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The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly.

https://arctichealth.org/en/permalink/ahliterature298452
Source
PLoS One. 2018; 13(9):e0204076
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
2018
Author
Kris A Christensen
Eric B Rondeau
David R Minkley
Jong S Leong
Cameron M Nugent
Roy G Danzmann
Moira M Ferguson
Agnieszka Stadnik
Robert H Devlin
Robin Muzzerall
Michael Edwards
William S Davidson
Ben F Koop
Author Affiliation
Fisheries and Oceans Canada, Centre for Aquaculture and Environmental Research, West Vancouver, British Columbia, Canada.
Source
PLoS One. 2018; 13(9):e0204076
Date
2018
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Adaptation, Physiological - genetics
Animals
Arctic Regions
Chromosome Mapping
Cold Temperature
Female
Genetic Linkage
Genetic markers
Genetic Speciation
Genome
Male
Oncorhynchus mykiss - classification - genetics
Phenotype
Phylogeny
Salmo salar - classification - genetics
Transcriptome
Trout - classification - genetics
Abstract
Arctic charr have a circumpolar distribution, persevere under extreme environmental conditions, and reach ages unknown to most other salmonids. The Salvelinus genus is primarily composed of species with genomes that are structured more like the ancestral salmonid genome than most Oncorhynchus and Salmo species of sister genera. It is thought that this aspect of the genome may be important for local adaptation (due to increased recombination) and anadromy (the migration of fish from saltwater to freshwater). In this study, we describe the generation of a new genetic map, the sequencing and assembly of the Arctic charr genome (GenBank accession: GCF_002910315.2) using the newly created genetic map and a previous genetic map, and present several analyses of the Arctic charr genes and genome assembly. The newly generated genetic map consists of 8,574 unique genetic markers and is similar to previous genetic maps with the exception of three major structural differences. The N50, identified BUSCOs, repetitive DNA content, and total size of the Arctic charr assembled genome are all comparable to other assembled salmonid genomes. An analysis to identify orthologous genes revealed that a large number of orthologs could be identified between salmonids and many appear to have highly conserved gene expression profiles between species. Comparing orthologous gene expression profiles may give us a better insight into which genes are more likely to influence species specific phenotypes.
PubMed ID
30212580 View in PubMed
Less detail

The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly.

https://arctichealth.org/en/permalink/ahliterature294866
Source
PLoS One. 2018; 13(9):e0204076
Publication Type
Journal Article
Date
2018
Author
Kris A Christensen
Eric B Rondeau
David R Minkley
Jong S Leong
Cameron M Nugent
Roy G Danzmann
Moira M Ferguson
Agnieszka Stadnik
Robert H Devlin
Robin Muzzerall
Michael Edwards
William S Davidson
Ben F Koop
Author Affiliation
Fisheries and Oceans Canada, Centre for Aquaculture and Environmental Research, West Vancouver, British Columbia, Canada.
Source
PLoS One. 2018; 13(9):e0204076
Date
2018
Language
English
Publication Type
Journal Article
Abstract
Arctic charr have a circumpolar distribution, persevere under extreme environmental conditions, and reach ages unknown to most other salmonids. The Salvelinus genus is primarily composed of species with genomes that are structured more like the ancestral salmonid genome than most Oncorhynchus and Salmo species of sister genera. It is thought that this aspect of the genome may be important for local adaptation (due to increased recombination) and anadromy (the migration of fish from saltwater to freshwater). In this study, we describe the generation of a new genetic map, the sequencing and assembly of the Arctic charr genome (GenBank accession: GCF_002910315.2) using the newly created genetic map and a previous genetic map, and present several analyses of the Arctic charr genes and genome assembly. The newly generated genetic map consists of 8,574 unique genetic markers and is similar to previous genetic maps with the exception of three major structural differences. The N50, identified BUSCOs, repetitive DNA content, and total size of the Arctic charr assembled genome are all comparable to other assembled salmonid genomes. An analysis to identify orthologous genes revealed that a large number of orthologs could be identified between salmonids and many appear to have highly conserved gene expression profiles between species. Comparing orthologous gene expression profiles may give us a better insight into which genes are more likely to influence species specific phenotypes.
Notes
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PubMed ID
30212580 View in PubMed
Less detail

Clinical and genetic epidemiology of Bardet-Biedl syndrome in Newfoundland: a 22-year prospective, population-based, cohort study.

