DNA barcodes and morphology of P. krempfi,  P. mekongensis, and P. elongatus

Three Pangasius species including P. krempfi, P. elongatus and P. mekongensis, are economically important. They can be mis-identified due to similar external appreance at small sizes. This study aimed to distinguish these species based on their differences in DNA barcode, COI (cytochrome c oxidase subunit I) gene, and morphological characteristics. Fish with various sizes (>90 samples/species) were sampled at the lower Mekong delta region. Kimura-2 parameter genetic distances based on COI sequences of three species (15 samples, in which, 4 unique sequences were assigned Genbank accession numbers from KT289877 to KT289880) are relatively high, ranging 9.33 – 12.10 %. Morphological measurements show that coutanble traits including numbers of fin rays and the first gill rakers vary in similar ranges but ratios of metric traits are significantly different among three species (P<0.01). Principle component analysis using metric traits sets three species apart. P. elongatus is characterized by elongated body, long caudal preduncle, large eyes, and retangle palatine tooth plates. P. krempfi differs from P. mekongesis in characteristics on their head. The number of sections, shape and length of barbel are different among three species. Phylogenetic relationship of three species based on morphology and COI sequences indicate that P. krempfi is closer to P. mekongenis rather than P. elongatus, and that the distance between P. mekongenis and P. elongatus is the largest.

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DNA barcodes identify medically important tick species in Canada

Genome ◽

10.1139/gen-2015-0179 ◽

2017 ◽

Vol 60 (1) ◽

pp. 74-84 ◽

Cited By ~ 10

Author(s):

Danielle A. Ondrejicka ◽

Kevin C. Morey ◽

Robert H. Hanner

Keyword(s):

Dna Barcode ◽

Nearest Neighbour ◽

Cryptic Diversity ◽

Dna Barcodes ◽

Genetic Cluster ◽

Potential Health ◽

Intraspecific Divergence ◽

Coi Sequences ◽

I Gene ◽

Barcode Gap

Medically important ticks (Acari: Ixodidae) are often difficult to identify morphologically. A standardized, molecular approach using a 658 base pair DNA barcode sequence (from the 5′ region of the mitochondrial cytochrome c oxidase subunit I gene) was evaluated for its effectiveness in discriminating ticks in North America, with an emphasis on Canadian ticks. DNA barcodes were generated for 96 of 154 specimens representing 26 ixodid species. A genetic cluster analysis was performed on the barcode sequences, which separated specimens into haplogroups closely corresponding with morphologically identified species. The tree topology was further supported by a BIN analysis. COI sequences generated were found to have a mean maximum intraspecific divergence of 1.59% and a mean nearest neighbour divergence of 12.8%, indicating a significant “barcode gap”. This study also revealed possible cryptic diversity among specimens morphologically identified as Ixodes soricis and Ixodes texanus. A PCR-based test for Borrelia burgdorferi determined that 18.1% of Lyme-competent ticks in this study were positive. This study is also the first to record a B. burgdorferi-positive exoskeleton. In conclusion, DNA barcoding is a powerful tool that clinicians can use to determine the identification of tick specimens which can help them to suggest whether an attached tick is a potential health risk.

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A Systematic Study on DNA Barcoding of Medicinally Important Genus Epimedium L. (Berberidaceae)

Genes ◽

10.3390/genes9120637 ◽

2018 ◽

Vol 9 (12) ◽

pp. 637 ◽

Cited By ~ 9

Author(s):

Mengyue Guo ◽

Yanqin Xu ◽

Li Ren ◽

Shunzhi He ◽

and Xiaohui Pang

Keyword(s):

Dna Barcode ◽

Morphological Characteristics ◽

Identification Accuracy ◽

Dna Barcodes ◽

Success Rates ◽

Data Set ◽

Herba Epimedii ◽

Potential Risks ◽

Medicinal Properties ◽

Species Being

Genus Epimedium consists of approximately 50 species in China, and more than half of them possess medicinal properties. The high similarity of species’ morphological characteristics complicates the identification accuracy, leading to potential risks in herbal efficacy and medical safety. In this study, we tested the applicability of four single loci, namely, rbcL, psbA-trnH, internal transcribed spacer (ITS), and ITS2, and their combinations as DNA barcodes to identify 37 Epimedium species on the basis of the analyses, including the success rates of PCR amplifications and sequencing, specific genetic divergence, distance-based method, and character-based method. Among them, character-based method showed the best applicability for identifying Epimedium species. As for the DNA barcodes, psbA-trnH showed the best performance among the four single loci with nine species being correctly differentiated. Moreover, psbA-trnH + ITS and psbA-trnH + ITS + rbcL exhibited the highest identification ability among all the multilocus combinations, and 17 species, of which 12 are medicinally used, could be efficiently discriminated. The DNA barcode data set developed in our study contributes valuable information to Chinese resources of Epimedium. It provides a new means for discrimination of the species within this medicinally important genus, thus guaranteeing correct and safe usage of Herba Epimedii.

