scholarly journals Species Identification of Rock Oysters Collected from the Dhofar Region, Sultanate of Oman

2012 ◽  
Vol 17 ◽  
pp. 61 ◽  
Author(s):  
Mikhail V. Chesalin ◽  
Salem A. Al-Ghassani ◽  
Mohammed A. Balkhair
Keyword(s):  
Phylogenetic Analysis ◽  
Species Composition ◽  
Species Identification ◽  
Dna Sequences ◽  
Dna Barcode ◽  
Rocky Shores ◽  
Data Systems ◽  
Sultanate Of Oman ◽  
Life Data ◽  
Taxonomic Studies

Oysters are commonly found on rocky shores along the Dhofar coast of Oman, but the species composition has not yet been studied. In an attempt to determine the species of these oysters, samples from four sites (Mirbat, Sadah, Hadbin, and Hasik) were collected and analyzed using DNA sequences that were compared with the database of GenBank/National Center for Biotechnology Information (NCBI) and Barcoding of Life Data Systems (BOLD). BLAST results of DNA sequences showed that there were no existing sequences available on NCBI/GenBank and BOLD. The DNA barcode sequences generated in this study can be employed as standards for this species and may be of use in taxonomic studies. Phylogenetic analysis demonstrated that the oysters from Oman exhibit homology with Saccostrea species cucullata or mordax. 

DNA barcoding the Lepidoptera inventory of a large complex tropical conserved wildland, Area de Conservacion Guanacaste, northwestern Costa Rica

Genome ◽  
2016 ◽  
Vol 59 (9) ◽  
pp. 641-660 ◽  
Author(s):  
Daniel H. Janzen ◽  
Winnie Hallwachs
Keyword(s):  
Costa Rica ◽  
Dna Barcoding ◽  
Dna Barcode ◽  
Species Level ◽  
Data Systems ◽  
Species Discovery ◽  
Life Data ◽  
And Behavior ◽  
Specimen Identification ◽  
Biodiversity Information

The 37-year ongoing inventory of the estimated 15 000 species of Lepidoptera living in the 125 000 terrestrial hectares of Area de Conservacion Guanacaste, northwestern Costa Rica, has DNA barcode documented 11 000+ species, and the simultaneous inventory of at least 6000+ species of wild-caught caterpillars, plus 2700+ species of parasitoids. The inventory began with Victorian methodologies and species-level perceptions, but it was transformed in 2004 by the full application of DNA barcoding for specimen identification and species discovery. This tropical inventory of an extraordinarily species-rich and complex multidimensional trophic web has relied upon the sequencing services provided by the Canadian Centre for DNA Barcoding, and the informatics support from BOLD, the Barcode of Life Data Systems, major tools developed by the Centre for Biodiversity Genomics at the Biodiversity Institute of Ontario, and available to all through couriers and the internet. As biodiversity information flows from these many thousands of undescribed and often look-alike species through their transformations to usable product, we see that DNA barcoding, firmly married to our centuries-old morphology-, ecology-, microgeography-, and behavior-based ways of taxonomizing the wild world, has made possible what was impossible before 2004. We can now work with all the species that we find, as recognizable species-level units of biology. In this essay, we touch on some of the details of the mechanics of actually using DNA barcoding in an inventory.

scholarly journals Scalable classification of organisms into a taxonomy using hierarchical supervised learners

2020 ◽  
Vol 18 (05) ◽  
pp. 2050026
Author(s):  
Gihad N. Sohsah ◽  
Ali Reza Ibrahimzada ◽  
Huzeyfe Ayaz ◽  
Ali Cakmak
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Kernel Method ◽  
Sequence Data ◽  
Genetic Material ◽  
Dna Barcode ◽  
Living Organism ◽  
Large Datasets ◽  
Data Systems ◽  
Hierarchical Classifier

Accurately identifying organisms based on their partially available genetic material is an important task to explore the phylogenetic diversity in an environment. Specific fragments in the DNA sequence of a living organism have been defined as DNA barcodes and can be used as markers to identify species efficiently and effectively. The existing DNA barcode-based classification approaches suffer from three major issues: (i) most of them assume that the classification is done within a given taxonomic class and/or input sequences are pre-aligned, (ii) highly performing classifiers, such as SVM, cannot scale to large taxonomies due to high memory requirements, (iii) mutations and noise in input DNA sequences greatly reduce the taxonomic classification score. In order to address these issues, we propose a multi-level hierarchical classifier framework to automatically assign taxonomy labels to DNA sequences. We utilize an alignment-free approach called spectrum kernel method for feature extraction. We build a proof-of-concept hierarchical classifier with two levels, and evaluated it on real DNA sequence data from barcode of life data systems. We demonstrate that the proposed framework provides higher f1-score than regular classifiers. Besides, hierarchical framework scales better to large datasets enabling researchers to employ classifiers with high classification performance and high memory requirement on large datasets. Furthermore, we show that the proposed framework is more robust to mutations and noise in sequence data than the non-hierarchical classifiers.

