DNA barcoding and taxonomic validation of Caranx spp. larvae

2021 ◽  
pp. 1-9
Author(s):  
Claudia A. Silva-Segundo ◽  
René Funes-Rodríguez ◽  
Jaime Gómez-Gutiérrez ◽  
Griselda Gallegos-Simental ◽  
Sergio Hernández-Trujillo ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Genetic Similarity ◽  
Fish Larvae ◽  
Coi Gene ◽  
Molecular Evidence ◽  
Nominal Species ◽  
Central Pacific ◽  
Diagnostic Characteristics ◽  
Coi Sequences ◽  
First Time

Abstract Of the five nominal species in the genus Caranx Lacepède 1801 distributed throughout the Eastern Central Pacific, Caranx caballus and Caranx sexfasciatus are the only two that have formal fish larval descriptions based on diagnostic characteristics (morphology, meristics and pigmentation). In this study, the diagnostic characteristics of three Caranx species larvae were validated using DNA barcoding analysis cytochrome c oxidase subunit I (COI; 651 bp). For the first time, the morphological taxonomic assignation of C. caballus fish larvae was confirmed using COI gene partial sequences of adults, with a genetic similarity between 99.8–100%. However, molecular evidence demonstrated that fish larvae previously described as C. sexfasciatus had high genetic similarity (99.7–100%) and low genetic distance (<1%) to Caranx caninus adults. An undescribed larval morphotype collected in the present study genetically matched (100%) with COI sequences of C. sexfasciatus adults. The diagnostic characteristics of this new morphotype were a lack of pigmentation in the supraoccipital crest, over the gut, and at the terminal region of the gut. The combination of diagnostic characteristics and DNA barcoding evidence allowed the discrimination and validation of C. caballus, C. caninus and C. sexfasciatus larvae. The diagnostic characteristics and COI sequences of Caranx lugubris and Caranx melampygus larvae, which are also distributed in the Eastern Central Pacific, remain to be investigated.

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 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 Initiating DNA barcoding of Eastern Mediterranean deep-sea biota

2018 ◽  
Author(s):  
GUY PAZ ◽  
YANA YUDKOVSKY ◽  
LEE SHAISH ◽  
NIR STERN ◽  
HADAS LUBINEVSKI ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Deep Sea ◽  
Eastern Mediterranean ◽  
Abundant Species ◽  
Coi Gene ◽  
Pcr Products ◽  
The Common ◽  
Coi Sequences ◽  
First Time ◽  
Deep Sea Fauna

Preliminary results of DNA barcoding survey of deep-sea mega-faunal biota are presented, collected by trawl and gillnet off the Israeli coast (SE Mediterranean, depths 700 to 1500 meters) during 2012-2013. 846 organisms were identified to 37 species, mainly fish and decapod crustaceans. The most abundant species were the blackmouth catshark Galeus melastomus, the cosmopolitan decapod Polycheles typhlops and the bivalve Abra longicallus. Two species were sampled for the first time from the southern Levant- the long armed chiroteuthid squid Chiroteuthis veranyi and the common mora, Mora moro. Four of the 18 fish species and two of the 10 crustacean species were abundant, representing 78% and 61%, respectively, of the organisms collected. Most other species are represented by fewer than 10 individuals. PCR products for the cytochrome c oxidase sub unit I (COI) gene for the 37 species were successfully sequenced. The identified and vouchered individuals are stored at the Steinhardt Museum of Natural History (Tel Aviv University, Israel) and their COI sequences were uploaded into the BoLD universal data center as part of the national marine barcoding project. The COI sequences of Acanthephyra eximia, Gryphus vitreus, Galeodea echinophora, Mesothuria intestinalis and Astropecten irregularis, constitute first records of these species in BoLD. When compared to the COI sequences in BoLD, the present results reveal some inconsistency in species identification, an outcome that should be taken into consideration primarily once the taxonomical verifications of collected taxa are elusive. This study is the first step in DNA barcoding of the Levant’s little-known benthic deep-sea 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.

New records and their associated DNA barcodes of the butterfly family Hesperiidae in Tibet, China

Zootaxa ◽  
2019 ◽  
Vol 4674 (4) ◽  
pp. 426-438
Author(s):  
CHENGLONG CAO ◽  
SIYAO HUANG ◽  
YONGQIANG XU ◽  
HAOMIN WU ◽  
TIANPENG CHEN ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Morphological Study ◽  
New Records ◽  
Coi Gene ◽  
Dna Barcodes ◽  
Species Cluster ◽  
The Family ◽  
Interspecific Genetic Distance ◽  
Coi Sequences ◽  
First Time

The specimens of the family Hesperiidae collected from Tibet during 2016–2018 are identified using morphology. COI sequences of 76 individuals are newly obtained. The result of our morphological study is congruent with COI gene analyses. Maximum likehood (ML) and Bayesina inferences (BI) analyses reveal that individuals identified morphologically as the same species cluster cohesively. The minimum interspecific genetic distance is 1.7% between Halpe aucma and H. filda, and the genetic distance between conspecific individuals ranged from 0 to 0.2% for the genus Halpe. A total of 51 species are recognized, and six of them, Celaenorrhinus consanguineus Leech, 1891, Barca bicolor (Oberthür, 1896), Aeromachus propinquus Alphéraky, 1897, Pedesta bivitta (Oberthür, 1886), Baoris penicillata chapmani Evans, 1937, and Ochlodes brahma Moore, 1878, are reported from Tibet for the first time, and the last species is new to China. 