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A new species of Litarachna Walter, 1925 (Acari: Hydrachnidia: Pontarachnidae) from Corozal Bay (Belize), described based upon morphology and DNA barcodes

Acarologia ◽

10.24349/r7no-ludg ◽

2021 ◽

Vol 61 (3) ◽

pp. 602-613

Author(s):

Lucia Montes-Ortiz ◽

Tom Goldschmidt ◽

Lourdes Vásquez-Yeomans ◽

Manuel Elías-Gutiérrez

Keyword(s):

Dna Barcode ◽

Morphological Description ◽

Estuarine System ◽

Dna Barcodes ◽

Sem Images ◽

The Family ◽

Coi Sequences ◽

First Time ◽

A New Species ◽

Electronic Microscope

A new planktonic species of the marine water mites of the family Pontarachnidae Koenike, 1910 is described from Corozal Bay, an estuarine system in Belize. The morphological description includes Scanning Electronic Microscope (SEM) images and is augmented by an analysis of DNA cytochrome c oxidase I (COI) sequences, the DNA barcode, used for the first time for a species description in this group.

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Using ITS-rDNA and matK gene nucleotide sequences for identification ginseng species in Panax in Phu Xai Lai Leng, Ky Son, Nghe An

Vietnam Journal of Biotechnology ◽

10.15625/1811-4989/18/1/15267 ◽

2020 ◽

Vol 18 (1) ◽

pp. 75-85

Author(s):

Vu Dinh Duy ◽

Tran Thi Viet Thanh ◽

Phan Ke Loc ◽

Nguyen Minh Tam ◽

Nguyen Thi Thanh Huong ◽

...

Keyword(s):

Success Rate ◽

Genetic Distances ◽

Its Rdna ◽

Dna Barcodes ◽

Phylogenetic Taxonomy ◽

Panax Species ◽

Pcr Product ◽

Matk Gene ◽

Close Relationship ◽

Relationship Of

DNA barcoding is a useful tool for species identification using standardized genomic DNA fragments. We used DNA barcodes (ITS-rDNA and matK gene) to explore Panax (32 samples collected from Phu Xai Lai Leng mountain and 19 samples collected from medicinal nursery of TH), and to investigate the phylogenetic taxonomy of Panax. In this study, the PCR success rate for ITS-rDNA and matK region was 100%. The success rate of bidirectional sequencing of PCR product was 100% of ITS-rDNA and matK region with length of 616 bp, 1433 bp, respectively. All 32 samples (Panax TB) of Phu Xai Lai Leng have a close relationship with P. stipuleanatus (MLBS = 99%, BPP = 100%). All 19 samples (Panax TH) of medicinal nursery have a close relationship with P. notoginseng (MLBS = 100%, BPP = 100%). Interspecific genetic distances within and among Panax species was varied from 0.2% to 7.9%, average (4%) (ITS-rDNA gene) and 0.1 to 2.9%, average (1.2%) (matK gene). The genetic relationship of species/gender belonging to the Panax genus showed that they have the same evolutionary origin and discovered that new distributed of P. stipuleanatus in Phu Xai Lai Leng mountain in Vietnam.

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Revalidation and redescription of Serranus knysnaensis Gilchrist, 1904, (Perciformes: Serranidae) with a new distribution record

Zootaxa ◽

10.11646/zootaxa.5057.1.6 ◽

2021 ◽

Vol 5057 (1) ◽

pp. 99-113

Author(s):

YONELA SITHOLE ◽

ELAINE HEEMSTRA ◽

MONICA MWALE

Keyword(s):

