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1238 records – page 1 of 124.

Second generation sequencing of three STRs D3S1358, D12S391 and D21S11 in Danes and a new nomenclature for sequenced STR alleles.

https://arctichealth.org/en/permalink/ahliterature261601
Source
Forensic Sci Int Genet. 2014 Sep;12:38-41
Publication Type
Article
Date
Sep-2014
Author
Chiara Gelardi
Eszter Rockenbauer
Sigrun Dalsgaard
Claus Børsting
Niels Morling
Source
Forensic Sci Int Genet. 2014 Sep;12:38-41
Date
Sep-2014
Language
English
Publication Type
Article
Keywords
Denmark
Gene Frequency
Humans
Microsatellite Repeats
Sequence Analysis, DNA - methods
Terminology as Topic
Abstract
Second generation sequencing (SGS) may revolutionize the field of forensic STR typing. Two of the essential requirements for implementation of an SGS based approach for forensic investigations are (1) establishment of adequate frequency databases and (2) adoption of a new STR nomenclature. We report the STR sequences and allele frequencies of three STR loci: D3S1358, D12S391 and D21S11 in 197 unrelated Danes. We used a new STR nomenclature that depicts the locus name used in forensic genetics, the length of the repeat region divided by the repeat length (typically 4 nucleotides) and detailed sequence information of possible sub-repeats and SNPs within the amplified fragment.
PubMed ID
24893347 View in PubMed
Less detail

A first glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus.

https://arctichealth.org/en/permalink/ahliterature258912
Source
J Exp Zool B Mol Dev Evol. 2014 May;322(3):177-89
Publication Type
Article
Date
May-2014
Author
Lorena Rivarola-Duarte
Christian Otto
Frank Jühling
Stephan Schreiber
Daria Bedulina
Lena Jakob
Anton Gurkov
Denis Axenov-Gribanov
Abdullah H Sahyoun
Magnus Lucassen
Jörg Hackermüller
Steve Hoffmann
Franz Sartoris
Hans-Otto Pörtner
Maxim Timofeyev
Till Luckenbach
Peter F Stadler
Source
J Exp Zool B Mol Dev Evol. 2014 May;322(3):177-89
Date
May-2014
Language
English
Publication Type
Article
Keywords
Amphipoda - genetics
Animals
Genes, Homeobox
Genome Size
Genome, Mitochondrial
Sequence Analysis, DNA
Siberia
Abstract
Eulimnogammarus verrucosus is an amphipod endemic to the unique ecosystem of Lake Baikal and serves as an emerging model in ecotoxicological studies. We report here on a survey sequencing of its genome as a first step to establish sequence resources for this species. From a single lane of paired-end sequencing data, we estimated the genome size as nearly 10 Gb and we obtained an overview of the repeat content. At least two-thirds of the genome are non-unique DNA, and a third of the genomic DNA is composed of just five families of repetitive elements, including low-complexity sequences. Attempts to use off-the-shelf assembly tools failed on the available low-coverage data both before and after removal of highly repetitive components. Using a seed-based approach we nevertheless assembled short contigs covering 33 pre-microRNAs and the homeodomain-containing exon of nine Hox genes. The absence of clear evidence for paralogs implies that a genome duplication did not contribute to the large genome size. We furthermore report the assembly of the mitochondrial genome using a new, guided "crystallization" procedure. The initial results presented here set the stage for a more complete sequencing and analysis of this large genome.
PubMed ID
24677529 View in PubMed
Less detail

First data on genetic diversity of burbot (Lota lota L.) in the Western Siberian.

https://arctichealth.org/en/permalink/ahliterature273364
Source
Dokl Biochem Biophys. 2015;463:255-8
Publication Type
Article
Date
2015
Author
Y Y Khrunyk
A V Borodin
V L Semerikov
L E Yalkovskaya
A R Koporikov
S B Rakitin
V D Bogdanov
Source
Dokl Biochem Biophys. 2015;463:255-8
Date
2015
Language
English
Publication Type
Article
Keywords
Animals
DNA, Mitochondrial - genetics
Gadiformes - genetics
Genetic Variation
Haplotypes
Sequence Analysis, DNA
Siberia
Abstract
Analysis of genetic diversity of burbot (Lota lota Linneus, 1758) mitochondrial control region (mtCR) haplotypes from geographically distant localities in the Ob-Irtysh River basin in comparison with distribution of known burbot haplotypes was conducted. mtCR fragments from burbot samples, obtained in two localities (longitudinal part of the Irtysh near Tobolsk and the Sob River, a left-bank tributary of the Ob River), were sequenced.
PubMed ID
26335825 View in PubMed
Less detail