scholarly journals Finding a suitable DNA barcode for Mesoamerican orchids

Lankesteriana ◽  
2015 ◽  
Vol 7 (1-2) ◽  
Author(s):  
Guillaume Gigot ◽  
Jonathan Van Alphen-Stahl ◽  
Diego Bogarín ◽  
Jorge Warner ◽  
Mark Chase ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Sequences ◽  
Dna Barcode ◽  
Molecular Technique ◽  
Biodiversity Inventories

Recently, DNA barcoding has emerged as an effec- tive tool for species identification. This has the poten- tial for many useful applications in conservation, such as biodiversity inventories, forensics and trade sur- veillance. It is being developed as an inexpensive and rapid molecular technique using short and standard- ized DNA sequences for species identification.  

scholarly journals Building a DNA barcode library of Alaska’s non-marine arthropods

Genome ◽  
2017 ◽  
Vol 60 (3) ◽  
pp. 248-259 ◽  
Author(s):  
Derek S. Sikes ◽  
Matthew Bowser ◽  
John M. Morton ◽  
Casey Bickford ◽  
Sarah Meierotto ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Dna Sequences ◽  
Dna Barcode ◽  
Data Systems ◽  
Dna Barcodes ◽  
Arthropod Species ◽  
Current State ◽  
The University ◽  
Trophic Mismatch ◽  
Insect Collection

Climate change may result in ecological futures with novel species assemblages, trophic mismatch, and mass extinction. Alaska has a limited taxonomic workforce to address these changes. We are building a DNA barcode library to facilitate a metabarcoding approach to monitoring non-marine arthropods. Working with the Canadian Centre for DNA Barcoding, we obtained DNA barcodes from recently collected and authoritatively identified specimens in the University of Alaska Museum (UAM) Insect Collection and the Kenai National Wildlife Refuge collection. We submitted tissues from 4776 specimens, of which 81% yielded DNA barcodes representing 1662 species and 1788 Barcode Index Numbers (BINs), of primarily terrestrial, large-bodied arthropods. This represents 84% of the species available for DNA barcoding in the UAM Insect Collection. There are now 4020 Alaskan arthropod species represented by DNA barcodes, after including all records in Barcode of Life Data Systems (BOLD) of species that occur in Alaska — i.e., 48.5% of the 8277 Alaskan, non-marine-arthropod, named species have associated DNA barcodes. An assessment of the identification power of the library in its current state yielded fewer species-level identifications than expected, but the results were not discouraging. We believe we are the first to deliberately begin development of a DNA barcode library of the entire arthropod fauna for a North American state or province. Although far from complete, this library will become increasingly valuable as more species are added and costs to obtain DNA sequences fall.

scholarly journals Barcode DNA berdasarkan Gen rbcL dan matK Anggrek Payus Limondok (Phaius tancarvilleae) (DNA Barcode of Payus Limondok Orchid (Phaius tancarvilleae) Based on the rbcL and matK genes)

2012 ◽  
Vol 4 (2) ◽  
Author(s):  
Beivy J Kolondam
Keyword(s):  
Polymerase Chain Reaction ◽  
Species Identification ◽  
Dna Sequences ◽  
Dna Barcode ◽  
Universal Primers ◽  
Chain Reaction ◽  
Barcode Dna ◽  
Polymerase Chain ◽  
Matk Sequence ◽  
Close Relatives

Metode identifikasi spesies telah disepakati menggunakan barcode DNA standar yaitu gen rbcL dan gen matK. Tujuan penelitian ini untuk menentukan tingkat kemiripan sekuens barcode DNA tanaman Anggrek Payus Limondok (Phaius tancarvilleae) dengan spesies kerabatnya yang sudah terdata dalam BOLD Systems, merekomendasi penggunaan barcode untuk mengidentifikasi atau mengkonfirmasi spesies ini, dan mengamati variasi intraspesifik. Teknik Polymerase Chain Reaction (PCR) digunakan untuk mengamplifikasi sekuens gen rbcL dan matK melalui primer universal. Barcode rbcL menunjukkan kemiripan 100% (identik) dengan dua spesies berbeda dalam famili yang sama (Orchidaceae), sehingga tidak bisa diandalkan untuk identifikasi spesies P. tancarvilleae secara akurat. Sekuens matK sampel menghasilkan kemiripan 100% dengan spesies sama yang sebelumnya telah terdata dalam BOLD Systems. Kemiripan ini mengindikasikan rendahnya variasi genetik intraspesies tetapi sekuens matK dapat diandalkan untuk identifikasi atau konfirmasi spesies anggrek P. tancarvilleae. Kata Kunci: barcode, rbcL, matK, Phaius tancarvilleae Abstract Species identification methods convention have been recommended to use standard DNA barcode for plants; the rbcL and matK genes. The aims of this research were to determine similarities in barcode DNA sequences of Payus Limondok Orchid (Phaius tancarvilleae) with its close relatives that listed in BOLD Systems, to recommend the use of DNA barcodes for identification or confirmation of this species, and to observe intraspecific variations. Polymerase Chain Reaction technique was employed to amplify rbcL and matK genes using universal primers. The rbcL barcode of Payus Limondok resulted identical hit with other two different species in the same family (Orchidaceae), therefore, unreliable for accurate P. tancarvilleae species identification. The matK sequence of this plant was 100% similar with the same plant species listed in BOLD Systems. This similarity indicated low genetic variation within the species, but the matK sequence was found to be reliable for P. tancarvilleae orchid species identification or confirmation. Keywords: barcode, rbcL, matK, Phaius tancarvilleae

scholarly journals The most northerly Black Witch (Ascalapha odorata): a tropical moth in the Canadian Arctic