Dna Barcode ◽

Taxonomic Status ◽

Molecular Data ◽

Genetic Distances ◽

Valid Species ◽

Eastern Atlantic Ocean ◽

Coi Sequences ◽

Morphological And Molecular Data ◽

Gill Raker ◽

Distribution Record

A southwestern Indian Ocean (SWIO) percoid fish Serranus knysnaensis Gilchrist, 1904, was long synonymised with the comber, Serranus cabrilla (Linnaeus, 1758), from the eastern Atlantic Ocean, Mediterranean and Black Sea. However, when the species was brought out of synonymy by Heemstra & Heemstra (2004), reasons for this decision were not given. This study aims to revalidate the present taxonomic status of S. knysnaensis using morphological and molecular assessments. The two species are distinguished by the number of circumpeduncular scales (26–34 in S. knysnaensis versus 34–38 in S. cabrilla) and total gill rakers (18–22 versus 22–24). Serranus knysnaensis is also distinct from S. novemcinctus Kner, 1864, the other SWIO species of Serranus, based on total gill raker counts (18–22 versus 31–35). Genetic analysis of mitochondrial DNA barcode (COI) sequences for 17 Serranus species revealed three closely-related monophyletic clusters corresponding to S. cabrilla, S. novemcinctus and S. knysnaensis that were supported (P <0.001) by species delimitation methods. Even though the genetic distances among the three species were the lowest in the genus (1.60−1.99%), these species may be ecomorphs or lineages that have only recently diverged from each other. These three species also have allopatric distributions and our morphological and molecular data thus confirm that S. knysnaensis is a valid species.

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Molecular identification and evolutionary relationships between the subspecies of Musa by DNA barcodes

BMC Genomics ◽

10.1186/s12864-020-07036-5 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

S. Dhivya ◽

S. Ashutosh ◽

I. Gowtham ◽

V. Baskar ◽

A. Baala Harini ◽

...

Keyword(s):

Dna Barcode ◽

Evolutionary Relationship ◽

Genetic Distances ◽

Its2 Region ◽

Potential Candidate ◽

Dna Barcodes ◽

Somaclonal Variations ◽

Distance Methods ◽

Significant Divergence ◽

Comprehensive Study

Abstract Background The banana (Musa sp., AAA) genome is constantly increasing due to high-frequency of somaclonal variations. Due to its large diversity, a conventional numerical and morphological based taxonomic identification of banana cultivars is laborious, difficult and often leads to subject of disagreements. Results Hence, in the present study, we used universal DNA barcode ITS2 region to identify and to find the genetic relationship between the cultivars and varieties of banana. Herein, a total of 16 banana cultivars were PCR amplified using ITS2 primer pair. In addition, 321 sequences which were retrieved from GenBank, USA, were used in this study. The sequences were then aligned using Clustal W and genetic distances were computed using MEGA V5.1. The study showed significant divergence between the intra- and inter-specific genetic distances in ITS2 region. BLAST1 and Distance methods proved that ITS2 DNA barcode region successfully identified and distinguished the cultivar and varieties of banana. Conclusion Thus, from the results of the present study, it is clear that ITS2 is not only an efficient DNA barcode to identify the banana species but also a potential candidate for enumerating the phylogenetic relationships between the subspecies and cultivars. This is the first comprehensive study to categorically distinguish the economically important banana subspecies and varieties using DNA barcodes and to understand its evolutionary relationship.

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Splitting the leafmining shield-bearer moth genus Antispila Hübner (Lepidoptera, Heliozelidae): North American species with reduced venation placed in Aspilanta new genus, with a review of heliozelid morphology

ZooKeys ◽

10.3897/zookeys.957.53908 ◽

2020 ◽

Vol 957 ◽

pp. 105-161

Author(s):

Erik J. van Nieukerken ◽

Charles S. Eiseman

Keyword(s):

Central America ◽

New Genus ◽

Dna Barcode ◽

Single Species ◽

Dna Barcodes ◽

Host Family ◽

Main Host ◽

Candidate Species ◽

Coi Sequences ◽

Rich Fauna

The new genus Aspilantagen. n. is described to harbour Nearctic heliozelid moths with reduced venation, previously placed in Antispila Hübner, 1825, with type species Antispila oinophylla van Nieukerken & Wagner, 2012. The erection of this genus has become possible now that monophyly has been supported by a recent phylotranscriptomics analysis. Six species are combined in this genus: Aspilanta oinophylla (van Nieukerken & Wagner, 2012), comb. n., A. hydrangaeella (Chambers, 1874), comb. n., A. ampelopsifoliella (Chambers, 1874), comb. n., A. voraginella (Braun, 1927), comb. n., A. argentifera (Braun, 1927), comb. n., A. viticordifoliella (Clemens, 1860), comb. n. and two candidate species are recognised. DNA barcode COI sequences of Malaise trapped specimens suggest a rich fauna of Aspilanta in Central America. All are leafminers, with Vitaceae as main host family, and single species feeding respectively on Hydrangeaceae and Myricaceae. The species are briefly diagnosed, and data on biology, DNA barcodes and distribution are provided. To place the genus in context, a review of heliozelid morphology and phylogeny is presented and a key to Nearctic genera is given. The genus is confined to North and Central America, possibly also occurring in South America. Aspilanta oinophylla is also an invasive species on grapevine in Italy. The genus is sister to Coptodisca Walsingham, 1895. Another species is removed from Antispila: Heliozela eugeniella (Busck, 1900), comb. n., feeding on Eugenia (Myrtaceae), from Florida.