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 On the Bennelongia barangaroo lineage (Crustacea, Ostracoda) in Western Australia, with the description of seven new species

2013 ◽  
Author(s):  
Koen Martens ◽  
Stuart Halse ◽  
Isa Schön
Keyword(s):  
New Species ◽  
Western Australia ◽  
Molecular Evidence ◽  
Nominal Species ◽  
Rock Pools ◽  
Additional Species ◽  
Coi Sequences ◽  
The Right ◽  
Genetic Species Concept ◽  
Genetic Species

The ostracod genus Bennelongia De Deckker & McKenzie, 1981 is endemic to Australia and New Zealand. Extensive sampling in Western Australia (WA) revealed a high specific and largely undescribed diversity. Here, we describe seven new species belonging to the B. barangaroo lineage: B. timmsi sp. nov., B. gnamma sp. nov., B. hirsuta sp. nov., B. ivanae sp. nov., B. mcraeae sp. nov., B. scanloni sp. nov. and B. calei sp. nov., and confirm the presence of an additional species, B. dedeckkeri, in WA. For five of these eight species, we could construct molecular phylogenies and parsimonious networks based on COI sequences. We also tested for cryptic diversity and specific status of clusters with a statistical method based on the evolutionary genetic species concept, namely Birky’s 4 theta rule. The analyses support the existence of these five species and a further three cryptic species in the WA B. barangaroo lineage. The molecular evidence was particularly relevant because most species described herein have very similar morphologies and can be distinguished from each other only by the shape, size and position of the antero-ventral lapel on the right valve, and, in sexual populations, by the small differences in shape of the hemipenes and the prehensile palps in males. Four species of the WA B. barangaroo lineage occur in small temporary rock pools (gnammas) on rocky outcrops. The other four species are mainly found in soft bottomed seasonal water bodies. One of the latter species, B. scanloni sp. nov., occurs in both claypans and deeper rock pools (pit gnammas). All species, except for B. dedeckkeri, originally described from Queensland, have quite clearly delimited distributions in WA. With the seven new species described here, the genus Bennelongia now comprises 25 nominal species but several more await formal description.

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 Molecular identification of Auxis spp. larvae (Pisces: Scombridae) from the Gulf of California: Solving morphological identification limits

2018 ◽  
Vol 53 (2) ◽  
pp. 157 ◽  
Author(s):  
María J. Ochoa-Muñoz ◽  
Noé Díaz-Viloria ◽  
Laura Sánchez-Velasco ◽  
Sylvia P. A. Jiménez-Rosenberg ◽  
Ricardo Pérez-Enríquez
Keyword(s):  
Molecular Identification ◽  
Gulf Of California ◽  
Fish Larvae ◽  
Morphological Characteristics ◽  
Species Level ◽  
Morphological Identification ◽  
Larval Stages ◽  
Marine Fish Larvae ◽  
Coi Sequences ◽  
First Time

The larvae of the Auxis genus are abundant in the Gulf of California during summer; however, their identification to the species level by morphological methods is a challenge. The goal of this study was to identify A. thazard and A. rochei larvae for first time, through molecular markers using COI sequences of mtDNA, and look for distinctive morphological characteristics between species, mainly in pigmentation patterns. Larvae were obtained by zooplankton tows in 3 oceanographic cruises in the southern Gulf of California and adjacent waters. The presence of A. thazard and A. rochei larvae was genetically confirmed. The sequences of 7 larvae showed genetic divergences lower than 1% when were compared to sequences of A. thazard adults, while 15 larvae showed genetic divergences lower than 2% when where compared to sequences of A. rochei adults. Genetic divergences between both Auxis species were higher than 2%. These results suggest the spawning of both species in the Gulf of California. On the other hand, pigmentation patterns and morphometric characteristics, in all larval stages, did not permit the secure differentiation between species. Thus, the use of molecular identification by COI is recommended to identify Auxis larvae to the species level, as well as in other marine fish larvae collected in other regions of the world, that have identification troubles.

Molecular Confirmation on the Presence of Anadara Kagoshimensis (Tokunaga, 1906) (Mollusca: Bivalvia: Arcidae) in the Black Sea / Confirmarea moleculară a prezenţei speciei Anadara Kagoshimensis (Tokunaga, 1906) (Mollusca: Bivalvia: Arcidae) în Marea Neagră

2015 ◽  
Vol 57 (1) ◽  
pp. 9-12 ◽  
Author(s):  
Ana Maria Krapal ◽  
Oana Paula Popa ◽  
Alexandra Levarda ◽  
Elena Iulia Iorgu ◽  
Luis Ovidiu Popa ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Genetic Markers ◽  
Black Sea ◽  
Genetic Similarity ◽  
Molecular Level ◽  
The Black Sea ◽  
Anadara Kagoshimensis ◽  
Ark Shell ◽  
Coi Sequences ◽  
High Genetic Similarity

Abstract The use of DNA barcoding in alien invasions has recently proved to be a powerful tool in delineating dispersal pathways and clarifying doubtful identifications. Morphological similarities between Anadara kagoshimensis (Tokunaga, 1906) and Anadara inaequivalvis (Bruguière, 1789) require the use of genetic markers in identifying the ark shell species that has recently invaded the Black Sea. The high genetic similarity (99.8-100%) hereby found between COI sequences obtained from the Black Sea samples and Japanese A. kagoshimensis confirms at a molecular level that the ark clam species invading the Romanian Black Sea belong to this taxon.

Sign in / Sign up

Export Citation Format

Share Document