| 1. |
- Kjaerner-Semb, Erik, et al.
(författare)
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Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection
- 2016
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 17
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Tidskriftsartikel (refereegranskat)abstract
- Background: Populations of Atlantic salmon display highly significant genetic differences with unresolved molecular basis. These differences may result from separate postglacial colonization patterns, diversifying natural selection and adaptation, or a combination. Adaptation could be influenced or even facilitated by the recent whole genome duplication in the salmonid lineage which resulted in a partly tetraploid species with duplicated genes and regions. Results: In order to elucidate the genes and genomic regions underlying the genetic differences, we conducted a genome wide association study using whole genome resequencing data from eight populations from Northern and Southern Norway. From a total of similar to 4.5 million sequencing-derived SNPs, more than 10 % showed significant differentiation between populations from these two regions and ten selective sweeps on chromosomes 5, 10, 11, 13-15, 21, 24 and 25 were identified. These comprised 59 genes, of which 15 had one or more differentiated missense mutation. Our analysis showed that most sweeps have paralogous regions in the partially tetraploid genome, each lacking the high number of significant SNPs found in the sweeps. The most significant sweep was found on Chr 25 and carried several missense mutations in the antiviral mx genes, suggesting that these populations have experienced differing viral pressures. Interestingly the second most significant sweep, found on Chr 5, contains two genes involved in the NF-KB pathway (nkap and nkrf), which is also a known pathogen target that controls a large number of processes in animals. Conclusion: Our results show that natural selection acting on immune related genes has contributed to genetic divergence between salmon populations in Norway. The differences between populations may have been facilitated by the plasticity of the salmon genome. The observed signatures of selection in duplicated genomic regions suggest that the recently duplicated genome has provided raw material for evolutionary adaptation.
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| 2. |
- Ozerov, Mikhail, et al.
(författare)
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Differential expression and alternative splicing analyses of multiple tissues reveal albinism-associated genes in the Wels catfish (Silurus glanis)
- 2024
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Ingår i: Comparative Biochemistry and Physiology - Part B: Biochemistry and Molecular Biology. - 1096-4959 .- 1879-1107. ; 271
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Tidskriftsartikel (refereegranskat)abstract
- Albinism is a widespread departure from a typical body colouration due to altered melanin production. The Wels catfish (Silurus glanis) is among the largest freshwater fish species in the world, and albino individuals occur both in the wild and in aquaculture. Here, we performed transcriptome-wide analysis of albino and normally pigmented S. glanis using four tissues (skin, dorsal fin, whole eye and liver) to identify genes associated with albinism by exploring patterns of differential expression (DE) and differential alternative splicing (DAS). Multitissue analyses revealed a large number of genes in skin (n = 1355) and fin (n = 614) tissue associated with the albino phenotype in S. glanis, while the number of DE genes in eye and liver tissues was lower (n = 188, n = 189, respectively). Several DE genes across multiple tissues were detected as the most promising candidates (e.g., hsp4, hsp90b1, raph1, uqcrfs1, adcy-family and wnt-family) potentially causally linked to the albino phenotype in Wels catfish. Moreover, our findings supported earlier observations of physiological differences between albino and normally pigmented individuals, particularly in energy metabolism and immune response. In contrast, there were only a few pigmentation-related genes observed among DAS genes (4 in skin, 2 in fin), the overlap between DAS and DE genes was low (n = 25) and did not include known pigmentation-related genes. This suggests that DAS and DE in Wels catfish are, to a large extent, independent processes, and the observed alternative splicing cases are probably not causally linked with albinism in S. glanis. This work provides the first transcriptome-wide multi-tissue insights into the albinism of Wels catfish and serves as a valuable resource for further understanding the genetic mechanisms of pigmentation in fish.
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| 3. |
- Ozerov, Mikhail, et al.
(författare)
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Distribution and prevalence of the myxozoan parasite Tetracapsuloides bryosalmonae in northernmost Europe: analysis of three salmonid species
- 2022
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Ingår i: Diseases of Aquatic Organisms. - : Inter-Research Science Center. - 0177-5103 .- 1616-1580. ; 151, s. 37-49
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Tidskriftsartikel (refereegranskat)abstract
- Global climate change is altering the abundance and spread of many aquatic parasites and pathogens. Proliferative kidney disease (PKD) of salmonids caused by the myxozoan Tetracapsuloides bryosalmonae is one such emerging disorder, and its impact is expected to increase with rising water temperature. Yet, the distribution and prevalence of T. bryosalmonae in Northern Europe remain poorly characterized. Here, we studied 43 locations in 27 rivers in northernmost Norway and Finland to describe T. bryosalmonae infection frequency and patterns in 1389 juvenile salmonids. T. bryosalmonae was discovered in 12 out of 27 rivers (44%) and prevalence ranged from 4.2 to 55.5% in Atlantic salmon and from 5.8 to 75% in brown trout among infected rivers. In sympatric populations, brown trout was more frequently infected with T. bryosalmonae than was salmon. Age-specific parasite prevalence patterns revealed that in contrast to lower latitudes, the infection of juvenile fish predominantly occurs during the second summer or later. Temperature monitoring over 2 yr indicated that the mean water temperature in June was 2.1 to 3.2 degrees C higher in rivers containing T. bryosalmonae compared to parasite-free rivers, confirming the important role of temperature in parasite occurrence. Temporal comparison in T. bryosalmonae prevalence over a 10 yr period in 11 rivers did not reveal any signs of contemporary parasite spread to previously uninfected rivers. However, the wide distribution of T. bryosalmonae in rivers flowing to the Barents Sea indicates that climate change and heat waves may cause new disease outbreaks in northern regions.