2014 ◽  
Vol 128 (1) ◽  
pp. 77
Author(s):  
Torbjørn Ekrem ◽  
Peter G. Kevan ◽  
Thomas S. Woodcock ◽  
Paul D. N. Hebert
Keyword(s):  
Geographical Area ◽  
Geographic Origin ◽  
Dna Barcode ◽  
Canadian Arctic ◽  
Current Data ◽  
Central American ◽  
Data Systems ◽  
Life Data ◽  
Extensive Analysis ◽  
Large Geographical Area

A specimen of the Black Witch (Ascalapha odorata) was collected in August 2006 near Churchill, Manitoba, at 58.7652°N. This represents the most northerly record for this species. DNA barcode comparison of 93 specimens of A. odorata in the Barcode of Life Data Systems revealed low genetic divergence even though these specimens were collected from a large geographical area. The haplotype of the Churchill specimen was shared by only one other individual (collected in the Yucatán Peninsula of Mexico) in the Barcode of Life Data Systems. A definite assignment of the geographic origin of the Churchill specimen is not possible with current data, but more extensive analysis of Central American populations with additional genetic markers might resolve this uncertainty.

Phylogenetic Analysis of Trichaptum Based on Nuclear 18S, 5.8S and ITS Ribosomal DNA Sequences

Mycologia ◽  
1997 ◽  
Vol 89 (5) ◽  
pp. 727 ◽  
Author(s):  
Kwan S. Ko ◽  
Soon G. Hong ◽  
Hack S. Jung
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Dna ◽  
Dna Sequences

scholarly journals The life-cycle of the avian haemosporidian parasite Haemoproteus majoris, with emphasis on the exoerythrocytic and sporogonic development

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Mikas Ilgūnas ◽  
Carolina Romeiro Fernandes Chagas ◽  
Dovilė Bukauskaitė ◽  
Rasa Bernotienė ◽  
Tatjana Iezhova ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Life Cycle ◽  
Dna Sequences ◽  
Parus Major ◽  
Life Cycles ◽  
Internal Organs ◽  
Haemosporidian Parasite ◽  
Biting Midges ◽  
Vector Identity ◽  
Bayesian Phylogeny

Abstract Background Haemoproteus parasites (Haemosporida, Haemoproteidae) are cosmopolitan in birds and recent molecular studies indicate enormous genetic diversity of these pathogens, which cause diseases in non-adapted avian hosts. However, life-cycles remain unknown for the majority of Haemoproteus species. Information on their exoerythrocytic development is particularly fragmental and controversial. This study aimed to gain new knowledge on life-cycle of the widespread blood parasite Haemoproteus majoris. Methods Turdus pilaris and Parus major naturally infected with lineages hPHYBOR04 and hPARUS1 of H. majoris, respectively, were wild-caught and the parasites were identified using microscopic examination of gametocytes and PCR-based testing. Bayesian phylogeny was used to determine relationships between H. majoris lineages. Exoerythrocytic stages (megalomeronts) were reported using histological examination and laser microdissection was applied to isolate single megalomeronts for genetic analysis. Culicoides impunctatus biting midges were experimentally exposed in order to follow sporogonic development of the lineage hPHYBOR04. Results Gametocytes of the lineage hPHYBOR04 are indistinguishable from those of the widespread lineage hPARUS1 of H. majoris, indicating that both of these lineages belong to the H. majoris group. Phylogenetic analysis supported this conclusion. Sporogony of the lineage hPHYBOR04 was completed in C. impunctatus biting midges. Morphologically similar megalomeronts were reported in internal organs of both avian hosts. These were big roundish bodies (up to 360 μm in diameter) surrounded by a thick capsule-like wall and containing irregularly shaped cytomeres, in which numerous merozoites developed. DNA sequences obtained from single isolated megalomeronts confirmed the identification of H. majoris. Conclusions Phylogenetic analysis identified a group of closely related H. majoris lineages, two of which are characterized not only by morphologically identical blood stages, but also complete sporogonic development in C. impunctatus and development of morphologically similar megalomeronts. It is probable that other lineages belonging to the same group would bear the same characters and phylogenies based on partial cytb gene could be used to predict life-cycle features in avian haemoproteids including vector identity and patterns of exoerythrocytic merogony. This study reports morphologically unique megalomeronts in naturally infected birds and calls for research on exoerythrocytic development of haemoproteids to better understand pathologies caused in avian hosts.

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