽  
T.V. Sajeev
Keyword(s):  
Cytochrome Oxidase ◽  
South India ◽  
The Body ◽  
Colour Polymorphism ◽  
Coi Gene ◽  
Body Colour ◽  
Cytochrome Oxidase Subunit ◽  
Cytochrome Oxidase Subunit I ◽  
Black And White ◽  
Oxidase Subunit

The presence of the body colour polymorphism in the tropical invasive pest giant African snail is reported for the first time from South India. Three different body colour polymorphs were recognised viz. grey, black and white. The grey body colour is the most common polymorph. The black and white colour polymorphs are found to be in almost equal proportions in the reported localities with the grey counterparts. The cytochrome oxidase subunit I (COI) sequences of the three colour polymorphs are found to be identical. The presence of the body colour polymorphism in south India may be attributed to the avian predation and other selection pressures.

Redefinition of Cornexcisia Fan & Kano, 2000 (Diptera: Sarcophagidae), with the first description of the female of Sarcophaga kurahashii (Shinonaga & Tumrasvin, 1979)

Zootaxa ◽  
2019 ◽  
Vol 4668 (3) ◽  
pp. 410-420
Author(s):  
CHAO WANG ◽  
YUNYUN GAO ◽  
THOMAS PAPE ◽  
DONG ZHANG
Keyword(s):  
Cytochrome Oxidase ◽  
Coi Gene ◽  
Mitochondrial Cytochrome ◽  
Gene Sequences ◽  
Cytochrome Oxidase Subunit ◽  
Cytochrome Oxidase Subunit I ◽  
Mitochondrial Cytochrome Oxidase Subunit ◽  
Senior Synonym ◽  
First Time ◽  
Mitochondrial Cytochrome Oxidase

Sarcophaga Meigen, 1826 is proposed as a senior synonym of Cornexcisia Fan & Kano, 2000, syn. nov. and Fanzideia Xue, Verves & Du, 2011, syn. nov. Cornexcisia Fan & Kano, 2000, stat. rev. is given status as a subgenus and is considered a senior synonym of Fanzideia Xue, Verves & Du, 2011, syn. nov. at the subgeneric level. Cornexcisia is argued to contain S. (Cornexcisia) longicornuta (Fan & Kano, 2000), comb. nov., S. (C.) cygnocerca (Xue, Verves & Du, 2011), comb. nov., S. (C.) kurahashii (Shinonaga & Tumrasvin, 1979), subgen. comb. nov. (from Phallosphaera Rohdendorf) and S. (C.) suthep Pape & Bänziger, 2003, subgen. comb. nov. (from Rosellea Rohdendorf). Sarcophaga (C.) kurahashii is newly recorded from China (Yunnan), the male is redescribed and the female is described for the first time, supported by photographs, illustrations and mitochondrial cytochrome oxidase subunit I (COI) gene sequences. Species of Cornexcisia share an exceptionally long postpedicel in the female and the following apomorphic distiphallic appendages in the male: juxta ventro-proximally with an apically divided arm with cuticular pile, and lateral styli bifurcated from the base with each branch elongate, gently curved and slightly expanded apically. A key to the species of Cornexcisia is provided. 

scholarly journals A Nation-wide Phylogenetic and Phylogeographic Investigation of the Endemic New Zealand Oyster Borers, Haustrum scobina and Haustrum albomarginatum

2021 ◽  
Author(s):  
Seamus O'Mahony
Keyword(s):  
New Zealand ◽  
Dna Sequences ◽  
Haplotype Diversity ◽  
Shell Morphology ◽  
Ice Age ◽  
Coi Gene ◽  
Rrna Gene ◽  
Similar Species ◽  
Migration Route ◽  
Outgroup Species