https://arctichealth.org/en/permalink/ahliterature176696
Source
Am J Med Genet A. 2005 Feb 1;132A(4):352-60
Publication Type
Article
Date
Feb-1-2005
Author
Susan J Moore
Jane S Green
Yanli Fan
Ashvinder K Bhogal
Elizabeth Dicks
Bridget A Fernandez
Mark Stefanelli
Christopher Murphy
Benvon C Cramer
John C S Dean
Philip L Beales
Nicholas Katsanis
Anne S Bassett
William S Davidson
Patrick S Parfrey
Author Affiliation
Clinical Epidemiology Unit, Memorial University, St John's, Newfoundland, Canada.
Source
Am J Med Genet A. 2005 Feb 1;132A(4):352-60
Date
Feb-1-2005
Language
English
Publication Type
Article
Keywords
Adolescent
Adult
Aged
Bardet-Biedl Syndrome - epidemiology - genetics - pathology
Child
Child, Preschool
Cohort Studies
Female
Genotype
Group II Chaperonins
Humans
Infant
Male
Microtubule-Associated Proteins
Middle Aged
Molecular Chaperones - genetics
Mutation
Newfoundland and Labrador - epidemiology
Pedigree
Phenotype
Prevalence
Proteins - genetics
Time Factors
Abstract
Bardet-Biedl syndrome (BBS) and Laurence-Moon syndrome (LMS) have a similar phenotype, which includes retinal dystrophy, obesity, and hypogenitalism. They are differentiated by the presence of spasticity and the absence of polydactyly in LMS. The aims of this study were to describe the epidemiology of BBS and LMS, further define the phenotype, and examine genotype-phenotype correlation. The study involved 46 patients (26 males, 20 females) from 26 families, with a median age of 44 years (range 1-68 years). Assessments were performed in 1986, 1993, and 2001 and included neurological assessments, anthropometric measurements, and clinical photographs to assess dysmorphic features. The phenotype was highly variable within and between families. Impaired co-ordination and ataxia occurred in 86% (18/21). Thirty percent (14/46) met criteria for psychiatric illness; other medical problems included cholecystectomy in 37% (17/46) and asthma in 28% (13/46). Dysmorphic features included brachycephaly, large ears, and short, narrow palpebral fissures. There was no apparent correlation of clinical or dysmorphic features with genotype. Two patients were diagnosed clinically as LMS but both had mutations in a BBS gene. The features in this population do not support the notion that BBS and LMS are distinct. The lack of a genotype-phenotype correlation implies that BBS proteins interact and are necessary for the development of many organs.
Notes
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PubMed ID
15637713 View in PubMed
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Clinical and genetic epidemiology of inherited renal disease in Newfoundland.

https://arctichealth.org/en/permalink/ahliterature190063
Source
Kidney Int. 2002 Jun;61(6):1925-34
Publication Type
Article
Date
Jun-2002
Author
Patrick S Parfrey
William S Davidson
Jane S Green
Author Affiliation
Department of Medicine and Biochemistry, Memorial University, St. John's, Newfoundland, Canada. pparfrey@mun.ca
Source
Kidney Int. 2002 Jun;61(6):1925-34
Date
Jun-2002
Language
English
Publication Type
Article
Keywords
Bardet-Biedl Syndrome - genetics
Female
Genes, Dominant
Genes, Recessive
Genetic Predisposition to Disease
Humans
Hypertension - genetics
Kidney Diseases - epidemiology - genetics
Kidney Failure, Chronic - genetics
Newfoundland and Labrador - epidemiology
Polycystic Kidney, Autosomal Dominant - genetics
Pre-Eclampsia - genetics
Pregnancy
Pregnancy Complications, Cardiovascular
Prevalence
von Hippel-Lindau Disease - genetics
Abstract
Clinical and genetic epidemiology of inherited renal disease in Newfoundland. Newfoundland's geography, settlement, and socioeconomic development have produced a population useful for the study of genetic diseases. This review examines the clinical and genetic epidemiologic studies of inherited renal diseases undertaken in this population in the past 15 years. Common founder effects and large families through each generation provided very extensive pedigrees with autosomal-dominant diseases, such as polycystic kidney disease (PKD) and von Hippel-Lindau disease. In the former disease the diagnostic utility of renal ultrasound was determined, as was the prognostic impact of genotype, the role of the renin-angiotensin system in the pre-hypertensive phase, the potential for somatic mutations of the PKD2 gene, or the combination of mutations in the PKD1 and PKD2 genes, in single cells to induce cysts, and the demonstration that human transheterozygotes of PKD1 and -2 are not embryonically lethal. The presence of multiple genetic isolates and the high coefficient of kinship have predisposed to autosomal recessive diseases such as Bardet-Biedl syndrome (BBS), autosomal-recessive PKD, primary hyperoxaluria, and dihydroxyadenine urolithiasis. We have reported the clinical manifestations and natural history of the BBS, with particular emphasis on the fact that renal abnormalities are cardinal manifestations of the disease, the presence of at least six different genotypes, the identity and function of the BBS6 gene, and the presence of three different BBS6 mutations. Because of its relatively homogenous origins and high coefficient of kinship, Newfoundland's population also may be useful for the study of complex diseases such as preeclampsia. Using unbiased ascertainment and strict diagnostic criteria, we have found a significant risk of preeclampsia and non-proteinuric gestational hypertension in sisters of probands with preeclampsia, particularly when probands are defined by severity of preeclampsia, an observation that supports a study to search for susceptibility genes. We conclude that collaborations between clinical epidemiologists and molecular geneticists, using the Newfoundland population, have provided important clinical and mechanistic insights into inherited renal diseases.
PubMed ID
12028433 View in PubMed
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Design and characterization of an 87k SNP genotyping array for Arctic charr (Salvelinus alpinus).

