A test of DNA barcoding in crayfish of the upper James River basin, Virginia

2015 ◽  
Vol 21 (1) ◽  
pp. 179-183
Author(s):  
Paul R. Cabe ◽  
Bradleigh E. Navalsky ◽  
Ainsley K. Bloomer ◽  
Ryan Doherty ◽  
Jordan Edgren ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
River Basin ◽  
Native Species ◽  
Biological Diversity ◽  
Coi Gene ◽  
Test Case ◽  
Accurate Identification ◽  
James River ◽  
Coi Sequences ◽  
Current Sequence

Abstract Crayfish populations in North America face many conservation threats, including habitat loss, degradation, and the introduction of non-native species. The management of biological diversity requires accurate identification of species, and for crayfish, many species are difficult to identify using standard morphological approaches. We investigated DNA barcoding using cytochrome oxidase I (COI) gene sequences to determine if this widely used method is useful in the identification of crayfish. As a test case, we sampled crayfish from the middle and upper James River basin in Virginia. This area had been recently surveyed by experienced crayfish biologists, and hosts a moderate number of species. We collected nearly 300 COI sequences, which clustered clearly into seven groups, mirroring the seven species reported for this watershed. Despite the unambiguous clustering, the range of sequence variation within species overlapped the range of variation between species; we detected no clear "barcode gap." Although this method holds promise as an aid to crayfish identification, current sequence databases (GenBank, BOLD) do not contain enough appropriate COI sequences to allow unequivocal identification in this unique and understudies fauna.

scholarly journals First results of Central Asiatic Euchalcia DNA-studies: comparison of nucleotide sequence differences in COI between Euchalcia herrichi and Euchalcia gyulai (Lepidoptera: Noctuidae)

2020 ◽  
Vol 6 ◽  
pp. 1-4
Author(s):  
Stanislav K Korb
Keyword(s):  
Nucleotide Sequence ◽  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Coi Gene ◽  
First Results ◽  
The Difference ◽  
Coi Sequences ◽  
Lepidoptera Noctuidae ◽  
Two Populations

We submitted first results of the DNA studies of the Central Asiatic owlet moths of the genus Euchalcia. Standard cytochrome C oxidase subunit I (COI) gene fragments were sequenced for DNA barcoding of six specimens belonging to Euchalcia herrichi and Euchalcia gyulai. We compared the received sequences between discussed species and with two European Euchalcia species (E. variabilis and E. consona). We found no variability within the COI sequences of the samples collected in the same locality (Alai Mts., Kyrgyzstan), whereas the difference in COI sequences between two populations (Ketmen Mts., Kazakhstan and Alai Mts., Kyrgyzstan) was 0.005.

scholarly journals DNA barcoding to resolve the confusion in identifying Tribolium confusum and Tribolium castaneum

2019 ◽  
Vol 47 (2) ◽  
pp. 333-342
Author(s):  
Abu Faiz Md Aslam ◽  
Sharmin Sultana ◽  
Sumita Rani Das ◽  
Abdul Jabber Howlader
Keyword(s):  
Dna Barcoding ◽  
Tribolium Castaneum ◽  
Life Stage ◽  
Dna Barcode ◽  
Tribolium Confusum ◽  
Likelihood Method ◽  
Coi Gene ◽  
Pest Species ◽  
Stored Grain ◽  
Accurate Identification

Tribolium confusum and Tribolium castaneum (Coleoptera: Tenebrionidae) are two very confusing pest species while identification is done on the basis of morphology only. Such pests are discovered in stored grain as immature stages, which further complicates the identification process. Accurate identification of these pests is urgently required for integrated pest management. In this research, DNA barcoding was used to identify these pests accurately at any life stage. A 658 bp fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene was analyzed. DNA barcode dataset of T. confusum (GeneBank Acc. no. MK120453.1) and T. castaneum (Acc. no. MK411585.1) were constructed. The nucleotide composition reveals that average AT contents (59.9%) were higher than the GC contents (38.6%). Phylogenetic analysis by maximum likelihood method showed that both the species were originated from a common major clade. About 17.13% nucleotide differences were noted between the CO1 sequences by multiple sequence alignment. The interspecies nucleotide genetic distance (0.200) was calculated using Kimura 2 parameter. Haplotype analysis showed high genetic diversity (112 mutaional steps) among them. Bangladesh J. Zool. 47(2): 333-342, 2019

scholarly journals First Record of Traumatic Myiasis Obtained From Forest Musk Deer (Moschus Berezovskii) Using DNA Barcoding

