| 1. |
- Bailey, Allison, et al.
(author)
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Regulation of gene expression is associated with tolerance of the Arctic copepod Calanus glacialis to CO2-acidified sea water
- 2017
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In: Ecology and Evolution. - : Wiley. - 2045-7758. ; 7:18, s. 7145-7160
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Journal article (peer-reviewed)abstract
- Ocean acidification is the increase in seawater pCO2 due to the uptake of atmospheric anthropogenic CO2, with the largest changes predicted to occur in the Arctic seas. For some marine organisms, this change in pCO2, and associated decrease in pH, represents a climate change-related stressor. In this study, we investigated the gene expression patterns of nauplii of the Arctic copepod Calanus glacialis cultured at low pH levels. We have previously shown that organismal-level performance (development, growth, respiration) of C. glacialis nauplii is unaffected by low pH. Here, we investigated the molecular-level response to lowered pH in order to elucidate the physiological processes involved in this tolerance. Nauplii from wild-caught C. glacialis were cultured at four pH levels (8.05, 7.9, 7.7, 7.5). At stage N6, mRNA was extracted and sequenced using RNA-seq. The physiological functionality of the proteins identified was categorized using Gene Ontology and KEGG pathways. We found that the expression of 151 contigs varied significantly with pH on a continuous scale (93% downregulated with decreasing pH). Gene set enrichment analysis revealed that, of the processes downregulated, many were components of the universal cellular stress response, including DNA repair, redox regulation, protein folding, and proteolysis. Sodium:proton antiporters were among the processes significantly upregulated, indicating that these ion pumps were involved in maintaining cellular pH homeostasis. C. glacialis significantly alters its gene expression at low pH, although they maintain normal larval development. Understanding what confers tolerance to some species will support our ability to predict the effects of future ocean acidification on marine organisms.
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| 2. |
- Bergin, Claudia, et al.
(author)
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Acquisition of a Novel Sulfur-Oxidizing Symbiont in the Gutless Marine Worm Inanidrilus exumae
- 2018
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In: Applied and Environmental Microbiology. - : AMER SOC MICROBIOLOGY. - 0099-2240 .- 1098-5336. ; 84:7
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Journal article (peer-reviewed)abstract
- Gutless marine oligochaetes (Annelida, Clitellata) lack a digestive and excretory system, and live in an obligate association with multiple bacterial endosymbionts that supply them with nutrition. In this study, we discovered an unusual symbiont community in the gutless oligochaete Inanidrilus exumae that differs markedly from the microbiome of all other 22 examined host species. Comparative 16S rRNA sequence analysis and fluorescence in situ hybridization revealed that I.exumae harboured co-occurring gamma-, alpha- and deltaproteobacterial symbionts, while all other host species harbour gamma- and either alpha- or deltaproteobacterial symbionts. Surprisingly, the primary chemoautotrophic, sulfur-oxidizer, Ca. Thiosymbion, which occurs in all other gutless oligochaetes, does not appear to be present in I.exumae. Instead, I. exumae harboured a bacterial endosymbiont that resembled Ca. Thiosymbion morphologically and metabolically, but originated from a novel lineage within the Gammaproteobacteria. This endosymbiont, named Gamma 4 symbiont here, had a 16S rRNA sequence that differed by at least 7% from those of other free-living and symbiotic bacteria and by 10% from Ca. Thiosymbion. Sulfur globules in the Gamma 4 symbiont cells, as well as the presence of genes characteristic for autotrophy (cbbL) and sulfur oxidation (aprA), suggest that this symbiont is a chemoautotrophic sulfur oxidizer. Our results indicate that a novel lineage of free-living bacteria was able to establish a stable and specific association with I. exumae, and displace the Ca. Thiosymbion symbionts originally associated with these hosts.
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| 3. |
- Calosi, Piero, et al.
