scholarly journals CURRENT PERSPECTIVES OF DNA BARCODING IN BOSNIA AND HERZEGOVINA THROUGH BOLD DATABASE

2021 ◽  
Vol 50 (1) ◽  
pp. 33-37
Author(s):  
Lejla Ušanović ◽  
Jasna Hanjalić ◽  
Semir Dorić ◽  
Lejla Lasić ◽  
Jasmina Šubara ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Data Storage ◽  
Bosnia And Herzegovina ◽  
Molecular Genetic ◽  
Sequence Evolution ◽  
Biodiversity Science ◽  
Its Gene ◽  
Continuous Progress ◽  
Nuclear Its ◽  
Analysis Platform

UDK: 577.212:574]:007.5(497.6) DNA barcoding is a method designed to provide rapid and precise species identifications by using one or more of short gene sequences called barcodes. In most plant and fungi studies, the standard barcodes of choice are three plastid (rbcL, matK and trnH-psbA) and one nuclear (ITS) gene regions. The relatively high, but comparatively conserved rate of sequence evolution of mtDNA has made COI the marker of choice in animals. BOLD is a freely available cloud-based data storage and analysis platform developed with the aim to advance biodiversity science through DNA barcoding species identification. To date, over 6 million barcodes have been deposited in BOLD with 196,000 animal species, 68,000 plant species and 22,000 species of fungi and other organism entries. In this database, there are currently 447 entries for organisms from Bosnia and Herzegovina, which makes 0.0067% of the total number of BOLD entries. According to BOLD statistics, only 1.11% of all organism entries from B&H were submitted by B&H institutions. Despite the fact that Bosnia and Herzegovina has valuable natural resources with a high percentage of endemic and autochthonous species, BOLD statistics elucidated the lack of coordinated and systematic DNA barcoding research so far. It is necessary to establish continuous progress of molecular-genetic characterization of these resources in the future. It is up to B&H institutions to decide if they want to continue the practice of submitting the data sporadically or if they will animate the research community to actively participate in this global project.

scholarly journals Evolutionary Analysis of Plastid Genomes of Seven Lonicera L. Species: Implications for Sequence Divergence and Phylogenetic Relationships

2018 ◽  
Vol 19 (12) ◽  
pp. 4039 ◽  
Author(s):  
Mi-Li Liu ◽  
Wei-Bing Fan ◽  
Ning Wang ◽  
Peng-Bin Dong ◽  
Ting-Ting Zhang ◽  
...  
Keyword(s):  
Molecular Genetic ◽  
Phylogenetic Reconstruction ◽  
Sequence Divergence ◽  
Genomic Analysis ◽  
Repeat Sequence ◽  
Biological Research ◽  
Comparative Genomic ◽  
Sequence Evolution ◽  
Evolutionary Analysis ◽  
Plastid Genomes

Plant plastomes play crucial roles in species evolution and phylogenetic reconstruction studies due to being maternally inherited and due to the moderate evolutionary rate of genomes. However, patterns of sequence divergence and molecular evolution of the plastid genomes in the horticulturally- and economically-important Lonicera L. species are poorly understood. In this study, we collected the complete plastomes of seven Lonicera species and determined the various repeat sequence variations and protein sequence evolution by comparative genomic analysis. A total of 498 repeats were identified in plastid genomes, which included tandem (130), dispersed (277), and palindromic (91) types of repeat variations. Simple sequence repeat (SSR) elements analysis indicated the enriched SSRs in seven genomes to be mononucleotides, followed by tetra-nucleotides, dinucleotides, tri-nucleotides, hex-nucleotides, and penta-nucleotides. We identified 18 divergence hotspot regions (rps15, rps16, rps18, rpl23, psaJ, infA, ycf1, trnN-GUU-ndhF, rpoC2-rpoC1, rbcL-psaI, trnI-CAU-ycf2, psbZ-trnG-UCC, trnK-UUU-rps16, infA-rps8, rpl14-rpl16, trnV-GAC-rrn16, trnL-UAA intron, and rps12-clpP) that could be used as the potential molecular genetic markers for the further study of population genetics and phylogenetic evolution of Lonicera species. We found that a large number of repeat sequences were distributed in the divergence hotspots of plastid genomes. Interestingly, 16 genes were determined under positive selection, which included four genes for the subunits of ribosome proteins (rps7, rpl2, rpl16, and rpl22), three genes for the subunits of photosystem proteins (psaJ, psbC, and ycf4), three NADH oxidoreductase genes (ndhB, ndhH, and ndhK), two subunits of ATP genes (atpA and atpB), and four other genes (infA, rbcL, ycf1, and ycf2). Phylogenetic analysis based on the whole plastome demonstrated that the seven Lonicera species form a highly-supported monophyletic clade. The availability of these plastid genomes provides important genetic information for further species identification and biological research on Lonicera.