2020 ◽  
Author(s):  
Yunyun Gao ◽  
Yajun Fu ◽  
Liping Yan ◽  
Defu Hu ◽  
Benmo Jiang ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Animal Husbandry ◽  
First Record ◽  
Coi Gene ◽  
Common Disease ◽  
Human Society ◽  
Musk Deer ◽  
Two Samples ◽  
Nucleotide Divergence ◽  
Coi Sequences

Abstract Background: Myiasis is a common disease occurring in humans and livestock all over the world. It is closely related to human society and of great significance to animal husbandry, forensic science, and medicine. Myiasis is known to occur in wild animals, while no information is reported in forest musk deer. On July 6, 2019, we found severe traumatic myiasis of an injured forest musk deer (Moschus berezovskii) (Flerov, 1929), infected by lots of maggots and clusters of eggs. However, the precise identification of the larvae that we collected was difficult with few specific morphology characteristics.Methods: DNA barcoding is an efficient technique for species diagnosis, therefore is employed to identify the samples collected from the infected forest musk deer. Firstly, we extracted genomic DNA from one larva and one egg respectively. The cytochrome oxidase I (COI) gene barcoding region was amplified by polymerase chain reaction (PCR) and bidirectionally sequenced by Sanger sequencing. The sequences were searched for similarity using BLAST and the best hits were Lucilia. To identify these blowflies accurately, these newly generated sequences were subsequently analyzed with COI sequences of Lucilia and Calliphora downloaded from GenBank, to calculate nucleotide divergence, and to construct a neighbor-joining tree.Results: Our results suggest that nucleotide divergence between the two samples is 0.0033cM, between two samples and Lucilia caesar (Diptera: Calliphoridae) (Linnaeus, 1758) is 0.0016–0.0050cM. Furthermore, the NJ tree construction indicates that the flies collected from the musk deer are Lucilia caesar.Conclusions: Our results indicate that DNA barcoding can successfully identify pathogenic species. As far as the authors know, this is the first time that myiasis is detected in forest musk deer caused by a traumatic infection in China. The affected individual was clinically treated immediately and apparently recovered.

scholarly journals DNA Barcoding and CITES-Listed Wedgefish (Rhynchobatidae, Rhinidae) from South Bangka, Indonesia

2021 ◽  
Vol 24 (2) ◽  
pp. 232-236
Author(s):  
Siti Aisyah ◽  
Novi Santia ◽  
Okto Supratman ◽  
Ahmad Fahrul Syarif ◽  
Anggraeni Anggraeni
Keyword(s):  
Dna Barcoding ◽  
Conservation Status ◽  
Marine Ecosystem ◽  
Iucn Red List ◽  
Coi Gene ◽  
Accurate Identification ◽  
Tissue Samples ◽  
Wild Fauna ◽  
The Status ◽  
Elasmobranch Species

Overfishing of wedgefish greatly affects its population and the balance of the marine ecosystem. This is exacerbated by their relatively low fecundity, slow growth, and late maturity results in one of the lowest population growth rate within elasmobranch species. However, lacking database information results in insufficient regulations and surveillance of wedgefish fishing. The current situation is feared to the risk of wedgefish’s survival, especially in Bangka Belitung Islands, Indonesia. Fundamental to a database is the accurate identification of wedgefish species based on mitochondrial DNA (mtDNA) analysis. This study aimed to use DNA barcodes to identify, determine the conservation status, and the status according to the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). We collected samples including unidentified fin samples from confiscated illegal fishing catches, the traditional markets and fishing docks, South Bangka. In this research, we used DNA Barcoding (mitocondrial DNA, COI gene) to identify and examine of wedgefish samples. The tissue samples used in this study were identified as species listed in CITES Appendix II, they are Rhynchobatus australiae, Rhynchobatus springeri and Rhina ancylostoma. According to the IUCN Red List, 100% of the wedgefish species found are Critical Endangered at the global level.

scholarly journals First results of Central Asiatic Euchalcia DNA-studies: comparison of nucleotide sequence differences in COI between Euchalcia herrichi and Euchalcia gyulai (Lepidoptera: Noctuidae)

