scholarly journals DNA barcoding of fishes from River Song, Dehradun, Uttarakhand using mitochondrial cytochrome-c oxidase-I gene

2013 ◽  
Vol 14 (3) ◽  
pp. 113-121
Author(s):  
Madhu Thapliyal ◽  
Bipin Kumar Sati ◽  
Ravi Kumar ◽  
Tribhuwan Chandra ◽  
Ashish Thapliyal
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Fresh Water ◽  
Fish Species ◽  
Molecular Taxonomy ◽  
Dna Barcode ◽  
Fish Fauna ◽  
Coi Gene ◽  
Cytochrome C Oxidase I ◽  
The Ganges

The entire Himalayan region is well known as a global hotspot for biodiversity. Many workers have documented different aspect of biodiversity.  The Uttarakhand Himalaya region, a part of Himalayan system, is very rich in fresh water aquatic biodiversity because it has many fresh water streams and rivers within a short distance of 200 miles. All these fresh water bodies harbor diverse aquatic fauna with fishes being the most extensively studied. There are many fish species reported by many authors in Uttarakhand. Many of the fishes have similar morphological characters (morpho-metrics) and are difficult to identify. Attempts have been made to generate the DNA barcode of fishes but most of the attempt are limited to major rivers i.e. the Ganges and the Yamuna. Besides these two prominent river (the Ganges & the Yamuna), there are many supporting streams and small tributaries that are also inhabited by many species. No “long term” and “entire river scan” for fish species has ever been conducted in Uttarakhand. Our research aims to generate a molecular database (DNA Barcode) for entire fish species fauna in each small river/stream of Uttarakhand.  Using a combination of morphometric & DNA bar-coding data will provide an efficient method for species level identification and contributes considerably to taxonomic and biodiversity research. The present study is first step towards establishing molecular taxonomy database of Uttarakhand based upon the bar coding pattern of cytochrome c oxidase I (COI) gene.  We carried out an “entire river scan” of River Song (a tributary of river Ganges).  50 samples were collected from various sampling sites along the entire stretch of river and analyzed.   Data was uploaded into the BOLD database and the analysis of data using this database suggests that the genetic variability (K2P distance) distribution of 50 individuals belonging with 15 species.The average intraspecific variation using K2P and NJ methods/models was assessed. The mean intraspecific distance was less than 1.45% for 32% of species. Mean K2P distance within species, genus and family was 0.1%, 16.3% and 21.70% respectively. Our results suggest that River Song has diverse fish fauna with substantial genetic diversity.  Data from Barillius species suggests that this species has a very high variation.  There is ahighly probability that as all the rivers are scanned new data on endemic and exotic fish fauna diversity will emerge which would be helpful in conservation efforts.

A new species of sponge-inhabiting barnacle Neoacasta (Archaeobalanidae, Acastinae) in Kyushu, Japan

Crustaceana ◽  
2020 ◽  
Vol 93 (11-12) ◽  
pp. 1515-1532
Author(s):  
Meng-Chen Yu ◽  
Takefumi Yorisue ◽  
Gregory A. Kolbasov ◽  
Benny K. K. Chan
Keyword(s):  
New Species ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Dna Barcode ◽  
Shell Morphology ◽  
Coi Gene ◽  
Cytochrome C Oxidase I ◽  
Morphological Examination ◽  
A New Species ◽  
I Gene

Abstract This paper describes a new species of sponge-inhabiting barnacle, Neoacasta liui sp. nov., collected in Fukuoka, Kyushu, Japan. In the present study we used both the morphological examination and DNA barcode (cytochrome c oxidase I gene) to distinguish this new species from acastine species including its congeners from Neoacasta Kolbasov, 1993. Neoacasta liui sp. nov. is similar to Neoacasta glans (Lamarck, 1818) in shell morphology, but the divergence in COI gene between them reached inter-specific differences. N. liui sp. nov. is characterized by externally latticed, narrow scutum, beak-shaped tergum with wider spur, and lack of six inwardly prominent teeth on margin of basis. N. glans having an Indo-West Pacific distribution may represent a complex of cryptic species.