The endemic New Zealand sea snails Haustrum scobina and Haustrum albomarginatum are rocky shore intertidal dogwhelks of the Muricidae family. They have direct developing young and are carnivores. Their radula is used to drill into the shells of their prey, and they are commonly referred to as oyster borers. The taxonomic status of these species is still unresolved and therefore the name Haustrum scobina sensu lato is used.<br><br>The overall goal of this thesis research was to investigate the phylogeny and phylogeography of Haustrum scobina sensu lato using mitochondrial DNA sequences. Comparisons made to phylogeographic studies of ecologically similar species such as Cominella spp. provide an opportunity to identify the common environmental determinates of population migration route, genetic differentiation and speciation whenever similar patterns are found.<br><br>A nation-wide collection of samples was used to generate 277 new sequences from a 610 bp portion of the cytochrome c oxidase subunit I (COI) gene. This enabled the formation of a dataset of 654 DNA sequences, which was comprised of the 277 new sequences, 16 retrieved from a published study that deposited them in GenBank, and 361 from a previous unpublished thesis study. An unexpectedly diverse phylogeny of 58 COI haplotypes from 31 sample sites was recovered. These formed three clusters using K-means clustering by pairwise mutational distance. The in-group species did not form reciprocal monophyly groups, and the expected closest outgroup species (Haustrum haustorium) appeared to be as similar to the in-group clusters as they were to each other. A dataset of 27 DNA sequences from an 827 bp portion of the large sub-unit 28S nuclear rRNA gene was produced with the intention of corroborating the findings from the analyses of the COI dataset. This consisted of 26 new sequences and one sequence from a published study that deposited the sequence on GenBank. The expected taxonomic arrangement of Haustrum scobina sensu lato could not be matched by COI sequences due to incongruence with the 28S phylogeny and shell morphology. <br><br>The 28S dataset and shell morphology indicated there are two species in Haustrum scobina sensu lato. These are most likely Haustrum scobina and Haustrum albomarginatum, but they could not clearly be identified in the COI data. As a result, the phylogeographic certainty was limited when using the COI dataset because of the lack of clarity between the haplotypes of the two putative species. Possible reasons for the complicated COI dataset are discussed. Phylogenetic analysis of both the 28S and COI datasets did not support the expected conclusion that members of Haustrum scobina sensu lato are each other’s closest relatives. Haustrum haustorium was the expected immediate outgroup species but formed a polytomy with the in-group. A decrease in COI haplotype diversity was observed in southern samples when they were compared to the samples collected at northern locations. Taranaki sites shared a haplotype with multiple South Island sites that had no haplotype diversity. This suggested post-glacial re-colonisation of southern sites after displacement by ice-age conditions from these locations, a hypothesis consistent with results from studies of the Cominella genus. Association between Purau Bay in Lyttleton Harbour, Titahi Bay, Port Ahuriri and Kawau Island with no associated haplotypes between these locations suggested human-mediated translocation events. A genetic disjunction was also apparent between the south Wellington/Wairarapa coast and the eastern Wairarapa coast. This pattern was consistent with one study of Cominella maculosa and other studies have attributed similar patterns of other species in the region to recent uplift events affecting coastal community composition. The phylogeny of Haustrum scobina sensu lato will require further investigation before it can be used to more confidently resolve the phylogeographic history of the species.

A new record of Ornithodoros (Pavlovskyella) verrucosus (Acari: Argasidae) from a porcupine burrow in western Iran

2019 ◽  
Vol 24 (5) ◽  
pp. 771
Author(s):  
Asadollah Hosseini Chegeni ◽  
Majid Tavakoli ◽  
Habibollah Koshki ◽  
Javad Khedri ◽  
Mohammad Hassan Kayedi
Keyword(s):  
Cytochrome Oxidase ◽  
18S Rdna ◽  
Genomic Dna ◽  
New Record ◽  
Morphological Characteristics ◽  
Species Group ◽  
Coi Gene ◽  
Cytochrome Oxidase Subunit ◽  
Western Iran ◽  
Blast Analysis

We found an Ornithodoros species with distinct morphological characteristics than Alveonasus genus and other O. (Pavlovskyella) species group. Tick specimens were collected from a porcupine burrow, located in Lorestan province, western Iran. Genomic DNA of tick was extracted using CTAB and then three gene fragments of cytochrome oxidase subunit I (COI) and 16S mtDNA & 18S rDNA were amplified by PCR. Tick specimens were identified as near to O. (P.) verrucosus and O. (P.) tholozani. So the identification was confirmed by BLAST analysis of 16S mtDNA & 18S rDNA and COI gene fragments. A taxonomic key to the native adult subfamily Ornithodorinae species of Iran are provided to facilitate their identification.