scholarly journals Filling gaps in the DNA barcode library - Aquatic insects (Ephemeroptera, Plecoptera, Trichoptera) from semi-mountainous and mountainous rivers of Ecoregion 6 (North Macedonia)

2021 ◽  
Vol 4 ◽  
Author(s):  
Biljana Rimcheska ◽  
Yanka Vidinova
Keyword(s):  
New Species ◽  
Dna Barcoding ◽  
Aquatic Insects ◽  
Molecular Genetic ◽  
Dna Barcode ◽  
Balkan Peninsula ◽  
Molecular Genetic Data ◽  
Medium Quality ◽  
Total Dna ◽  
Data Library

This research provides pivotal molecular genetic data on the community structure of aquatic insects from semi-mountainous and mountainous rivers from the 6th Ecoregion that belongs to the territory of North Macedonia. The aim of this research is to fill the gaps for barcoding the aquatic macroinvertebrates from the Balkan Peninsula and check if the existing barcode library could provide improved identifications for the specimens that were not taxonomically determined to the lowest level possible. We analyzed 95 specimens from which total DNA was extracted and the COI barcode region amplified and sequenced. The taxa were selected from 20 different localities of the territory of western part of North Macedonia. The selected specimens were not determined to species-level in order to test the efficiency of the DNA barcoding methodology and what is missing in the DNA barcoding data library. From the result from one plate (95 specimens) we obtained: 16 samples without barodes, or failed and 10 samples did not have a match in the BOLD database. In the remining 69 samples, three were misidentified. In the total of 69 barcoded species new for the fauna of North Macedonia, 11 are mayflies: Baetis melanonyx, Ecdyonurus vitoshensis, E. macani; stonefly Isoperla vjose; and caddisflies: Agapetus delicatulus, Athripsodes bilineatus, Glossosoma klotho, Lepidostoma basale, Helicopsyche bacescui, Tinodes unicolor and Odontocerum hellenicum. We have also four rarely found species: Zwicknia bifrons, Drussus tenellus, Hydropsyche botosaneanui and Hydropsyche bulbifera, and one species without barcode available as Ecdyonurus sp. SK2 (potential new species). We found 83% efficiency of DNA barcoding, where some samples failed or were with low or medium quality for some specimens, as for the representatives from the genera Baetis, Oxietyra and Rhyacophila. In conclusion we can confirm that 10 of the selected vouchers need to be further identified by morphology and to be added in the BOLD barcode library, and maybe we'll have the possibility to describe a new species as well.

scholarly journals DNA barcoding of native Caucasus herbal plants: potentials and limitations in complex groups and implications for phylogeographic patterns

2021 ◽  
Vol 9 ◽  
Author(s):  
Parvin Aghayeva ◽  
Salvatore Cozzolino ◽  
Donata Cafasso ◽  
Valida Ali-zade ◽  
Silvia Fineschi ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Dna Barcode ◽  
Species Level ◽  
Floristic Survey ◽  
Barcoding Gap ◽  
Plant Groups ◽  
History Of ◽  
Nuclear Its ◽  
Species Assignment ◽  
Assignment Success