scholarly journals Occurrence and molecular identification of an invasive rice strain of fall armyworm Spodoptera frugiperda (Lepidoptera: Noctuidae) from Sindh, Pakistan, using mitochondrial cytochrome c oxidase I gene sequences

2021 ◽  
Author(s):  
Sumaira Yousaf ◽  
Abdul Rehman ◽  
Mariyam Masood ◽  
Kazam Ali ◽  
Nazia Suleman
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Spodoptera Frugiperda ◽  
Fall Armyworm ◽  
Coi Gene ◽  
Invasive Pest ◽  
Mitochondrial Cytochrome ◽  
Cytochrome C Oxidase I ◽  
Gene Sequences ◽  
Rice Strain

AbstractThe fall armyworm (FAW), an invasive pest of maize, is an emerging threat in Southern Asia after America and Europe. Recently, this notorious pest has also been found in different areas of Pakistan. To assess its presence in Pakistan, a survey was carried out in the provinces of Punjab, Sindh, and Khyber Pakhtunkhwa during May–October 2019. We observed the highest incidence of FAW in Sindh with maximum impact in districts Tando-Allahyar and Hyderabad. These samples were identified as Spodoptera frugiperda on the morphological and taxonomical bases. However, morphological identification of this pest is very difficult at early larval instars. Here, we use the mitochondrial cytochrome c oxidase I (COI) gene region for the precise identification of larva of this invasive pest at species level. Two different regions of COI gene (COI-5′ and COI-3′) were used as molecular markers for the identification of this species. DNA sequence similarity searches of the obtained COI gene sequences (NCBI GenBank Accession Nos. MW241537, MW241538, MW349515, MW349516, MW349493 and MW349494) revealed that genetically it is more than 99% identical to S. frugiperda. The phylogenetic analysis indicated it as the rice-strain (R-strain). Both 3′- and 5′-fragment tree topologies showed that the collected samples of the FAW species belong to the R-strain. To the best of our knowledge, this is the first report providing molecular evidence for the existence of R-strain of S. frugiperda that was found feeding on maize crop in Sindh, Pakistan, using COI gene sequences as a marker.

scholarly journals Variasi Genetik Plutella xylostella L. (Lepidoptera: Plutellidae) berdasarkan Gen Cytochrome C Oxidase I

Jurnal MIPA ◽  
2019 ◽  
Vol 8 (1) ◽  
pp. 1
Author(s):  
Claudius F. Kairupan ◽  
Jantje Pelealu ◽  
Juliet M.E. Mamahit
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Plutella Xylostella ◽  
Coi Gene ◽  
Cytochrome C Oxidase I ◽  
Base Pairs ◽  
Insecticide Application ◽  
Nucleotide Base ◽  
North Sulawesi ◽  
Relationship Of