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| 4. |
- Ozerov, Mikhail, et al.
(författare)
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DNA metabarcoding reveals spatial and temporal variation of fish eye fluke communities in lake ecosystems
- 2024
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Ingår i: International Journal for Parasitology. - 0020-7519 .- 1879-0135. ; 54, s. 33-46
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Tidskriftsartikel (refereegranskat)abstract
- Eye flukes (Diplostomidae) are diverse and abundant trematode parasites that form multi-species communities in fish with negative effects on host fitness and survival. However, the environmental factors and host-related characteristics that determine species diversity, composition, and coexistence in such communities remain poorly understood. Here, we developed a cost-effective cox1 region-specific DNA metabarcoding approach to characterize parasitic diplostomid communities in two common fish species (Eurasian perch and common roach) collected from seven temperate lakes in Estonia. We found considerable inter- and intra-lake, as well as inter-host species, variation in diplostomid communities. Sympatric host species characterization revealed that parasite communities were typically more diverse in roach than perch. Additionally, we detected five positive and two negative diplostomid species associations in roach, whereas only a single negative association was observed in perch. These results indicate that diplostomid communities in temperate lakes are complex and dynamic systems exhibiting both spatial and temporal heterogeneity. They are influenced by various environmental factors and by hostparasite and inter-parasite interactions. We expect that the described methodology facilitates ecological and biodiversity research of diplostomid parasites. It is also adaptable to other parasite groups where it could serve to improve current understanding of diversity, distribution, and interspecies interactions of other understudied taxa.
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| 5. |
- Ozerov, Mikhail, et al.
(författare)
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Draft genome assembly of the freshwater apex predator wels catfish (Silurus glanis) using linked-read sequencing
- 2020
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Ingår i: G3. - : Oxford University Press (OUP). - 2160-1836. ; 10, s. 3897-3906
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Tidskriftsartikel (refereegranskat)abstract
- The wels catfish (Silurus glanis) is one of the largest freshwater fish species in the world. This top predator plays a key role in ecosystem stability, and represents an iconic trophy-fish for recreational fishermen. S. glanis is also a highly valued species for its high-quality boneless flesh, and has been cultivated for over 100 years in Eastern and Central Europe. The interest in rearing S. glanis continues to grow; the aquaculture production of this species has almost doubled during the last decade. However, despite its high ecological, cultural and economic importance, the available genomic resources for S. glanis are very limited. To fulfill this gap we report a de novo assembly and annotation of the whole genome sequence of a female S. glanis. The linked-read based technology with 10X Genomics Chromium chemistry and Supernova assembler produced a highly continuous draft genome of S. glanis: ∼0.8Gb assembly (scaffold N50 = 3.2 Mb; longest individual scaffold = 13.9 Mb; BUSCO completeness = 84.2%), which included 313.3 Mb of putative repeated sequences. In total, 21,316 protein-coding genes were predicted, of which 96% were annotated functionally from either sequence homology or protein signature searches. The highly continuous genome assembly will be an invaluable resource for aquaculture genomics, genetics, conservation, and breeding research of S. glanis.
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| 6. |
- Ozerov, Mikhail, et al.
(författare)
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Humic-acid-driven escape from eye parasites revealed by RNA-seq and target-specific metabarcoding
- 2020
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Ingår i: Parasites and Vectors. - : Springer Science and Business Media LLC. - 1756-3305. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Background: Next generation sequencing (NGS) technologies are extensively used to dissect the molecular mechanisms of host-parasite interactions in human pathogens. However, ecological studies have yet to fully exploit the power of NGS as a rich source for formulating and testing new hypotheses.Methods: We studied Eurasian perch (Perca fluviatilis) and its eye parasite (Trematoda, Diplostomidae) communities in 14 lakes that differed in humic content in order to explore host-parasite-environment interactions. We hypothesised that high humic content along with low pH would decrease the abundance of the intermediate hosts (gastropods), thus limiting the occurrence of diplostomid parasites in humic lakes. This hypothesis was initially invoked by whole eye RNA-seq data analysis and subsequently tested using PCR-based detection and a novel targeted metabarcoding approach.Results: Whole eye transcriptome results revealed overexpression of immune-related genes and the presence of eye parasite sequences in RNA-seq data obtained from perch living in clear-water lakes. Both PCR-based and targeted-metabarcoding approach showed that perch from humic lakes were completely free from diplostomid parasites, while the prevalence of eye flukes in clear-water lakes that contain low amounts of humic substances was close to 100%, with the majority of NGS reads assigned toTylodelphys clavata.Conclusions: High intraspecific diversity ofT. clavataindicates that massively parallel sequencing of naturally pooled samples represents an efficient and powerful strategy for shedding light on cryptic diversity of eye parasites. Our results demonstrate that perch populations in clear-water lakes experience contrasting eye parasite pressure compared to those from humic lakes, which is reflected by prevalent differences in the expression of immune-related genes in the eye. This study highlights the utility of NGS to discover novel host-parasite-environment interactions and provide unprecedented power to characterize the molecular diversity of cryptic parasites.