[Genetic polymorphism, haplotype distribution, and phylogeny of Daphnia (Cladocera: Anomopoda) species from the water bodies of russia as inferred from the 16S mtDNA gene sequencing].

https://arctichealth.org/en/permalink/ahliterature289713
Source
Genetika. 2016 Jun; 52(6):672-84
Publication Type
Journal Article
Date
Jun-2016
Author
E I Zuykova
N A Bochkarev
N G Sheveleva
Source
Genetika. 2016 Jun; 52(6):672-84
Date
Jun-2016
Language
Russian
Publication Type
Journal Article
Keywords
Animals
DNA, Mitochondrial - genetics
Daphnia - genetics
Haplotypes
Phylogeny
Polymorphism, Genetic
Russia
Sequence Analysis, DNA
Abstract
The data on the genetic polymorphism of the most widespread Daphnia species occupying different water bodies of Russia are presented. The phylogenetic relationships between the examined species were established, and the haplotype networks were constructed. A fragment of the 16S mitochondrial DNA gene was used as a genetic marker. The results of molecular phylogenetic analysis generally coincided with modern concepts in the systematics of the genus Daphnia. The representatives of the divergent mitochondrial lineages within the D. longispina, D. pulex, and D. magna complex remain poorly investigated morphologically. For D. dentifera, a new habitat on the territory of Russia, namely, the water bodies of the Lake Baikal basin, was identified. A conclusion was made that the 16S mtDNA gene could be successfully used in phylogeographic analysis of the genus Daphnia.
PubMed ID
29368496 View in PubMed
Less detail

[Genetic polymorphism, haplotype distribution, and phylogeny of Daphnia (Cladocera: Anomopoda) species from the water bodies of russia as inferred from the 16S mtDNA gene sequencing].

https://arctichealth.org/en/permalink/ahliterature289555
Source
Genetika. 2016 Jun; 52(6):672-84
Publication Type
Journal Article
Date
Jun-2016
Author
E I Zuykova
N A Bochkarev
N G Sheveleva
Source
Genetika. 2016 Jun; 52(6):672-84
Date
Jun-2016
Language
Russian
Publication Type
Journal Article
Keywords
Animals
DNA, Mitochondrial - genetics
Daphnia - genetics
Haplotypes
Phylogeny
Polymorphism, Genetic
Russia
Sequence Analysis, DNA
Abstract
The data on the genetic polymorphism of the most widespread Daphnia species occupying different water bodies of Russia are presented. The phylogenetic relationships between the examined species were established, and the haplotype networks were constructed. A fragment of the 16S mitochondrial DNA gene was used as a genetic marker. The results of molecular phylogenetic analysis generally coincided with modern concepts in the systematics of the genus Daphnia. The representatives of the divergent mitochondrial lineages within the D. longispina, D. pulex, and D. magna complex remain poorly investigated morphologically. For D. dentifera, a new habitat on the territory of Russia, namely, the water bodies of the Lake Baikal basin, was identified. A conclusion was made that the 16S mtDNA gene could be successfully used in phylogeographic analysis of the genus Daphnia.
PubMed ID
29368496 View in PubMed
Less detail

Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb).

