The seas of the North Pacific Ocean are characterized by a large variety of fish fauna, including endemic species. Molecular genetic methods, often based on DNA barcoding approaches, have been recently used to determine species boundaries and identify cryptic diversity within these species. This study complements the DNA barcode library of fish from the Northeast Pacific area. A library based on 154 sequences of the mitochondrial gene from 44 species was assembled and analyzed. It was found that 39 species (89%) can be unambiguously identified by the clear thresholds forming a barcoding gap. Deviations from the standard 2% threshold value resulted in detection of the species in the sample, which is not typical for the eastern part of the Bering Sea. This barcoding gap also made it possible to identify naturally occurring low values of interspecific divergence of eulittoral taxa and the deep-sea genus . Synonymy of the genus in favor of the genus is suggested based on both the original and previously published data.
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http://dx.doi.org/10.1139/gen-2020-0192 | DOI Listing |
Sci Rep
December 2024
School of Health and Life Sciences, Teesside University, Middlesbrough, UK.
Outdoor microcosms, metabarcoding with next-generation sequencing of the 16S rRNA bacterial gene, total body score (TBS) and physicochemical analyses were used to monitor Mus musculus decomposition aboveground (A) and in the subsurface (S), and compared to soil-only controls (C). As determined by MaAsLin2 analysis, significant shifts in bacterial communities at 30 cm depths within the A, S and C treatments distinguished control from experimental soils, and between aboveground and subsurface deposition, demonstrating the potential for gravesoil discrimination during the first 90 days. For example, Dokdonella (p = 0.
View Article and Find Full Text PDFBiotechniques
December 2024
Laboratorio de Parasitología Molecular, Vicerrectoría de Investigaciones, Universidad El Bosque, Bogotá, Colombia.
In 2006, a PCR method was introduced to subtype by Sanger sequencing of an ≈610 bp amplicon of the 18S rRNA gene. This method, known as barcoding-PCR, has become widespread, although the primer pair used can amplify non- sequences, which can result in false positives. Barcoding-PCR is most effective with DNA extracted from cultures, limiting its sensitivity when used directly with stool samples.
View Article and Find Full Text PDFSci Rep
December 2024
National Center for Biotechnology, 13/5, Korgalzhyn Road, 010000, Astana, Kazakhstan.
Ribes janczewskii is a rare and valuable plant known for its resistance to spring frosts, pests, and diseases. It is used in hybridization to develop resistant currant varieties but is on the verge of extinction, listed in Kazakhstan Red Book. This study developed a micropropagation and slow-growth storage protocol for conservation.
View Article and Find Full Text PDFMethods Mol Biol
December 2024
The James Hutton Institute, Dundee, UK.
We describe a protocol to amplify DNA barcodes of known and unknown taxa of Phytophthora and related plant pathogenic oomycetes from a range of environments. The methods focus on sampling pathogen propagules from water using in situ sampling and filtration equipment and buffers that enable efficient storage and DNA extraction for later downstream processing.
View Article and Find Full Text PDFMethods Protoc
December 2024
Department of Natural Sciences, University of South Carolina Beaufort, 1 University Boulevard, Bluffton, SC 29909, USA.
The multifunctional catalytic hemoglobin from the terebellid polychaete , also named dehaloperoxidase (DHP), utilizes the typical oxygen transport function in addition to four observed activities involved in substrate oxidation. The multifunctional ability of DHP is presently a rare observation, and there exists a limitation for how novel dehaloperoxidases can be identified from macrobenthic infauna. In order to discover more infaunal DHP-bearing candidates, we have devised a facilitated method for an accurate taxonomic identification that places visual and molecular taxonomic approaches in parallel.
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