Molecular characterization and phylogenetic analysis of cyclopoid copepod Mesocyclops leuckarti using mtCOI

2017 ◽  
Vol 6 (04) ◽  
pp. 5365
Author(s):  
Gomathi Jeyam ◽  
Ramanibai R*
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Barcode ◽  
Coi Gene ◽  
Universal Primers ◽  
Cyclopoid Copepod ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
Mesocyclops Leuckarti ◽  
Coi Sequences ◽  
The Individual

Copepods are the most abundant metazoan zooplankton amongst multicellular animals. The present study was performed to establish the sequence variation of partial mitochondrial Cytochrome c Oxidase I gene (COI) from Mesocyclops leuckarti collected from the Retteri Lake, Chennai in order to identify and describe their genetic divergence along with the phylogenetic relatedness with other species. DNA of individual M. leuckarti was extracted and the partial mitochondrial COI gene was successfully amplified using the universal primers LCO-1490 and HCO-2198. A 576bp partial mitochondrial COI gene sequence was obtained. Analysis of partial COI sequences of M. leuckarti exposed 93% similarity amongst all the individual of copepods selected from Genbank. The obtained COI sequences of Cyclopoid copepod was confirmed with BLAST analysis. Phylogenetic analysis of M. leuckarti along with selected out groups from different taxa level further supports the clarity and maintained the authentic of taxonomy up to the subclass level: Copepoda. The results showed that, the COI barcoding of cyclopoid copepod species could be distinguished from the others very clearly. Thus, it strongly indicated that COI may be a useful construction of a comprehensive DNA barcode database for copepods inhabiting the freshwater bodies in Chennai.

scholarly journals Species detections in environmental DNA using metabarcoding: a useful tool in estuaries monitoring

2015 ◽  
Author(s):  
Adrián Mártinez-Marqués ◽  
Carlos Enrique Carleos ◽  
Eva García-Vazquez ◽  
Yaisel J. Borrell Pichs
Keyword(s):  
Dna Analysis ◽  
Anthropogenic Activities ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Coi Gene ◽  
Universal Primers ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
Cantabrian Coast ◽  
Taxonomic Groups

Estuaries are amongst the most productive habitats in Earth, producing more organic materia than forests, meadows or agricultural lands. In addition, estuaries exhibit high, and precious, biodiversity levels. In this study an environmental DNA analysis of the two most important estuaries in Asturias (Cantabrian Coast, north Iberia) in terms of food production (Ría del Eo and Ría de Villaviciosa) was carried out. The objective was to monitor aquatic biodiversity and also to detect alien species that can be associated with anthropogenic activities (e.g.: aquaculture). To achieve these objectives, a metabarcoding methodology based in NGS (next generation sequencing) and the mitochondrial COI gene as a DNA Barcode was used. Results showed that this methodology was useful to detect the presence of three different non-native genera (Crepidula, Lymnaea, Macrobrachium) that are probably parasitating species cultured in these estuaries. It is true that Metabarcoding has still unsolved problems such as the lack of 100% universal primers and paucity of referenced sequences for some taxonomic groups in the databases. However, it represents already a powerful tool to manage the resources of these important ecosystems and to guarantee their long-term sustainailibity.

scholarly journals Species detections in environmental DNA using metabarcoding: a useful tool in estuaries monitoring

2015 ◽  
Author(s):  
Adrián Mártinez-Marqués ◽  
Carlos Enrique Carleos ◽  
Eva García-Vazquez ◽  
Yaisel J. Borrell Pichs
Keyword(s):  
Dna Analysis ◽  
Anthropogenic Activities ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Coi Gene ◽  
Universal Primers ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
Cantabrian Coast ◽  
Taxonomic Groups

Estuaries are amongst the most productive habitats in Earth, producing more organic materia than forests, meadows or agricultural lands. In addition, estuaries exhibit high, and precious, biodiversity levels. In this study an environmental DNA analysis of the two most important estuaries in Asturias (Cantabrian Coast, north Iberia) in terms of food production (Ría del Eo and Ría de Villaviciosa) was carried out. The objective was to monitor aquatic biodiversity and also to detect alien species that can be associated with anthropogenic activities (e.g.: aquaculture). To achieve these objectives, a metabarcoding methodology based in NGS (next generation sequencing) and the mitochondrial COI gene as a DNA Barcode was used. Results showed that this methodology was useful to detect the presence of three different non-native genera (Crepidula, Lymnaea, Macrobrachium) that are probably parasitating species cultured in these estuaries. It is true that Metabarcoding has still unsolved problems such as the lack of 100% universal primers and paucity of referenced sequences for some taxonomic groups in the databases. However, it represents already a powerful tool to manage the resources of these important ecosystems and to guarantee their long-term sustainailibity.