(author)
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Will Life find a Way? Evolution of Marine Species Under Global Change
- 2016
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In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 9:9, s. 1035-1042
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Journal article (peer-reviewed)abstract
- Projections of marine biodiversity and implementation of effective actions for its maintenance in face of current rapid global environmental change are constrained by our limited understanding of species’ adaptive responses, including, transgenerational plasticity, epigenetics, natural selection. This special issue presents 13 novel studies, which employ experimental and modeling approaches to: (1) Investigate plastic and evolutionary responses of marine species to major global change drivers; (2) ask relevant broad eco-evolutionary questions, implementing well-designed multiple species and populations studies; (3) show the advantages of using advanced experimental designs and tools; (4) construct novel model organisms for marine evolution; (5) help identifying future challenges for the field, and (6) highlight the importance of incorporating existing evolutionary theory into management solutions for the marine realm. What emerges is that at least some populations of marine species are able to adapt to future global change conditions. However, marine organisms’ capacity for adaptation appears finite, due to evolutionary trade-offs and possible rapid losses in genetic diversity. This further corroborate the idea that acquiring an evolutionary perspective on how marine life will respond to the selective pressure of future global changes will guide us in better identifying which conservation efforts will be most needed, and most effective.
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| 4. |
- De Wit, Pierre, 1978, et al.
(author)
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Diet-dependent gene expression highlights the importance of Cytochrome P450 in detoxification of algal secondary metabolites in a marine isopod
- 2018
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 8
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Journal article (peer-reviewed)abstract
- Isopods of the genus Idotea have an unusual ability to feed on algae containing high amounts of chemical defense molecules, such as species of the genera Fucus and Ulva. In this study, we compared gene expression patterns of Idotea balthica individuals fed with Fucus vesiculosus to individuals fed with Ulva lactuca. We generated the rst-ever transcriptome assembly for this species, and found 3,233 di erentially expressed genes across feeding regimes. However, only a handful of biological functions were enriched with regard to di erentially expressed genes, the most notable being “alkaloid metabolic process”. Within this category, we found eight di erentially expressed cytochrome P450 (CYP) unigenes, all of which had a higher expression in the U. lactuca diet treatment. A phylogenetic analysis showed that the di erentially expressed CYP genes are closely related to a CYP gene described from the hepatopancreas of the spiny lobster Panulirus argus, and we hypothesize that these transcripts are involved in metabolite detoxi cation. This is a rst step in the understanding of this algae-grazer interaction, and will form a basis for future work to characterize cytochrome P450 functioning in marine crustaceans.
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| 5. |
- De Wit, Pierre, 1978, et al.
(author)
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Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms
- 2018
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 19
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Journal article (peer-reviewed)abstract
- Background: Despite recent work to characterize gene expression changes associated with larval development in oysters, the mechanism by which the larval shell is first formed is still largely unknown. In Crassostrea gigas, this shell forms within the first 24 h post fertilization, and it has been demonstrated that changes in water chemistry can cause delays in shell formation, shell deformations and higher mortality rates. In this study, we use the delay in shell formation associated with exposure to CO2-acidified seawater to identify genes correlated with initial shell deposition. Results: By fitting linear models to gene expression data in ambient and low aragonite saturation treatments, we are able to isolate 37 annotated genes correlated with initial larval shell formation, which can be categorized into 1) ion transporters, 2) shell matrix proteins and 3) protease inhibitors. Clustering of the gene expression data into co-expression networks further supports the result of the linear models, and also implies an important role of dynein motor proteins as transporters of cellular components during the initial shell formation process. Conclusions: Using an RNA-Seq approach with high temporal resolution allows us to identify a conceptual model for how oyster larval calcification is initiated. This work provides a foundation for further studies on how genetic variation in these identified genes could affect fitness of oyster populations subjected to future environmental changes, such as ocean acidification.
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| 6. |
- De Wit, Pierre, 1978, et al.
(author)
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Selection on oxidative phosphorylation and ribosomal structure as a multigenerational response to ocean acidification in the common copepod Pseudocalanus acuspes
- 2016
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In: Evolutionary Applications. - : Wiley. - 1752-4571. ; 9:9, s. 1112-1223
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Journal article (peer-reviewed)abstract
- Ocean acidification is expected to have dramatic impacts on oceanic ecosystems, yet surprisingly few studies currently examine long-term adaptive and plastic responses of marine invertebrates to pCO2 stress. Here, we exposed populations of the common copepod Pseudocalanus acuspes to three pCO2 regimes (400, 900 and 1550 μatm) for two generations, after which we conducted a reciprocal transplant experiment. A de novo transcriptome was assembled, annotated, and gene expression data revealed that genes involved in RNA transcription were strongly down-regulated in populations with long-term exposure to a high pCO2 environment, even after transplantation back to control levels. In addition, 747,000 SNPs were identified, out of which 1513 showed consistent changes in nucleotide frequency between replicates of control and high pCO2 populations. Functions involving RNA transcription and ribosomal function, as well as ion transport and oxidative phosphorylation were highly overrepresented. We thus conclude that pCO2 stress appears to impose selection in copepods on RNA synthesis and translation, possibly modulated by helicase expression. Using a physiological hypothesis-testing strategy to mine gene expression data, we herein increase the power to detect cellular targets of ocean acidification. This novel approach seems promising for future studies of effects of environmental changes in ecologically important non- model organisms.