2020 ◽  
Vol 6 ◽  
pp. 1-4
Author(s):  
Stanislav Korb
Keyword(s):  
Nucleotide Sequence ◽  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Coi Gene ◽  
First Results ◽  
The Difference ◽  
Coi Sequences ◽  
Lepidoptera Noctuidae ◽  
Two Populations

We submitted first results of the DNA studies of the Central Asiatic owlet moths of the genus Euchalcia. Standard cytochrome C oxidase subunit I (COI) gene fragments were sequenced for DNA barcoding of six specimens belonging to Euchalcia herrichi and Euchalcia gyulai. We compared the received sequences between discussed species and with two European Euchalcia species (E. variabilis and E. consona). We found no variability within the COI sequences of the samples collected in the same locality (Alai Mts., Kyrgyzstan), whereas the difference in COI sequences between two populations (Ketmen Mts., Kazakhstan and Alai Mts., Kyrgyzstan) was 0.005.

scholarly journals Karyotype and COI sequences of Chironomus sokolovae Istomina, Kiknadze et Siirin, 1999 (Diptera,Chironomidae) from the bay of Orkhon River, Mongolia

2021 ◽  
Vol 15 (2) ◽  
pp. 149-157
Author(s):  
Viktor V. Bolshakov ◽  
Alexander A. Prokin
Keyword(s):  
Bayesian Inference ◽  
Phylogenetic Tree ◽  
Genetic Distance ◽  
Dna Barcoding ◽  
Molecular Genetic ◽  
Species Level ◽  
Coi Gene ◽  
High Similarity ◽  
Coi Sequences ◽  
First Time

Chironomus sokolovae Istomina, Kiknadze et Siirin, 1999 (Diptera, Chironomidae) is recorded from Mongolia for the first time. Eleven banding sequences determined in the Mongolian population were previously known from Altai and Yenisei populations: sokA1, sokB1, sokB2, sokC1, sokC2, sokD1, sokD2, sokE1, sokF1, sokF2 and sokG1. The additional B-chromosomes are absent. DNA-barcoding of COI gene was carried out for this species for the first time. The phylogenetic tree estimated by Bayesian inference showed a high similarity of the studied species with Ch. acutiventris Wülker, Ryser et Scholl, 1983 from the Chironomus obtusidens-group. The estimated genetic distance K2P between Ch. sokolovae and Ch. acutiventris is much lower (0.38%) than the commonly accepted threshold of 3% for species of genus Chironomus Meigen, 1803. Our results show that the accepted cytogenetic criteria of species level in the genus Chironomus are more in accordance with morphological ones of the same level, than with molecular-genetic criteria accepted for species COI genetic distance.

scholarly journals First record of non-native platyfish, Xiphophorus maculatus (Günther, 1866) (Cyprinodontiformes, Poeciliidae), in the Jaguaribe River basin, northeastern Brazil

Check List ◽  
2020 ◽  
Vol 16 (5) ◽  
pp. 1159-1164
Author(s):  
Telton Pedro Anselmo Ramos ◽  
Yuri Gomes Ponce de Carvalho Rocha ◽  
Silvia Yasmin Lustosa Costa ◽  
José Etham de Lucena Barbosa
Keyword(s):  
River Basin ◽  
Native Species ◽  
Biological Diversity ◽  
First Record ◽  
Northeastern Brazil ◽  
Fish Populations ◽  
Native Fish ◽  
Total Length ◽  
Xiphophorus Maculatus

We provide the first record of Xiphophorus maculatus (Günther, 1866) in a river basin in the northeastern Brazil. Specimens were collected in the Jaguaribe River basin, João Pessoa, Paraíba state, Brazil. Two hundred eighty-one specimens, corresponding to 143 males and 138 females of X. maculatus, were collected at nine sites along the basin, from 2017 to 2019. Specimens total length ranged from 17.5 to 26.6 mm in males and from 11.7 to 32.7 mm in females. Introduction of non-native species greatly threatens the biological diversity worldwide. When introduced into a new habitat, X. maculatus usually decreases microcrustacean, macroinvertebrate and native fish populations.

scholarly journals Identifikasi ikan gabus, Channa spp. (Scopoli 1777) stok liar dan generasi I hasil domestikasi berdasarkan gen Cytochrome C Oxidase Subunit I (COI)

