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- Stjelja Arvelius, Suzana
(författare)
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Evolutionary history and adaptive significance of the polymorphic Pan I in migratory and stationary populations of Atlantic cod (Gadus morhua)
- 2015
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Ingår i: Marine Genomics. - : Elsevier BV. - 1874-7787. ; 22, s. 45-54
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Tidskriftsartikel (refereegranskat)abstract
- The synaptophysin (SYP) family comprises integral membrane proteins involved in vesicle-trafficking events, but the physiological function of several members has been enigmatic for decades. The presynaptic SYP protein controls neurotransmitter release, while SYP-like 2 (SYPL2) contributes to maintain normal Ca2+-signaling in the skeletal muscles. The polymorphic pantophysin (Pan I) of Atlantic cod shows strong genetic divergence between stationary and migratory populations, which seem to be adapted to local environmental conditions. We have investigated the functional involvement of Pan I in the different ecotypes by analyzing the 1) phylogeny, 2) spatio-temporal gene expression, 3) structure-function relationship of the Pan I-A and I-B protein variants, and 4) linkage to rhodopsin (rho) recently proposed to be associated with different light sensitivities in Icelandic populations of Atlantic cod. We searched for SYP family genes in phylogenetic key species and identified a single syp-related gene in three invertebrate chordates, while four members, Syp, Sypl1, Sypl2 and synaptoporin (Synpr), were found in tetrapods, Comoran coelacanth and spotted gar. Teleost fish were shown to possess duplicated syp, sypl2 and synpr genes of which the sypl2b paralog is identical to Pan I. The ubiquitously expressed cod Pan I codes for a tetra-spanning membrane protein possessing five amino acid substitutions in the first intravesicular loop, but only minor structural differences were shown between the allelic variants. Despite sizable genomic distance (>2.5 Mb) between Pan land rho, highly significant linkage disequilibrium was found by genotyping shallow and deep water juvenile settlers predominated by the Pan I-A-rho(A) and Pan I-B-rho(B) haplotypes, respectively. However, the predicted rhodopsin protein showed no amino add changes, while multiple polymorphic sites in the upstream region might affect the gene expression and pigment levels in stationary and migratory cod. Alternatively, other strongly linked genes might be responsible for the sharp settling stratification of juveniles and the different vertical behavior patterns of adult Atlantic cod. (C) 2015 Elsevier B.V. All rights reserved.
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- Stjelja Arvelius, Suzana, et al.
(författare)
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Genetic characterisation of canine cardiomyopathies
- 2013
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Canine domestication and breed creation have shaped a genome with a structure advantageous for genetic disease mapping. Within a dog breed, linkage disequilibrium (LD) is extensive and haplotype blocks with no recombination are long (0.5-1 mega bases), while between breeds LD and haplotype blocks are short (~10 kilo bases). Genetic diseases are common among different dog breeds and several such diseases are breed-specific. Therefore, genetic risk factors are more easily identified. Moreover, dogs and humans share the majority of their genes as well as common environment and similar diseases affect both species. Identification of causative and risk variants for canine genetic disease requires fewer markers and fewer individuals compared with humans and it may result in improved diagnostic settings and treatment options in both dogs and humans. In several genome-wide association studies (GWAS) conducted at the Swedish University of Agricultural Sciences, genetic risk factors underlying both monogenic Mendelian traits (e.g. the white coat color in Boxers and the ridge phenotype in Rhodesian Ridgebacks) and complex diseases in dogs (e.g. Systemic Lupus Erythematosus (SLE)-related disease in Nova Scotia duck tolling retriever and Atopic Dermatitis (AD) in German shepherds) have been successfully identified. The principles for disease-mapping procedures and advantages and challenges of GWAS, and how such results can be applied will be discussed. Dilated Cardiomyopathy (DCM) in the high-risk Great Dane and New Foundland breeds will be discussed as examples. DCM is one of the most prevalent and the most heterogeneous cardiomyopathies in both humans and large-sized dog breeds. The disease is characterized by dilation, enlargement and weakened contraction of the left ventricular cardiac chamber. In later disease states all four chambers may be affected, often leading to development of congestive heart failure. GWAS have been performed using clinically well-defined case-control populations, mapped using a high density 173.000 Single Nucleotide Polymorphism (SNP) Illumina array and analyzed with PLINK and GenABEL softwares.
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- Stjelja Arvelius, Suzana
(författare)
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Genomics of Plasmodiophora brassicae
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Plasmodiophora brassicae is a soil-borne pathogen that infects roots of plants in Brassicaceae and causes enlarged roots or clubs known as the clubroot disease. Details of its complex life cycle and particularly the molecular basis of its strategies to master defenses and alter metabolism of plant hosts are still largely unknown. The general aim of this thesis was to enhance the genomic knowledge on P. brassicae and its intimate relationship with a plant host. We developed a protocol for extraction of large amounts of high-quality DNA from pathogen resting spores that allowed us to apply long-read PacBio sequencing. De-novo assembly of the P. brassicae e3 strain generated a 25.2 Mb nuclear genome and a mitochondrial genome (114.6 kb). Twenty nuclear contigs were assembled of which 13 from telomere-to-telomere, thanks to the resolution of highly repetitive sequences. As much as 11.5% of the genome was assigned to repetitive sequences, a higher proportion than previously estimated. The most abundant were transposable elements (TEs) such as Copia and Gypsy and unclassified interspersed repeats. They were particularly clustered in telomeric, sub-telomeric and large regions with complex structural variation found on each contig. Among 9,231 predicted protein-coding genes in the nuclear genome, we identified 314 small, secreted proteins as P. brassicae effector candidates. They were distributed along all contigs. TEs and unclassified repeats were found within a 3 kb distance from more than a third of the predicted effectors. We further detected enrichment of the effector candidates with a motif rich in valine, leucine and alanine amino acids. Annotation of the circular mitochondrial genome revealed a compact and complex sequence organization with intron-rich genes, a new splicing mechanism and a previously not resolved 12 kb repetitive region. Our findings and the new genome sequences, currently representing the only P. brassicae long-read assembly, form a valuable resource for comparative and functional analyses.
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- Stjelja Arvelius, Suzana, et al.
(författare)
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The architecture of the Plasmodiophora brassicae nuclear and mitochondrial genomes
- 2019
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Plasmodiophora brassicae is a soil-borne pathogen that attacks roots of cruciferous plants causing clubroot disease. The pathogen belongs to the Plasmodiophorida order in Phytomyxea. Here we used long-read SMRT technology to clarify the P. brassicae e3 genomic constituents along with comparative and phylogenetic analyses. Twenty contigs representing the nuclear genome and one mitochondrial (mt) contig were generated, together comprising 25.1 Mbp. Thirteen of the 20 nuclear contigs represented chromosomes from telomere to telomere characterized by [TTTTAGGG] sequences. Seven active gene candidates encoding synaptonemal complex-associated and meiotic-related protein homologs were identified, a finding that argues for possible genetic recombination events. The circular mt genome is large (114,663 bp), gene dense and intron rich. It shares high synteny with the mt genome of Spongospora subterranea, except in a unique 12 kb region delimited by shifts in GC content and containing tandem minisatellite- and microsatellite repeats with partially palindromic sequences. De novo annotation identified 32 protein-coding genes, 28 structural RNA genes and 19 ORFs. ORFs predicted in the repeat-rich region showed similarities to diverse organisms suggesting possible evolutionary connections. The data generated here form a refined platform for the next step involving functional analysis, all to clarify the complex biology of P. brassicae.
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