scholarly journals DNA barcoding of Naididae (Annelida, Oligochaeta) based on COI and ITS2 genes in China

2021 ◽  
Author(s):  
Tingting Zhou ◽  
Hongzhu Wang ◽  
Yongde Cui
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Genetic Distances ◽  
Coi Gene ◽  
Tubifex Tubifex ◽  
Morphological Identification ◽  
Lumbriculus Variegatus ◽  
Mitochondrial Coi ◽  
Aquatic Oligochaete ◽  
Barcode Gap

Exploring the effectiveness of DNA barcoding in species identification is prerequisite for biodiversity conservation and environmental monitoring. Aquatic oligochaete could serve as an excellent indicator in aquatic monitoring programs. However, few studies have examined the effectiveness of DNA barcoding in these specific organisms. The mitochondrial COI gene and nuclear ITS2 gene of 83 specimens belonging to 36 species of 18 genera were sequenced in this study. The results showed that there was a barcode gap between species of Naididae, and the intraspecific genetic distances of each species were smaller than interspecific genetic distances. The classification results of ABGD (Automatic Barcode Gap Discovery) were consistent with those of morphological identification except for Tubifex tubifex and Lumbriculus variegatus. All species were successfully distinguished in the phylogenetic tree based on ITS2 gene, which was coincident with morphological result. Our results provided evidence that DNA barcoding can be used as an effective and convenient tool for species identification of the family Naididae and even aquatic oligochaete.

scholarly journals DNA barcoding of Naididae (Annelida, Oligochaeta), based on cytochrome C oxidase gene and ITS2 region in China

2021 ◽  
Vol 9 ◽  
Author(s):  
Tingting Zhou ◽  
Wei Jiang ◽  
Hongzhu Wang ◽  
Yongde Cui
Keyword(s):  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Species Identification ◽  
Genetic Distances ◽  
Coi Gene ◽  
Tubifex Tubifex ◽  
Its2 Region ◽  
Aquatic Oligochaetes ◽  
Barcode Gap

Exploring the effectiveness of DNA barcoding in species identification is a prerequisite for biodiversity conservation and environmental monitoring. Aquatic oligochaetes could serve as excellent indicators in aquatic monitoring programmes. However, few studies have examined the effectiveness of DNA barcoding in these specific organisms. The mitochondrial cytochrome C oxidase (COI) gene of 83 specimens belonging to 40 species of 18 genera were sequenced in this study. The results showed that there was a barcode gap between species of Naididae and the intraspecific genetic distances of each species were smaller than interspecific genetic distances. The classification results of ABGD (Automatic Barcode Gap Discovery) were consistent with those of morphological identification, except for Tubifex tubifex and Lumbriculus variegatus. All species were successfully distinguished in the phylogenetic tree, based on the ITS2 region, which was coincident with the morphological result. Our results provided evidence that DNA barcoding can be used as an effective and convenient tool for species identification of the family Naididae and even for other aquatic oligochaetes.

DNA barcoding of bats (Chiroptera) from the Colombian northern region

Mammalia ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Álvaro J. Benítez ◽  
Dina Ricardo-Caldera ◽  
María Atencia-Pineda ◽  
Jesús Ballesteros-Correa ◽  
Julio Chacón-Pacheco ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Genetic Distances ◽  
Northern Region ◽  
Coi Gene ◽  
Individual Species ◽  
Species Variation ◽  
Molossus Molossus ◽  
Artibeus Lituratus

Abstract Bats are mammals of great ecological and medical importance, which have associations with different pathogenic microorganisms. DNA barcoding is a tool that can expedite species identification using short DNA sequences. In this study, we assess the DNA barcoding methodology in bats from the Colombian Northern region, specifically in the Córdoba department. Cytochrome oxidase subunit I (COI) gene sequences of nine bat species were typified, and their comparison with other Neotropic samples revealed that this marker is suitable for individual species identification, with ranges of intra-species variation from 0.1 to 0.9%. Bat species clusters are well supported and differentiated, showing average genetic distances ranging from 3% between Artibeus lituratus and Artibeus planirostris, up to 27% between Carollia castanea and Molossus molossus. C. castanea and Glossophaga soricina show geographical structuring in the Neotropic. The findings reported in this study confirm DNA barcoding usefulness for fast species identification of bats in the region.

scholarly journals Species diversity of freshwater shrimp in Henan Province, China, based on morphological characters and COI mitochondrial gene

2021 ◽  
Author(s):  
Chuanjiang Zhou ◽  
Mengxia Feng ◽  
Yongtao Tang ◽  
Changxing Yang ◽  
Xiaolin Meng ◽  
...  
Keyword(s):  
Species Diversity ◽  
Cryptic Species ◽  
Dna Barcoding ◽  
Species Identification ◽  
High Efficiency ◽  
Morphological Characteristics ◽  
Henan Province ◽  
Coi Gene ◽  
Morphological Identification ◽  
Freshwater Shrimp