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Efficiency of ITS1-5.8S-ITS2 region in identifying Cordyceps species

Vietnam Journal of Biotechnology ◽

10.15625/1811-4989/16/4/13220 ◽

2020 ◽

Vol 16 (4) ◽

pp. 705-712

Author(s):

Le Thi Thu Hien ◽

Ha Hong Hanh

Keyword(s):

Dna Sequences ◽

Phylogenetic Trees ◽

Nearest Neighbor ◽

Dna Barcode ◽

Morphological Characteristics ◽

Pcr Amplification ◽

Cordyceps Sinensis ◽

Its2 Region ◽

Dna Barcodes ◽

Plastid Genomes

Cordyceps genus is a well-known traditional medicine worldwide. It contains abundant physiological active compounds that were demonstrated to perform benefit in reducing progression of cancer as well as protecting human health. Accurately classifying species in this genus is essential in order to prevent commercial counterfeit medicines. Nowadays, a taxonomic classification of species based on DNA sequences can overcome the existed limitation in identifying by using only morphological characteristics of this genus. DNA barcodes are standard short genomic regions that are universally present in target lineages and has sufficient sequence variation to discriminate species in the genus. A variety of loci has been suggested as DNA barcodes for plants, including genes and non-coding regions in the nuclear and plastid genomes such as psbA-trnH, matK, rbcL, and ITS. Thus, the objective of this study was to identify selected species of Cordyceps genus using DNA barcodes. Seven strains of Cordyceps were collected. Total DNA extraction and purification, PCR amplification and DNA sequencing were performed with standard chemicals and kits. The candidate ITS1-5.8S-ITS2 region was amplified and sequenced. Data were analyzed using Bioedit 7.2.6 and MEGA 7 softwares. Analysis of seven obtained DNA barcode sequences of collected samples revealed that the ITS1-5.8S-ITS2 region provided high species discriminating power for Cordyceps genus. Accordingly, phylogenetic trees based on this DNA barcode exhibited six samples had closed relationship to Cordyceps militaris, while another specimen was the nearest neighbor to Cordyceps sinensis with average similarities at 99.82% and 99.81%, respectively. Our results support the identification of valuable medicinal plant species within Cordyceps genus.

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DNA barcodes of birds from northern Colombia

Biodiversity Data Journal ◽

10.3897/bdj.9.e64842 ◽

2021 ◽

Vol 9 ◽

Author(s):

Paulo Pulgarín-R ◽

Martha Olivera-Angel ◽

Luisa Ortíz ◽

Duván Nanclares ◽

Sara Velásquez-Restrepo ◽

...

Keyword(s):

South America ◽

Tropical Forest ◽

Dna Barcode ◽

Bird Species ◽

Taxonomic Identification ◽

Dna Barcodes ◽

Laboratory Methods ◽

Blood Samples ◽

Lowland Tropical Forest ◽

Coi Sequences

DNA barcode datasets are a useful tool for conservation and aid in taxonomic identification, particularly in megadiverse tropical countries seeking to document and describe its biota, which is dropping at an alarming rate during recent decades. Here we report the barcodes for several low elevation bird species from northern Colombia with the goal to provide tools for species identification in this region of South America. We blood-sampled birds in a lowland tropical forest with various degrees of intervention using standard 3 × 12 m mist-nets. We extracted DNA and sequenced the COI barcode gene using standard primers and laboratory methods. We obtained 26 COI sequences from 18 species, 10 families and three orders and found that barcodes largely matched (but not always) phenotypic identification (> 90%) and they also facilitated the identification of several challenging passerine species. Despite our reduced sampling, our study represents the first attempt to document COI barcodes for birds (from blood samples) in this part of Colombia, which fills a considerable gap of sampling in this part of South America.

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Description of Chaetocladius longivirgatus sp. n., with a review of C. suecicus (Kieffer) (Diptera: Chironomidae)

Zootaxa ◽

10.11646/zootaxa.2762.1.3 ◽

2011 ◽

Vol 2762 (1) ◽

pp. 37 ◽

Cited By ~ 5

Author(s):

ELISABETH STUR ◽

MARTIN SPIES

Keyword(s):

Species Group ◽

Genetic Distances ◽

Dna Barcodes ◽

Single Male ◽

Male Specimen ◽

Coi Sequences

The male imago of Chaetocladius longivirgatus sp. n. is described and diagnosed against a refined characterization of the species understood as C. suecicus (Kieffer) since Edwards (1929). The two species are separated by both morphology and partial COI sequences (DNA barcodes). An additional single male specimen shows pairwise genetic distances to C. suecicus and C. longivirgatus sp. n. as high as those between the latter two species, thus may represent a third European member in this species group. Morphologically, however, that male is inseparable from those of C. suecicus.

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