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| 7. |
- Ozerov, Mikhail, et al.
(författare)
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Temporally stable small-scale genetic structure of Northern pike (Esox lucius) in the coastal Baltic Sea
- 2022
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Ingår i: Fisheries Research. - : Elsevier BV. - 0165-7836 .- 1872-6763. ; 254
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Tidskriftsartikel (refereegranskat)abstract
- The Northern pike (Esox lucius) is an important predator in freshwater and brackish water environments. In the Baltic Sea, Northern pike follows isolation by distance pattern across wide geographical scale. However, relatively little is known about the fine-scale population divergence and temporal genetic variation of Baltic pike, especially for populations inhabiting the eastern part of the Baltic Sea. Here, we characterize the population genetic structure of Northern pike and its temporal stability in six freshwater and one brackish water locations on the Island of Saaremaa (Estonia). To accomplish this, we collected 274 young-of-the-year (YOY) of two consecutive cohorts and 218 older specimens that were genotyped using ten microsatellite loci. Our results indicate a temporally stable population differentiation between geographically close locations and reduced diversity of the north-western Saaremaa populations. Furthermore, the correspondence analysis and a discriminant analysis of principal components showed a clear differentiation between north-western and the Gulf of Riga spawning grounds. Our findings support the idea that natal homing behavior, limited dispersal and facultative anadromy in Baltic pike likely promotes the existence of temporally stable genetic divergence among different populations at small geographical scale, representing an essential prerequisite for development of local adaptations. Thus, conservation, management and restoration efforts of coastal Baltic Sea pike should preserve the existing genetic differences between different populations and avoid actions, which potentially increase genetic homogenization.
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| 8. |
- Ozerov, Mikhail, et al.
(författare)
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The strength and form of natural selection on transcript abundance in the wild
- 2021
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 30, s. 2724–2737-
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Tidskriftsartikel (refereegranskat)abstract
- Gene transcription variation is known to contribute to disease susceptibility and adaptation, but we currently know very little about how contemporary natural selection shapes transcript abundance. Here, we propose a novel analytical framework to quantify the strength and form of ongoing natural selection at the transcriptome level in a wild vertebrate. We estimated selection on transcript abundance in a cohort of a wild salmonid fish (Salmo trutta) affected by an extracellular myxozoan parasite (Tetracapsuloides bryosalmonae) through mark-recapture field sampling and the integration of RNA-sequencing with classical regression-based selection analysis. We show, based on fin transcriptomes of the host, that infection by the parasite and subsequent host survival is linked to upregulation of mitotic cell cycle process. We also detect a widespread signal of disruptive selection on transcripts linked to host immune defence, host-pathogen interactions, cellular repair and maintenance. Our results provide insights into how selection can be measured at the transcriptome level to dissect the molecular mechanisms of contemporary evolution driven by climate change and emerging anthropogenic threats. We anticipate that the approach described here will enable critical information on the molecular processes and targets of natural selection to be obtained in real time.
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| 9. |
- Ozerov, Mikhail, et al.
(författare)
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Whole-genome sequencing illuminates multifaceted targets of selection to humic substances in Eurasian perch
- 2022
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 31, s. 2367-2383
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Tidskriftsartikel (refereegranskat)abstract
- Extreme environments are inhospitable to the majority of species, but some organisms are able to survive in such hostile conditions due to evolutionary adaptations. For example, modern bony fishes have colonized various aquatic environments, including perpetually dark, hypoxic, hypersaline and toxic habitats. Eurasian perch (Perca fluviatilis) is among the few fish species of northern latitudes that is able to live in very acidic humic lakes. Such lakes represent almost "nocturnal" environments; they contain high levels of dissolved organic matter, which in addition to creating a challenging visual environment, also affects a large number of other habitat parameters and biotic interactions. To reveal the genomic targets of humic-associated selection, we performed whole-genome sequencing of perch originating from 16 humic and 16 clear-water lakes in northern Europe. We identified over 800,000 single nucleotide polymorphisms, of which >10,000 were identified as potential candidates under selection (associated with >3000 genes) using multiple outlier approaches. Our findings suggest that adaptation to the humic environment may involve hundreds of regions scattered across the genome. Putative signals of adaptation were detected in genes and gene families with diverse functions, including organism development and ion transportation. The observed excess of variants under selection in regulatory regions highlights the importance of adaptive evolution via regulatory elements, rather than via protein sequence modification. Our study demonstrates the power of whole-genome analysis to illuminate the multifaceted nature of humic adaptation and provides the foundation for further investigation of causal mutations underlying phenotypic traits of ecological and evolutionary importance.
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| 10. |
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