Freshwater shrimp is an extremely rich species group with a long and problematic taxonomic history, attributed to its wide distribution, numerous species and similar morphology. Shrimp diversity and species identification is utmost important for fisheries management. However, identification based on morphological characteristics is difficult and complex for a non-specialist to perform. The water system of Henan Province is relatively abundant, but there are few investigations of freshwater shrimps and no description of molecular features. The aim of this study was to uncover the species diversity and phylogenetic of freshwater shrimp in Henan province by combining morphological identification and molecular species delimitation (barcoding gene: COI gene). About 1,200 freshwater shrimp samples from 46 sampling sites were collected for preliminary traditional morphological identification, 222 samples of these were been further microscopic examination and molecular delimitation. Here we used tree based method (NJ, ML) and distance based method (ABGD, bPTP) mainly to define species, detect the cryptic species and assess the validity of the barcoding in molecular. Comprehensive morphological identification and molecular delimitation results, there were 9 effective species and more than one cryptic species of freshwater shrimp in the province and moreover all of them can be identified by DNA barcoding. The results of morphological identification and molecular identification show high consistency, which proves the high efficiency in freshwater shrimp species identification of the DNA barcoding and the presence of cryptic species.

DNA Barcoding of Simulium asakoae (Diptera: Simuliidae) From Northern Thailand

2020 ◽  
Vol 57 (5) ◽  
pp. 1675-1678 ◽  
Author(s):  
Van Lun Low ◽  
Wichai Srisuka ◽  
Atiporn Saeung ◽  
Tiong Kai Tan ◽  
Zubaidah Ya’cob ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Barcoding ◽  
Genetic Divergence ◽  
Species Complex ◽  
Morphological Variability ◽  
Single Species ◽  
Genetic Distances ◽  
Morphological Identification ◽  
Dna Barcodes ◽  
Barcode Gap

Abstract Previous studies suggested the presence of species complex in the so-called Simulium asakoae Takaoka & Davies (Diptera: Simuliidae) in Thailand due to its high morphological variability and genetic divergence. To investigate whether the true S. asakoae is present in Thailand, we performed a detailed morphological identification of S. asakoae and compared its DNA barcodes with the morphospecies S. asakoae from Myanmar and the typical S. asakoae from Malaysia. Phylogenetic analysis revealed the Thai materials analyzed in this study were indeed genetically similar with those from Myanmar and Malaysia, though genetic distances 0–2.27% were observed. We tentatively regard this divergence as intraspecific variation, and the automatic barcode gap discovery analysis further supports them as a single species.

Morphological description and DNA barcoding of Hydrobaenus golovinensis sp. nov. (Diptera: Chironomidae: Orthocladiinae) from the Russian Far East

Zootaxa ◽  
2017 ◽  
Vol 4286 (2) ◽  
pp. 277
Author(s):  
EUGENYI A. MAKARCHENKO ◽  
MARINA A. MAKARCHENKO ◽  
ALEXANDER A. SEMENCHENKO ◽  
OLEG A. VELIAEV
Keyword(s):  
Dna Barcoding ◽  
Russian Far East ◽  
Far East ◽  
Instar Larva ◽  
Genetic Distances ◽  
Coi Gene ◽  
Morphological Description ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
The Russian Far East

Illustrated descriptions of adult male, pupa and fourth instar larva, as well as DNA barcoding results of Hydrobaenus golovinensis sp. nov. in comparison with closely related species H. majus Makarchenko et Makarchenko and H. sikhotealinensis Makarchenko et Makarchenko from the Russian Far East are provided. Partial mitochondrial COI gene (DNA barcoding) of the new species has been sequenced and uploaded to GenBank. Comparisons with corresponding regions of COI between H. golovinensis and other species in the genus produce K2P genetic distances of 10.3–14.3%, the values well above those associated with intraspecific variation. In contrast, genetic distances among 18 specimens are all within the range of 0–3.5%. The ML tree is also constructed using DNA barcodes obtained in the present study and those of other species of Hydrobaenus Fries from GenBank. 

A review of genus Agriocnemis larva (Odonata: Coenagrionidae) from Thailand including a description of the final stadium larva of Agriocnemis minima Selys, 1877 with supporting molecular (COI) data

Zootaxa ◽  
2019 ◽  
Vol 4711 (3) ◽  
pp. 579-599
Author(s):  
TOSAPHOL SAETUNG ◽  
BOONSATIEN BOONSOONG
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Ventral View ◽  
Coi Gene ◽  
Compound Eyes ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
First Time

The larva of Agriocnemis minima Selys, 1879 is described and illustrated for the first time, based on reared specimens collected from Thailand. Selected larvae of Agrioncnemis Selys, 1877 were matched with their adults by DNA barcoding. The mitochondrial COI gene (658 bp) of three species (A. minima, A. femina femina (Brauer, 1868), and A. pygmaea (Rambur, 1842)) occurring in Thailand was analysed to confirm the species identification and to determine the association between the larva and adult stages. The larva of A. minima can be distinguished from known species by the following combination of characteristics: 1) long simple setae on the antennomeres I and II, 2) protrusion of the male cerci as long as 0.5× the S10, and 3) tufts of spiniform setae on the lateral occiput margin and on the ventral view of the compound eyes. Comparisons to known larvae of Agriocnemis and those of some other subfamily Agriocnemidinae members are also provided. 