New species of Sargassum-boring Limnoria Leach, 1814 (Crustacea, Isopoda, Limnoriidae) from Japan

Zootaxa ◽  
2021 ◽  
Vol 4970 (1) ◽  
pp. 119-130
Author(s):  
HIROKI YOSHINO ◽  
YURIKO KAMBARA ◽  
SHOTA KAJIWARA ◽  
TAKESHI A. OHSAWA
Keyword(s):  
New Species ◽  
The Other ◽  
Coi Gene ◽  
Congeneric Species ◽  
Japanese Species ◽  
Mitochondrial Coi ◽  
Chiba Prefecture ◽  
Mitochondrial Coi Gene ◽  
Mandibular Palp ◽  
Coi Sequences

A new marine Sargassum-boring species of Limnoria (Limnoriidae) is described on the basis of specimens obtained at Kamogawa-shi, Chiba Prefecture, Japan. Limnoria aspera sp. nov. shares a reduced mandibular palp to a seta, algal-feeding, and the clavate shaped epipod of the maxilliped with the other species of non-mandibular-palp group. L. aspera sp. nov. differs morphologically from the congeneric species by secondary unguis of pereopods and unique carinae of pleonite 5 and pleotelson. We describe the sequences of the mitochondrial COI gene and the nuclear 28S rDNA gene. L. aspera sp. nov. differs by 14.2–18.0% in p-distance based on COI sequences from other Japanese species, L. furca and L. nagatai. 

DNA barcoding and phylogenetic analysis of bagrid catfish in China based on mitochondrial COI gene

2020 ◽  
Vol 31 (2) ◽  
pp. 73-80
Author(s):  
Rui Zou ◽  
Cong Liang ◽  
Mengmeng Dai ◽  
Xiaodong Wang ◽  
Xiuyue Zhang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Barcoding ◽  
Coi Gene ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene

scholarly journals Phortica eparmata species complex (Diptera, Drosophildae) from the Oriental Region, with DNA barcoding information of Chinese species

2018 ◽  
Author(s):  
Lin Zhu ◽  
Huiluo Cao ◽  
Hongwei Chen
Keyword(s):  
New Species ◽  
Species Complex ◽  
Coi Gene ◽  
Oriental Region ◽  
Mitochondrial Coi ◽  
Species Complexes ◽  
Mitochondrial Coi Gene ◽  
Coi Sequences ◽  
Two Parameter ◽  
A New Species

A new species complex, the eparmata complex, is established within the subgenus Phortica s. str., based on eight known and five new species, all of which are endemic to the Oriental Region: P. bipartita (Toda & Peng, 1992), P. eparmata (Okada, 1977), P. lanuginosa Chen & Toda, 2007, P. latipenis Chen & Gao, 2005, P. pangi Chen & Wen, 2005, P. setitabula Chen & Gao, 2005, P. unipetala Chen & Wen, 2005 and P. zeta Chen & Toda, 2007; P. jadete sp. nov., P. kava sp. nov., P. mengda sp. nov., P. wongding sp. nov. and P. yena sp. nov. A key to all species of this complex is provided. Barcoding sequences (mitochondrial COI gene) were obtained for 22 specimens of five known and the five above-mentioned new species. The intra- and inter-specific pairwise K-2P (Kimura’s two-parameter) distances of COI were determined. Phylogenetic analysis was performed using Bayesian inference based on COI sequences, confirming the monophyletic status of the eparmata complex, which is distinct from the species complexes of magna, omega, variegata and another two ungrouped species

scholarly journals Molecular identification and characterization of medically and veterinary important flies of Bangladesh based on mitochondrial COI gene sequences

2019 ◽  
pp. 69-79
Author(s):  
Faria Farhana Rain ◽  
Abdul Jabber Howlader ◽  
Abu Faiz Md. Aslam
Keyword(s):  
Research Work ◽  
Dna Barcode ◽  
Haplotype Network ◽  
First Record ◽  
Coi Gene ◽  
Gene Sequences ◽  
Accurate Identification ◽  
Haematobia Irritans ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene

Flies are considered serious pests which cause health problems of human and animal, transmitting many pathogenic microbes. Pest management programs depend on proper identification of pests. The present research work is an initiative to identify the medically and veterinary important flies based on mitochondrial COI gene sequences. Eleven species of the fly pests were identified. Among them, four fly species were the first record from Bangladesh. The phylogenetic analysis of retrieved sequences confirmed that the evolution of these species occurred from a common ancestor. Highest AT percentage (69.9%) was found in Haematobia irritans exigua and lowest GC percentage (30.4%) was found in Haematobia irritans exigua. The substitution rate of codon was found 1.88 in 1st position, 0.73 in 2nd position and 1.22 in 3rd position, respectively. Interspecific genetic divergence range of flies sequences was 5-20%. Haplotype network showed that Atylotus agrestis was mostly diverged from its common ancestors by 37 mutational steps. This research is the first molecular approach to identify the medically and veterinary important flies based on MT-COI gene sequences along with the establishment of first DNA barcode dataset for accurate identification in Bangladesh.

Pairing of two highly sexually dimorphic species within the genus Lophocampa Harris, 1841 (Lepidoptera: Erebidae: Arctiini)

Zootaxa ◽  
2021 ◽  
Vol 4927 (1) ◽  
pp. 104-112
Author(s):  
MICHEL LAGUERRE ◽  
BENOIT VINCENTCENT
Keyword(s):  
Dna Barcode ◽  
Original Description ◽  
Coi Gene ◽  
Sexually Dimorphic ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
First Time ◽  
Dimorphic Species

Two Lophocampa species previously known only by females are paired with morphologically highly different male specimens. This pairing was initiated after the discovery of a mosaic gynandromorph specimen and then confirmed using the mitochondrial COI gene (the so-called DNA barcode). Following the discovery of a labeling error by Rothschild during the original description of two species, two recombinations are proposed. Pairs for each species are illustrated and the male specimens are described for the first time. 

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