DNA barcoding has rapidly become a useful complementary tool in floristic investigations particularly for identifying specimens that lack diagnostic characters. Here, we assess the capability of three DNA barcode markers (chloroplast rpoB, accD and nuclear ITS) for correct species assignment in a floristic survey on the Caucasus. We focused on two herbal groups with potential for ornamental applications, namely orchids and asterids. On these two plant groups, we tested whether our selection of barcode markers allows identification of the “barcoding gap” in sequence identity and to distinguish between monophyletic species when employing distance-based methods. All markers successfully amplified most specimens, but we found that the rate of species-level resolution amongst selected markers largely varied in the two plant groups. Overall, for both lineages, plastid markers had a species-level assignment success rate lower than the nuclear ITS marker. The latter confirmed, in orchids, both the existence of a barcoding gap and that all accessions of the same species clustered together in monophyletic groups. Further, it also allowed the detection of a phylogeographic signal.The ITS marker resulted in its being the best performing barcode for asterids; however, none of the three tested markers showed high discriminatory ability. Even if ITS were revealed as the most promising plant barcode marker, we argue that the ability of this barcode for species assignment is strongly dependent on the evolutionary history of the investigated plant lineage.

scholarly journals Study of the microbiome species of the flowers phytophages based on the DNA-barcoding data

2019 ◽  
Vol 63 (2) ◽  
pp. 175-180
Author(s):  
S. V. Panteleev ◽  
O. Yu. Baranov ◽  
L. A. Golovchenko ◽  
A. V. Konstantinov ◽  
L. V. Mozharovskaya ◽  
...  
Keyword(s):  
Species Composition ◽  
Dna Barcoding ◽  
Molecular Genetic ◽  
Genetic Identification ◽  
Molecular Genetic Identification

Based on the DNA-barcoding data, a molecular-genetic identification of the dominant microbiome species composition of the perennial floral plants phytophages was carried out. Various variants of species combinations in the microbiota–phytophagous system, as well as the ways of phytophagous transmission of pathogenic microflora have been identified.

Dichrorampha dinarica, new species, a century of confusion in European lepidopterology (Lepidoptera: Tortricidae) resolved by combining morphology and DNA barcoding

Zootaxa ◽  
2012 ◽  
Vol 3389 (1) ◽  
pp. 41 ◽  
Author(s):  
PETER HUEMER ◽  
BOYAN ZLATKOV ◽  
JOAQUIN BAIXERAS
Keyword(s):  
New Species ◽  
Dna Barcoding ◽  
Bosnia And Herzegovina ◽  
Morphological Characters ◽  
Dinaric Mountains ◽  
Significant Divergence ◽  
The Alps

Dichrorampha dinarica, new species, is described from the Dinaric mountains (Macedonia, Bosnia and Herzegovina). The newspecies was formerly confused with D. ligulana (Herrich-Schäffer, 1851) from the Alps and D. rilana Drenowsky, 1909 fromthe Rila mountains (Bulgaria). Therefore, a re-description of D. rilana is provided based on topotypical specimens. The diag-nostic morphological characters of the involved species, supported by significant divergence of the mtDNA barcode (COI fragment of 658 bp), are discussed in detail.

The current approaches to the study of algae: DNA barcoding and DNA taxonomy

2021 ◽  
pp. 124-130
Author(s):  
Anna D. Temraleeva ◽  
Elena S. Krivina ◽  
Yury S. Bukin
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequencing ◽  
Dna Barcoding ◽  
Species Identification ◽  
Green Algae ◽  
Molecular Genetic ◽  
Algal Species ◽  
Species Boundaries ◽  
Sequencing Technology ◽  
Dna Taxonomy

The understanding of the impossibility of distinguishing algal species based on morphological features came with the development of DNA sequencing technology, which today is a necessary tool for defining species boundaries and testing traditional species concepts. The paper discusses popular approaches to species identification (DNA barcoding) and the description of new and revision of known species (DNA taxonomy) using molecular genetic methods. The requirements and limitations in their work are given, as well as examples of phylogenetic analysis of green algae from the clade Moewusinia and Parachlorella, including the genus Micractinium.