Daerah Modoinding dan Tomohon di Sulawesi Utara, dikenal sebagai  daerah penghasil sayuran kubis di Indonesia. Sayuran kubis memiliki hama utama yaitu Plutella xylostella. Penyebab serangga ini dapat bertahan hingga saat ini karena adanya sifat resistensi akibat pemberian insektisida yang berlebihan. Penelitian ini dilakukan untuk menganalisis variasi pada gen cytochrome C oxidase IPlutella xylostella yang diperoleh dari dua lokasi yang berbeda, yaitu Modoinding dan Tomohon. Analisis sekuens menunjukkan adanya perbedaan pasang basa nukleotida dari sampel yang berbeda lokasi. Selain itu, variasi juga ditunjukkan pada sampel yang diperoleh dari basis data GenBank dengan adanya perbedaan 1-14 pasang basa nukleotida dengan spesimen pada penelitian ini. Hubungan kekerabatan gen COI P. xylostella keseluruhan sampel tergolong dalam variasi intraspesies dengan nilai jarak genetik berkisar antara 0-0,022 (0-2,20%).Modoinding and Tomohon areas in North Sulawesi, are known as regions in Indonesia that produce a cabbage. The main pest of cabbage, Plutella xylostella. This insect can survive due to its resistance resulted from prolonged insecticide application. This study aims to analyze genetic variation of COI genes in P. xylostella from Modoinding and Tomohon areas. Sequence analysis showed there were differences in nucleotide base pairs between these locations. In addition, variations were also shown in samples obtained from the GenBank database with differences in 1-14 nucleotide base pairs with specimens in this study. The genetic relationship of P. xylostella COI gene in all samples was classified as intraspecific variation with genetic distance values ranging from 0-0,022 (0-2,20%).D aerah Modoinding dan Tomohon di Sulawesi Utara, dikenal sebagaidaerah penghasil sayuran kubis di Indonesia. Sayuran kubis memilikihama utama yaitu Plutella xylostella. Penyebab serangga ini dapatbertahan hingga saat ini karena adanya sifat resistensi akibat pemberianinsektisida yang berlebihan. Penelitian ini dilakukan untuk menganalisisvariasi pada gen cytochrome C oxidase I Plutella xylostella yang diperolehdari dua lokasi yang berbeda, yaitu Modoinding dan Tomohon. Analisissekuens menunjukkan adanya perbedaan pasang basa nukleotida darisampel yang berbeda lokasi. Selain itu, variasi juga ditunjukkan padasampel yang diperoleh dari basis data GenBank dengan adanyaperbedaan 1-14 pasang basa nukleotida dengan spesimen padapenelitian ini. Hubungan kekerabatan gen COI P. xylostella keseluruhansampel tergolong dalam variasi intraspesies dengan nilai jarak genetikberkisar antara 0-0,022 (0-2,20%).

scholarly journals Phylogenetic analysis of Anguilla marmorata population in Thua Thien Hue, Vietnam based on the cytochrome c oxidase I (COI) gene fragments

2020 ◽  
Author(s):  
Nguyen Quang Linh ◽  
Kieu Thi Huyen
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Gene Segment ◽  
Coi Gene ◽  
Molecular Characteristics ◽  
Cytochrome C Oxidase I ◽  
Anguilla Marmorata ◽  
Data Book ◽  
Population Numbers ◽  
Adenine Thymine

Abstract The giant mottled eel is a species with high commercial value so overfishing, river management, and water pollution have negatively affected its movement and population numbers. Anguilla marmorata (eel) was listed in the Vietnam Red Data Book 2007 with a description of Vulnerability. This study used a barcode technique to analyze molecular characteristics and build genetic plants based on the cytochrome c oxidase I gene segment isolated from the mitochondrial genome of 48 individuals of A. marmorata collected in five different ecological regions of Thua Thien Hue, Vietnam. The isolated the cytochrome c oxidase I sequence has a length of 843 nucleotides, four base nucleotides of 30.03% Thymine, 25.15% Cytosine, 27.49% Adenine, and 17.43% Guanine. The percentage of Guanine + Cytosine content (42.58%) is acceptable, lower than the Adenine + Thymine content. The replacement capacity of Adenine and Guanine is 22.45% highest, the ratio between Thymine and Guanine; Cytosine and Guanine are the lowest at 2.72%. The establishment of genetically modified plants has shown the high genetic similarity of individuals in eel populations in Thua Thien Hue. The population of Anguilla marmorata eels in Thua Thien Hue, Vietnam is divided into two separate groups that are guided by the migration process and specific ecological. This is particularly important in building strategies to conserve and develop the gene for eel in Vietnam and Thua Thien Hue.

Monitoring the seasonal dynamics of microalgae in the South Sea of Korea by use of a cytochrome c oxidase I DNA barcode

2018 ◽  
Vol 21 (1) ◽  
pp. 10-18 ◽  
Author(s):  
Mirye Park ◽  
So Yun Park ◽  
Jinik Hwang ◽  
Juyun Lee ◽  
Seung Won Jung ◽  
...  
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Seasonal Dynamics ◽  
Dna Barcode ◽  
Cytochrome C Oxidase I ◽  
The South ◽  
South Sea
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