https://arctichealth.org/en/permalink/ahliterature298409
Source
BMC Bioinformatics. 2019 Feb 05; 20(Suppl 1):37
Publication Type
Journal Article
Date
Feb-05-2019
Author
Dmitry A Kuzmin
Sergey I Feranchuk
Vadim V Sharov
Alexander N Cybin
Stepan V Makolov
Yuliya A Putintseva
Natalya V Oreshkova
Konstantin V Krutovsky
Author Affiliation
Laboratory of Forest Genomics, Genome Research and Education Center, Siberian Federal University, 660036, Krasnoyarsk, Russia.
Source
BMC Bioinformatics. 2019 Feb 05; 20(Suppl 1):37
Date
Feb-05-2019
Language
English
Publication Type
Journal Article
Keywords
Arabidopsis - genetics
Genome, Plant
Larix - genetics
Prunus - genetics
Sequence Analysis, DNA - methods
Time Factors
Abstract
De novo assembling of large genomes, such as in conifers (~?12-30 Gbp), which also consist of ~?80% of repetitive DNA, is a very complex and computationally intense endeavor. One of the main problems in assembling such genomes lays in computing limitations of nucleotide sequence assembly programs (DNA assemblers). As a rule, modern assemblers are usually designed to assemble genomes with a length not exceeding the length of the human genome (3.24 Gbp). Most assemblers cannot handle the amount of input sequence data required to provide sufficient coverage needed for a high-quality assembly.
An original stepwise method of de novo assembly by parts (sets), which allows to bypass the limitations of modern assemblers associated with a huge amount of data being processed, is presented in this paper. The results of numerical assembling experiments conducted using the model plant Arabidopsis thaliana, Prunus persica (peach) and four most popular assemblers, ABySS, SOAPdenovo, SPAdes, and CLC Assembly Cell, showed the validity and effectiveness of the proposed stepwise assembling method.
Using the new stepwise de novo assembling method presented in the paper, the genome of Siberian larch, Larix sibirica Ledeb. (12.34 Gbp) was completely assembled de novo by the CLC Assembly Cell assembler. It is the first genome assembly for larch species in addition to only five other conifer genomes sequenced and assembled for Picea abies, Picea glauca, Pinus taeda, Pinus lambertiana, and Pseudotsuga menziesii var. menziesii.
PubMed ID
30717661 View in PubMed
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Refugia, differentiation and postglacial migration in arctic-alpine Eurasia, exemplified by the mountain avens (Dryas octopetala L.).

https://arctichealth.org/en/permalink/ahliterature82240
Source
Mol Ecol. 2006 Jun;15(7):1827-40
Publication Type
Article
Date
Jun-2006
Author
Skrede Inger
Eidesen Pernille Bronken
Portela Rosalía Piñeiro
Brochmann Christian
Author Affiliation
National Centre for Biosystematics, Natural History Museum, University of Oslo, PO Box 1172, Blindern, NO-0318 Oslo, Norway. inger.skrede@nhm.uio.no
Source
Mol Ecol. 2006 Jun;15(7):1827-40
Date
Jun-2006
Language
English
Publication Type
Article
Keywords
Arctic Regions
Environment
Gene Flow
Geography
Phylogeny
Polymorphism, Genetic
Rosaceae - classification - genetics
Sequence Analysis, DNA
Abstract
Many arctic-alpine organisms have vast present-day ranges across Eurasia, but their history of refugial isolation, differentiation and postglacial expansion is poorly understood. The mountain avens, Dryas octopetala sensu lato, is a long-lived, wind-dispersed, diploid shrub forming one of the most important components of Eurasian tundras and heaths in terms of biomass. We address differentiation and migration history of the species with emphasis on the western and northern Eurasian parts of its distribution area, also including some East Greenlandic and North American populations (partly referred to as the closely related D. integrifolia M. Vahl). We analysed 459 plants from 52 populations for 155 amplified fragment length polymorphisms (AFLP) markers. The Eurasian plants were separated into two main groups, probably reflecting isolation and expansion from two major glacial refugia, situated south and east of the North European ice sheets, respectively. Virtually all of northwestern Europe as well as East Greenland have been colonized by the Southern lineage, whereas northwest Russia, the Tatra Mountains and the arctic archipelago of Svalbard have been colonized by the Eastern lineage. The data indicate a contact zone between the two lineages in northern Scandinavia and possibly in the Tatra Mountains. The two single populations analysed from the Caucasus and Altai Mountains were most closely related to the Eastern lineage but were strongly divergent from the remaining eastern populations, suggesting survival in separate refugia at least during the last glaciation. The North American populations grouped with those from East Greenland, irrespective of their taxonomic affiliation, but this may be caused by independent hybridization with D. integrifolia and therefore not reflect the true relationship between populations from these areas.
PubMed ID
16689901 View in PubMed
Less detail

Pseudo-parallel patterns of disjunctions in an Arctic-alpine plant lineage.