2018 ◽  
Vol 17 (2) ◽  
pp. 165 ◽  
Author(s):  
Irmawati Irmawati ◽  
Joeharnani Tresnati ◽  
Liestiaty Fachruddin ◽  
Nur Rahmawaty Arma ◽  
Andi Haerul
Keyword(s):  
Cytochrome C ◽  
Dna Barcoding ◽  
Cytochrome C Oxidase ◽  
Native Species ◽  
First Generation ◽  
Coi Gene ◽  
Oxidase Subunit ◽  
South Sulawesi ◽  
Phylogenetic Resolution ◽  
Channa Striata

The snakehead fish (Channidae) is widely distributed in inland water of Indonesia. This fish is native species in Suma-tera, Java and Kalimantan, but non-native species in Sulawesi and Papua. Study on molecular identification and phylo-geny of this fish using cytochrome c oxidase subunit I (COI) gene has only been conducted on snakehead fish origin from Tasikmalaya, Ambarawa, Bali, Aceh, Pontianak, and Banjarmasin waters, but none is available in South Sulawesi waters. The objectives of this research are to identify species of snakehead fish from Towuti Lake Sorowako and the first generation (F1) of domesticated snakehead fish from Bantaeng waters of South Sulawesi using COI gene for DNA barcoding, and to analyze the phylogenetic resolution of the fish. Partial sequences of the COI gene of the snakehead fish were aligned with sequences of snakehead fish deposited in GenBank. The phylogenetic tree was constructed using MEGA 7.0.20 program. The result indicated that COI gene nucleotides of snakehead fish from Towuti Lake Sorowako showed 99% homology with Channa striata acc no. KU692418 and KU692421, and showed 98% homology with those of acc no. KU852443. Therefore it can be conclude that Channa striata exist in Towuti Lake Sorowako. Nucleotide sequences of the first generation (F1) of domesticated snakehead fish from Bantaeng waters showed 65% homology with Channa pleurophthalma (acc no. KJ937390) origins from Banjarmasin waters and Channa gachua (acc no. KX389277). Based on this result, it assumed that snakehead fish from Towuti Lake Sorowako are distantly in gene to those from Bantaeng waters, and further analyses are required to identify the population of snakehead fish from Bantaeng waters. Abstrak Populasi ikan gabus (famili Channidae) tersebar luas di wilayah perairan tawar Indonesia. Ikan gabus merupakan ikan asli di Sumatera, Jawa, dan Kalimantan) tetapi merupakan ikan introduksi di Sulawesi dan Papua. Identifikasi berdasar-kan gen cytochrome c oxidase subunit I (COI) telah dilakukan terhadap ikan gabus dari perairan di Tasikmalaya, Amba-rawa, Bali, Aceh, Pontianak dan Banjarmasin, tetapi ikan gabus dari perairan Sulawesi Selatan belum dilakukan. Tuju-an penelitian adalah untuk mengidentifikasi species ikan gabus dari Danau Towuti Sorowako dan ikan gabus generasi I (F1) hasil domestikasi dari induk yang berasal dari perairan tawar Kabupaten Bantaeng Sulawesi Selatan menggunakan gen COI untuk DNA barcoding, dan untuk menganalisis filogeni ikan gabus tersebut. Sekuen gen COI ikan gabus terse-but disejajarkan dengan sekuen nukleotida ikan gabus yang terdeposit di GenBank. Pohon filogenetik dikonstruksi de-ngan menggunakan program MEGA 7.0.20. Hasil penelitian menunjukkan bahwa nukleotida gen COI sampel ikan gabus dari Danau Towuti Sorowako memiliki kemiripan 99% dengan Channa striata nomor aksesi KU692418 dan KU692421 dan 98% dengan Channa striata nomor aksesi KU852443 sehingga dapat disimpulkan bahwa di Danau To-wuti terdapat ikan gabus jenis Channa striata. Tingkat kemiripan sekuen nukleotida ikan gabus F1dari perairan Kabu-paten Bantaeng adalah 65% dengan ikan gabus Channa pleurophthalma (KJ937390) asal perairan Banjarmasin dan ikan gabus Channa gachua (KX389277). Berdasarkan hasil tersebut maka diduga bahwa ikan gabus dari Danau Towu-ti Sorowako berkerabat jauh dengan ikan gabus dari perairan Bantaeng, dan diperlukan analisis yang lebih lanjut untuk menentukan jenis populasi ikan gabus F1 asal perairan tawar Kabupaten Bantaeng tersebut.