Comment on “Molecular identification of seven new Zygopteran genera from South China through partial cytochrome oxidase subunit I (COI) gene”

Meta Gene ◽  
2020 ◽  
Vol 25 ◽  
pp. 100759
Author(s):  
Yesenia Margarita Vega-Sánchez ◽  
María Olalla Lorenzo-Carballa ◽  
Diogo Silva Vilela ◽  
Rhainer Guillermo-Ferreira ◽  
Ricardo Koroiva
Keyword(s):  
Cytochrome Oxidase ◽  
Molecular Identification ◽  
South China ◽  
Coi Gene ◽  
Cytochrome Oxidase Subunit ◽  
Cytochrome Oxidase Subunit I ◽  
Oxidase Subunit

scholarly journals Genetic Profile Assessment of Giant Clam Genus Tridacna as a Basis for Resource Management at Wakatobi National Park Waters

2017 ◽  
Vol 22 (2) ◽  
pp. 67-74
Author(s):  
Muhammad Nur Findra ◽  
Isdradjad Setyobudiandi ◽  
Nurlisa Alias Butet ◽  
Dedy Duryadi Solihin
Keyword(s):  
Resource Management ◽  
Cytochrome Oxidase ◽  
National Park ◽  
Coi Gene ◽  
Genetic Profile ◽  
Giant Clam ◽  
Cytochrome Oxidase Subunit ◽  
Cytochrome Oxidase Subunit I ◽  
Oxidase Subunit ◽  
Specific Nucleotide

Giant clam population has been decreased in a few years. Resource management requires information from various aspects, such as ecological, population, and other aspects. This study was aimed at assessing the genetic profile of Tridacna giant clam in Wakatobi National Park waters using Cytochrome oxidase subunit I (COI) genetic marker. Sample collection was conducted around the three main islands, i.e., Wangi-wangi, Kaledupa, and Tomia. Genetic analysis using COI gene may contribute in identifying giant clams up to the species level and showed the relationship among species. The research found 41 specific nucleotide sites for the clams. T. crocea, T. squamosa and T. maxima had 2, 15 and 24 sites, respectively. COI gene as a biological marker was able to separate groups of giant clam by species. Nucleotide variation of T. crocea from Wakatobi was the highest among other locations, so it could be used as a genetic source for translocation and domestication. Keywords: cytochrome oxidase subunit I, specific nucleotide, Tridacna, Wakatobi National Park

Characteristics of Crassostrea Oyster Cytochrome Oxidase Subunit I (Coi) Gene As Species Identity In Delta Cimanuk, West Java

2020 ◽  
Vol 4 (1) ◽  
pp. 8-16
Author(s):  
Dian Rezki Muliani ◽  
Fredinan Yulianda ◽  
Nurlisa A Butet
Keyword(s):  
Cytochrome Oxidase ◽  
Morphological Changes ◽  
Coi Gene ◽  
Morphological Identification ◽  
Cytochrome Oxidase Subunit ◽  
Species Identity ◽  
Cytochrome Oxidase Subunit I ◽  
Oxidase Subunit ◽  
Identification Of Species ◽  
Crassostrea Oyster

Oysters belong to the Crassostrea, which is a type of shellfish that lives as benthos in waters under the same substrate and environmental conditions will exhibit similar morphological changes in response. There are many types of oysters that have a similar shape are often an obstacle to differentiate of Crassostrea species through morphological identification. The purpose of this research was to identify the types of oysters found in the waters of Delta Cimanuk through analysis of the morphology and nucleotide diversity of Cytochrome Oxidase subunit I (COI) gene, as basic information on proper management and conservation. The morphological identification results show that there were two species of the Crassostrea. Identification of species through the Barcoding DNA technique shows that there is one type of oyster: Crassostrea iredalei with an accuracy of 99.5%.

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