scholarly journals DNA barcoding of Deltocephalus Burmeister leafhoppers (Cicadellidae, Deltocephalinae, Deltocephalini) in China

ZooKeys ◽  
2019 ◽  
Vol 867 ◽  
pp. 55-71 ◽  
Author(s):  
Hong Zhang ◽  
Yalin Zhang ◽  
Yani Duan
Keyword(s):  
Dna Barcoding ◽  
Phylogenetic Analyses ◽  
Dna Barcode ◽  
Distinct Species ◽  
Genetic Distances ◽  
Coi Gene ◽  
Mitochondrial Coi ◽  
Chinese Populations ◽  
The Status ◽  
Morphological Variants

We investigated the feasibility of using the DNA barcode region in identifying Deltocephalus from China. Sequences of the barcode region of the mitochondrial COI gene were obtained for 98 specimens (Deltocephalusvulgaris – 88, Deltocephaluspulicaris – 5, Deltocephalusuncinatus – 5). The average genetic distances among morphological and geographical groups of D.vulgaris ranged from 0.9% to 6.3% and among the three species of Deltocephalus ranged from 16.4% to 21.9% without overlap, which effectively reveals the existence of a “DNA barcoding gap”. It is important to assess the status of these morphological variants and explore the genetic variation among Chinese populations of D.vulgaris because the status of this species has led to taxonomic confusion because specimens representing two distinct morphological variants based on the form of the aedeagus are often encountered at a single locality. Forty-five haplotypes (D.vulgaris – 36, D.pulicaris – 5, D.uncinatus – 4) were defined to perform the phylogenetic analyses; they revealed no distinct lineages corresponding either to the two morphotypes of D.vulgaris or to geographical populations. Thus, there is no evidence that these variants represent genetically distinct species.

scholarly journals DNA Barcoding for Selected Mangrove-Based Estuary Fishes from Way Kambas National Park, Lampung Province, Indonesia

2021 ◽  
Vol 11 (2) ◽  
pp. 151-160
Author(s):  
Yanti Ariyanti ◽  
◽  
Ika Rini ◽  
Indah Oktaviani ◽  
Sovia Leksikowati ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Fish Species ◽  
National Park ◽  
Conservation Status ◽  
Genetic Distances ◽  
Coi Gene ◽  
Species Discovery ◽  
Mitochondrial Coi ◽  
Identification Of Species ◽  
Way Kambas National Park

Over the past decade, DNA barcoding has provided new insight into fish ecology and biosystematics and led to new species' discovery. DNA barcoding is a method for the recognition and identification of species using short, standardised DNA fragments. The correct taxonomic identification of species is critical for the assessment and monitoring of biodiversity. This study applied DNA barcoding techniques to identify selected fish species from a mangrove-based estuary in Way Kambas National Park, Lampung Province, Indonesia. The gene encoding cytochrome c oxidase subunit I (COI) was amplified and bi-directionally sequenced from 22 specimens. The resulting 680 base pairs (bp) sequence was used to identify species, obtain phylogenetic information, and analyse genetic distances. A neighbour-joining tree was constructed based on the mitochondrial COI gene using the Kimura two-parameter model. This study also exhibits conservation status for those identified species. Our findings will facilitate future studies of fish species diversity in mangrove estuary-based ecosystems and provide preliminary data in policymaking in conservation areas such as National Park.

scholarly journals Identification of Megaselia scalaris (Diptera : Phoridae) based on morphology and mitochondrial 16S rRNA and COI gene sequences

2016 ◽  
Vol 25 (2) ◽  
pp. 149-159 ◽  
Author(s):  
Mohammad Shamimul Alam ◽  
Khandaker Asif Ahmed ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
Model Organism ◽  
Coi Gene ◽  
Morphological Identification ◽  
Rrna Gene ◽  
Neighbor Joining ◽  
Mitochondrial Coi ◽  
Molecular Approaches ◽  
Megaselia Scalaris ◽  
Rrna Sequences

Megaselia scalaris (Diptera: Phoridae), commonly known as scuttle fly, is widely distributed all over the world. It is easily cultured in the laboratory condition making it a potential model organism. Besides, it has forensic importance. However, no report from Bangladesh could be retrieved about this fly. So, in the present study, identification of this species was attempted using both morphological and molecular approaches. Characteristics of male hypopygium and legs played key roles in morphological identification. To strengthen identification, mitochondrial COI and 16S rRNA gene fragments were amplified and sequenced. Blast search at NCBI provided highest hits to available COI and 16S rRNA sequences of M. scalaris. A neighbor joining phylogenetic tree was built using sequences of respective COI gene region to show its relationship among other closely related dipteran flies. Dhaka Univ. J. Biol. Sci. 25(2): 149-159, 2016 (July)

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