scholarly journals DNA Barcoding for Delimitation of Putative Mexican Marine Nematodes Species

Diversity ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 107 ◽  
Author(s):  
Arely Martínez-Arce ◽  
Alberto De Jesús-Navarrete ◽  
Francesca Leasi
Keyword(s):  
Dna Barcoding ◽  
Low Cost ◽  
Nematode Species ◽  
Molecular Data ◽  
Coi Gene ◽  
Taxonomic Resolution ◽  
Species List ◽  
Nematode Diversity ◽  
Coi Sequences ◽  
Morphological And Molecular Data

Nematode biodiversity is mostly unknown; while about 20,000 nematode species have been described, estimates for species diversity range from 0.1 to 100 million. The study of nematode diversity, like that of meiofaunal organisms in general, has been mostly based on morphology-based taxonomy, a time-consuming and costly task that requires well-trained specialists. This work represents the first study on the taxonomy of Mexican nematodes that integrates morphological and molecular data. We added eleven new records to the Mexican Caribbean nematode species list: Anticomidae sp.1, Catanema sp.1, Enoploides gryphus, Eurystomina sp.1, Haliplectus bickneri, Metachromadora sp.1, Odontophora bermudensis, Oncholaimus sp.1, Onyx litorale, Proplatycoma fleurdelis, and Pontonema cf. simile. We improved the COI database with 57 new sequences from 20 morphotypes. All COI sequences obtained in this work are new entries for the international genetic databases GenBank and BOLD. Among the studied sites, we report the most extensive species record (12 species) at Cozumel. DNA barcoding and species delineation methods supported the occurrence of 20 evolutionary independent entities and confirmed the high taxonomic resolution of the COI gene. Different approaches provided consistent results: ABGD and mPTP methods disentangled 20 entities, whereas Barcode Index Numbers (BINs) recovered 22 genetic species. Results support DNA barcoding being an efficient, fast, and low-cost method to integrate into morphological observations in order to address taxonomical shortfalls in meiofaunal organisms.

scholarly journals A Beetle in a Haystack: Are There Alternate Hosts of the Coffee Berry Borer (Hypothenemus hampei) in Puerto Rico?

Agronomy ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 228 ◽  
Author(s):  
Victor J. Vega ◽  
Yobana A. Mariño ◽  
Daymara Deynes ◽  
Elsie B. Greco ◽  
Donald E. Bright ◽  
...  
Keyword(s):  
Puerto Rico ◽  
Dna Barcoding ◽  
Management Strategies ◽  
Coi Gene ◽  
Hypothenemus Hampei ◽  
Coffee Berry ◽  
Coffee Berry Borer ◽  
Accurate Identification ◽  
Alternate Hosts ◽  
Preference Tests

Can the coffee berry borer (Hypothenemus hampei, or CBB) use host plants other than coffee for food and shelter? The use of fruits other than coffee has been reported. However, the validity of these reports depends on accurate identification of CBB, which is sometimes uncertain. In this study we sampled potential alternate hosts in coffee farms in Puerto Rico. Fruits with perforations were collected and examined for the presence of scolytid beetles (Coleoptera: Curculionidae: Scolytinae). Scolytids were identified by morphology and DNA barcoding of the COI gene. Association between the presence of Inga vera and Guarea guidonia trees and infestation rate of CBB in coffee fruits was evaluated. Food preference tests were performed in the laboratory. A total of 3563 beetles were found and 587 were identified as Hypothenemus spp.; of these, 85 identifications were confirmed by DNA barcoding. Twenty-seven of the beetles identified were H. hampei, mostly in I. vera fruits in periods between coffee crops. Most scolytids identified were H. obscurus. In preference tests, some CBB initially penetrated G. guidonia fruits, but eventually chose coffee. There was no evidence of feeding or reproduction in fruits of G. guidonia or Cajanus cajan. The results show that in Puerto Rico it is rare to find CBB in fruits of alternate hosts. The scarcity of coffee fruits in the off-season might cause some CBBs to take refuge in other fruits, but they did not feed or reproduce in them in laboratory tests. Understanding the refugia of CBB in the off-season may be useful for designing effective management strategies.

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