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.

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 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. 

scholarly journals Pelacakan Gen Sitokrom Oksidase Sub Unit I (COI) DNA Mitokondria Itik Tegal (Anas domesticus) Menggunakan Primer Universal

2013 ◽  
Vol 15 (1) ◽  
pp. 20 ◽  
Author(s):  
Sarwo Edi Wibowo ◽  
Muhammad Anwar Djaelani ◽  
Hermin Pancasakti Kusumaningrum
Keyword(s):  
Mitochondrial Dna ◽  
Native Species ◽  
Egg Production ◽  
Genetic Characterization ◽  
Coi Gene ◽  
Universal Primers ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
Gene Data ◽  
Pcr Conditions

Currently local ducks are generally quite difficult to find in a big farm in Inonesia, including Tegal ducks. Tegal ducks is one of the genetic resources native to Indonesia with it’s advantages in terms of high and large egg production. Conservation and development of local ducks have strived to maintain our existence of Indonesian livestock germplasm. If such information is not superior to native species exist, the opportunity to increase his lead further also getting smaller. Tracking the mitochondrial COI gene DNA of Tegal ducks may underlie the process of an organism's genetic characterization. Information about Tegal duck mitochondrial DNA has not been done. The information obtained can be used for optimization of duck products native to Indonesia both in physiological aspects, phylogeny and genetic engineering. The research method used in this research is tracking COI gene data from Gen Bank with the programs Clustal X and Genedoc. Tracking then continued using universal primers HCO and LCO. The results of the data followed up with the isolation and amplification of COI gene mitochondrial DNA as well as the optimization of PCR conditions. The results showed mitochondrial DNA COI gene Tegal ducks were amplified with primer LCO obtain DNA fragments of length less than 250 bp. Kata kunci: duck’s from Tegal, COI gene, mitochondrial DNA

Fixation, description and DNA barcode of a neotype for Botryllus schlosseri (Pallas, 1766) (Tunicata, Ascidiacea)

Zootaxa ◽  
2017 ◽  
Vol 4353 (1) ◽  
pp. 29 ◽  
Author(s):  
RICCARDO BRUNETTI ◽  
LUCIA MANNI ◽  
FRANCESCO MASTROTOTARO ◽  
CARMELA GISSI ◽  
FABIO GASPARINI
Keyword(s):  
Developmental Stages ◽  
Dna Barcode ◽  
Molecular Data ◽  
Coi Gene ◽  
Morphological Description ◽  
Botryllus Schlosseri ◽  
Colonial Ascidian ◽  
History Museum ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene

Botryllus schlosseri is a widespread colonial ascidian commonly considered cosmopolitan and amply used as model for researches ranging from developmental biology to immunobiology. Recently, molecular data lead to hypothesize that the species named B. schlosseri may consist of more than a single taxon. Indeed, five highly divergent clades, named A-E, have been genetically identified and are referred as cryptic species. In this context, and lacking both a type and a detailed morphological description, we believe that it is necessary, as a taxonomic reference point, to designate a neotype and re-describe the species. Therefore, a sample from the Lagoon of Venice (Adriatic Sea, Italy) was deposited as neotype in the Natural History Museum of Venice (Italy), preserved both in formalin and in 90% ethanol. Here we provide a morphological description of the suggested neotype of B. schlosseri that takes into account several developmental stages (oozooid, zooid of first blastogenic generations, and mature zooid) and is carefully compared with the previous descriptions of samples coming from other European and non-European localities. Finally, we associate our morphological description to a “DNA barcode”, consisting in a long fragment of the mitochondrial COI gene. Our description is associated to clade A, although at now we cannot guarantee that this association is univocal.

Description of Idaea josephinae sp. n. from the Iberian Peninsula (Lepidoptera: Geometridae)

Zootaxa ◽  
2021 ◽  
Vol 4990 (2) ◽  
Author(s):  
JUAN-JOSE GUERRERO ◽  
AXEL HAUSMANN ◽  
ANTONIO S. ORTIZ
Keyword(s):  
Iberian Peninsula ◽  
Dna Barcode ◽  
Sister Species ◽  
Coi Gene ◽  
North African ◽  
External Appearance ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
Differential Characters

Idaea josephinae sp. n. is described from the Iberian Peninsula. Differential characters from its North African sister species Idaea lobaria (Chrétien, 1909) in external appearance and genitalia, and in the 5’ barcode fragment of the mitochondrial COI gene (the DNA barcode) are presented.

A review of the genus Forficuloecus Conci (Phthiraptera: Philopteridae) from parrots (Psittaciformes: Psittacidae), with descriptions of four new species

Zootaxa ◽  
2008 ◽  
Vol 1859 (1) ◽  
pp. 49 ◽  
Author(s):  
ROGER D. PRICE ◽  
KEVIN P. JOHNSON ◽  
RICARDO L. PALMA
Keyword(s):  
New Species ◽  
Coi Gene ◽  
Chewing Louse ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
Genetic Distinctiveness

Ten species, including four new species, of the chewing louse genus Forficuloecus Conci, 1941, are recognized from Australasian parrots, and a key is given for their identification. The new species and their type hosts are: F. cameroni ex the Red-winged Parrot, Aprosmictus erythropterus (J.F. Gmelin, 1788); F. banksi ex the Mulga Parrot, Psephotus varius Clark, 1910; F. wilsoni ex the Northern Rosella, Platycercus venustus (Kuhl, 1820); and F. josephi ex the Bourke's Parrot, Neopsephotus bourkii (Gould, 1841). Partial sequences of the mitochondrial COI gene support the genetic distinctiveness of these new species.

Are Tetranychus macfarlanei Baker & Pritchard and Tetranychus malaysiensis Ehara (Acari: Tetranychidae) one species? Morphological and molecular evidences for synonymy between these two spider mite species and a note on invasiveness of T. macfarlanei on okra and eggplant in India

2017 ◽  
Vol 22 (4) ◽  
pp. 467
Author(s):  
Mahran Zeity ◽  
Nagappa Srinivas ◽  
Chinnamade Channegowde Gowda
Keyword(s):  
Spider Mite ◽  
Morphological Characters ◽  
Molecular Data ◽  
Mite Species ◽  
Coi Gene ◽  
High Similarity ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
High Degree ◽  
Degree Of Similarity

Study of morphological characters of Tetranychus macfarlanei Baker & Pritchard and Tetranychus malaysiensis Ehara revealed high similarity by comparing all the important characters in addition to the characters pointed out by Ehara to separate those two species. Molecular phylogeny of seven Indian populations of T. macfarlanei and one population of T. malaysiensis from Philippines along with few distantly related species of Tetranychus was attempted. High degree of similarity between these two species at mitochondrial COI gene (96%) as well as ITS2 (rDNA) (96–99%) region was evident. Based on both morphological features and molecular data, T. malaysiensis is proposed as a junior synonym of T. macfarlanei based on ICZN’s law of priority. Also more female characters are prompted in this study to distinctly discriminate T. macfarlanei from its most resembling species, Tetranychus ludeni Zacher. Tetranychus macfarlanei has emerged as a pest of several cultivated crop plants in India. 

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