https://arctichealth.org/en/permalink/ahliterature296093
Source
Mol Phylogenet Evol. 2018 06; 123:88-100
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Date
06-2018
Author
Rebecca L Stubbs
Ryan A Folk
Chun-Lei Xiang
Douglas E Soltis
Nico Cellinese
Author Affiliation
Department of Biology, University of Florida, Gainesville, FL 32611, USA; Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA. Electronic address: stubbsrl@ufl.edu.
Source
Mol Phylogenet Evol. 2018 06; 123:88-100
Date
06-2018
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Keywords
Biodiversity
Ecosystem
Likelihood Functions
North America
Phylogeny
Phylogeography
Saxifragaceae - classification
Sequence Analysis, DNA
Species Specificity
Abstract
Disjunct distributions have intrigued biologists for centuries. Investigating these biogeographic patterns provides insight into speciation and biodiversity at multiple spatial and phylogenetic scales. Some disjunctions have been intensively studied, yet others have been largely overlooked and remain poorly understood. Among the lesser-known disjunction patterns is that between the mountain ranges of western North America. Flora and fauna endemic to the mountains of this region provide important systems for investigating causes and results of disjunctions, given the relatively recent geological formation of this area and the intense climatic fluctuations that have occurred since its formation. In Micranthes (Saxifragaceae), which has high rates of montane endemism, two species, M. bryophora and M. tolmiei, show this biogeographical pattern. By reconstructing a time-calibrated phylogeny based on 518 low-copy nuclear markers and including multiple populations of each species from the Coast Ranges, Cascades, Sierra Nevada, and Rocky Mountains, this study provides a biogeographical and temporal framework for the evolution of Micranthes in western North America. Strongly supported east-west differentiated clades are recovered for M. bryophora and M. tolmiei in both maximum likelihood and coalescent-based species tree reconstructions. Biogeographic analysis suggests different patterns of dispersal for both taxa and the dating analyses recovered contrasting ages for each clade. Due to both the different geographic patterns and the timing of the initial diversification of each taxon corresponding to different geologic and climatic events, the disjunction patterns shown for these taxa are suggested to be an example of biogeographical pseudocongruence.
PubMed ID
29496541 View in PubMed
Less detail

Complete genome of Marinobacter psychrophilus strain 20041(T) isolated from sea-ice of the Canadian Basin.

https://arctichealth.org/en/permalink/ahliterature282526
Source
Mar Genomics. 2016 Aug;28:1-3
Publication Type
Article
Date
Aug-2016
Author
Lai Song
Lufeng Ren
Li Wang
Yong Yu
Xumin Wang
Guiming Liu
Source
Mar Genomics. 2016 Aug;28:1-3
Date
Aug-2016
Language
English
Publication Type
Article
Keywords
Arctic Regions
Canada
Genome, Bacterial
Ice Cover - microbiology
Marinobacter - classification - genetics
Phylogeny
Sequence Analysis, DNA
Abstract
Marinobacter psychrophilus strain 20041(T) was isolated from sea-ice of the Canadian Basin. Here we report the complete sequence of the 3.9-Mb genome of this strain. The complete genome sequence will facilitate the study of the physiology and evolution of Marinobacter species.
PubMed ID
26908308 View in PubMed
Less detail

Identification of the novel HLA-DQB1*02:85 and HLA-DRB1*01:01:30 alleles in Russian individuals.

https://arctichealth.org/en/permalink/ahliterature291005
Source
HLA. 2017 Aug; 90(2):135-136
Publication Type
Journal Article
Date
Aug-2017
Author
E Kuzmich
S Tyapushkina
A Alyanskiy
B Afanasyev
Author Affiliation
HLA Laboratory, Pavlov First Saint Petersburg State Medical University, Saint Petersburg, Russia.
Source
HLA. 2017 Aug; 90(2):135-136
Date
Aug-2017
Language
English
Publication Type
Journal Article
Keywords
Alleles
HLA-DQ beta-Chains - genetics
HLA-DRB1 Chains - genetics
Humans
Russia
Sequence Analysis, DNA
Abstract
Two novel HLA class II alleles, HLA-DQB1*02:85 and HLA-DRB1*01:01:30, were detected in Russian individuals.
PubMed ID
28470933 View in PubMed
Less detail

1238 records – page 1 of 124.