https://arctichealth.org/en/permalink/ahliterature299045
Source
PLoS One. 2019; 14(4):e0215008
Publication Type
Journal Article
Date
2019
Author
Cameron M Nugent
Jong S Leong
Kris A Christensen
Eric B Rondeau
Matthew K Brachmann
Anne A Easton
Christine L Ouellet-Fagg
Michelle T T Crown
William S Davidson
Ben F Koop
Roy G Danzmann
Moira M Ferguson
Author Affiliation
University of Guelph, Department of Integrative Biology, Guelph, Ontario, Canada.
Source
PLoS One. 2019; 14(4):e0215008
Date
2019
Language
English
Publication Type
Journal Article
Abstract
We have generated a high-density, high-throughput genotyping array for characterizing genome-wide variation in Arctic charr (Salvelinus alpinus). Novel single nucleotide polymorphisms (SNPs) were identified in charr from the Fraser, Nauyuk and Tree River aquaculture strains, which originated from northern Canada and fish from Iceland using high coverage sequencing, reduced representation sequencing and RNA-seq datasets. The array was designed to capture genome-wide variation from a diverse suite of Arctic charr populations. Cross validation of SNPs from various sources and comparison with previously published Arctic charr SNP data provided a set of candidate SNPs that generalize across populations. Further candidate SNPs were identified based on minor allele frequency, association with RNA transcripts, even spacing across intergenic regions and association with the sex determining (sdY) gene. The performance of the 86,503 SNP array was assessed by genotyping Fraser, Nauyuk and Tree River strain individuals, as well as wild Icelandic Arctic charr. Overall, 63,060 of the SNPs were polymorphic within at least one group and 36.8% were unique to one of the four groups, suggesting that the array design allows for characterization of both within and across population genetic diversity. The concordance between sdY markers and known phenotypic sex indicated that the array can accurately determine the sex of individuals based on genotype alone. The Salp87k genotyping array provides researchers and breeders the opportunity to analyze genetic variation in Arctic charr at a more detailed level than previously possible.
PubMed ID
30951561 View in PubMed
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Retraction: The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly.

https://arctichealth.org/en/permalink/ahliterature303539
Source
PLoS One. 2021; 16(2):e0247083
Publication Type
Retraction of Publication
Date
2021

Ribosomal genes and heat shock proteins as putative markers for chronic, sub-lethal heat stress in Arctic charr: applications for aquaculture and wild fish.

https://arctichealth.org/en/permalink/ahliterature101495
Source
Physiol Genomics. 2011 Jul 12;
Publication Type
Article
Date
Jul-12-2011
Author
Nicole L Quinn
Colin R McGowan
Glenn A Cooper
Ben F Koop
William S Davidson
Author Affiliation
Simon Fraser University.
Source
Physiol Genomics. 2011 Jul 12;
Date
Jul-12-2011
Language
English
Publication Type
Article
Abstract
Arctic charr thrive at high densities and can live in freshwater year round, making this species especially suitable for inland, closed containment aquaculture. However, it is a cold water salmonid, which both limits where the species can be farmed and places wild populations at particular risk to climate change. Previously, we identified genes associated with tolerance and intolerance to acute, lethal temperature stress in Arctic charr. However, there remained a need to examine the genes involved in the stress response to more realistic temperatures that could be experienced during a summer heat wave in grow-out tanks that are not artificially cooled, or under natural conditions. Here, we exposed Arctic charr to sub-lethal heat stress of 15-18°C for 72 hours, and gill tissues extracted before, during (i.e., at 72 hrs), immediately after cooling and after 72 hours of recovery at ambient temperature (6°C) were used for gene expression profiling by microarray and qPCR analyses. The results revealed an expected pattern for heat shock protein (Hsp) expression, which was highest during heat exposure, with significantly reduced expression (approaching control levels) quickly thereafter. We also found that the expression of numerous ribosomal proteins was significantly elevated immediately and 72 hrs after cooling, suggesting that the gill tissues were undergoing ribosome biogenesis while recovering from damage caused by heat stress. We suggest that these are candidate gene targets for the future development of genetic markers for broodstock development or for monitoring temperature stress and recovery in wild or cultured conditions.
PubMed ID
21750231 View in PubMed
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7 records – page 1 of 1.