Slow Mitochondrial COI Sequence Evolution at the Base of the Metazoan Tree and Its Implications for DNA Barcoding

2008 ◽  
Vol 66 (2) ◽  
pp. 167-174 ◽  
Author(s):  
Danwei Huang ◽  
Rudolf Meier ◽  
Peter A. Todd ◽  
Loke Ming Chou
Keyword(s):  
Dna Barcoding ◽  
Sequence Evolution ◽  
Mitochondrial Coi

scholarly journals Imagining Sisyphus happy: DNA barcoding and the unnamed majority

2016 ◽  
Vol 371 (1702) ◽  
pp. 20150329 ◽  
Author(s):  
Mark Blaxter
Keyword(s):  
Dna Barcoding ◽  
Time Frame ◽  
Morphological Identification ◽  
Dna Barcodes ◽  
Species Definition ◽  
Operational Taxonomic Units ◽  
The Earth ◽  
Biodiversity Science ◽  
Reasonable Time Frame

The vast majority of life on the Earth is physically small, and is classifiable as micro- or meiobiota. These organisms are numerically dominant and it is likely that they are also abundantly speciose. By contrast, the vast majority of taxonomic effort has been expended on ‘charismatic megabionts’: larger organisms where a wealth of morphology has facilitated Linnaean species definition. The hugely successful Linnaean project is unlikely to be extensible to the totality of approximately 10 million species in a reasonable time frame and thus alternative toolkits and methodologies need to be developed. One such toolkit is DNA barcoding, particularly in its metabarcoding or metagenetics mode, where organisms are identified purely by the presence of a diagnostic DNA sequence in samples that are not processed for morphological identification. Building on secure Linnaean foundations, classification of unknown (and unseen) organisms to molecular operational taxonomic units (MOTUs) and deployment of these MOTUs in biodiversity science promises a rewarding resolution to the Sisyphean task of naming all the world's species. This article is part of the themed issue ‘From DNA barcodes to biomes’.

scholarly journals Identification of Nepeta olgae Regel and phylogenetic status of some genera in subtribe Nepetinae (Lamiaceae) using DNA markers

2021 ◽  
Vol 38 ◽  
pp. 00087
Author(s):  
Elena Nikitina ◽  
Abdurashid Rakhmatov
Keyword(s):  
Dna Barcoding ◽  
Large Scale ◽  
Dna Barcode ◽  
Dna Barcodes ◽  
Biodiversity Monitoring ◽  
Reference Library ◽  
Accurate Identification ◽  
Unknown Species ◽  
Phylogenetic Status ◽  
Nuclear Its

The species level diversity is the reference unit for biodiversity accounting, should be systematized and include full information about the species. Reliable identification of any species is critical for a large-scale biodiversity monitoring and conservation. A DNA barcode is a DNA sequence that identifies a species by comparing the sequence of an unknown species with barcodes of a known species sequence database. Accurate identification of important plants is essential for their conservation, inventory. The species diversity assessing exampled on the subtribe Nepetinae (Lamiaceae) representatives, growing in Uzbekistan is given, using DNA barcoding method. The study was aimed to identify indigenous important plants with the nuclear (ITS) and plastid (matK, rbcL, trnL-F) genomes. This work demonstrates the phylogenetic relationships of some genera within the subtribe Nepetinae Coss. & Germ. (Lamiaceae), based on ITS locus gene. All results indicate that the DNA barcoding tool can be successfully used to reliably identify important plants, to inventory the botanical resources of Uzbekistan and to create a reference library of DNA barcodes. So, the combination of three-four locus gene is a good candidate for this approach.

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.

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