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| 7. |
- De Wit, Pierre, 1978
(author)
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SNP Discovery Using Next Generation Transcriptomic Sequencing
- 2016
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In: Marine Genomics - Methods and Protocols. - New York : Springer Science + Business Media. - 9781493937721
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Book chapter (peer-reviewed)abstract
- In this chapter, I will guide the user through methods to find new SNP markers from expressed sequence (RNA-Seq) data, focusing on the sample preparation and also on the bioinformatic analyses needed to sort through the immense flood of data from high-throughput sequencing machines. The general steps included are as follows: sample preparation, sequencing, quality control of data, assembly, mapping, SNP discovery, filtering, validation. The first few steps are traditional laboratory protocols, whereas steps following the sequencing are of bioinformatic nature. The bioinformatics described herein are by no means exhaustive, rather they serve as one example of a simple way of analyzing high-throughput sequence data to find SNP markers. Ideally, one would like to run through this protocol several times with a new dataset, while varying software parameters slightly, in order to determine the robustness of the results. The final validation step, although not described in much detail here, is also quite critical as that will be the final test of the accuracy of the assumptions made in silico. There is a plethora of downstream applications of a SNP dataset, not covered in this chapter. For an example of a more thorough protocol also including differential gene expression and functional enrichment analyses, BLAST annotation and downstream applications of SNP markers, a good starting point could be the “Simple Fool’s Guide to population genomics via RNA-Seq,” which is available at http://sfg.stanford.edu.
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| 8. |
- De Wit, Pierre, 1978, et al.
(author)
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SNP genotyping and population genomics from expressed sequences –current advances and future possibilities : RNA-Seq for population genomics
- 2015
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In: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 24:10, s. 2310-2323
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Journal article (peer-reviewed)abstract
- With the rapid increase in production of genetic data from new sequencing technologies, a myriad of new ways to study genomic patterns in non-model organisms are currently possible. Because genome assembly still remains a complicated procedure, and because the functional role of much of the genome is unclear, focusing on SNP genotyping from expressed sequences provides a cost-effective way to reduce complexity while still retaining functionally relevant information. This review summarizes current methods, identifies ways that using expressed sequence data benefits population genomic inference, and explores how current practitioners evaluate and overcome challenges that are commonly encountered. We focus particularly on the additional power of functional analysis provided by expressed sequence data and how these analyses push beyond allele pattern data available from non-function genomic approaches. The massive datasets generated by these approaches create opportunities and problems as well – especially false positives. We discuss methods available to validate results from expressed SNP genotyping assays, new approaches that sidestep use of mRNA, and review follow up experiments that can focus on evolutionary mechanisms acting across the genome.
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| 9. |
- Erséus, Christer, 1951, et al.
(author)
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Molecular data reveal a tropical freshwater origin of Naidinae (Annelida, Clitellata, Naididae)
- 2017
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In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 115, s. 115-127
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Journal article (peer-reviewed)abstract
- The phylogenetic relationships within Naidinae (Annelida, Clitellata, Naididae) were investigated, using six molecular markers, both mitochondrial (12S rDNA, 16S rDNA, the COI gene) and nuclear (18S rDNA, 28S rDNA, the ITS region). Thirty-seven nominal species, representing 16 of the 22 genera recognized in the subfamily, were included, and the Nais conmmmunis/variabilis species complex was represented by six different morphotypes. Ten other species of Naididae were selected as outgroups. The data were analysed by Bayesian inference and Maximum Likelihood. The phylogeny corroborates monophyly of the Naidinae, and the separate status of the genus Pristina (Pristininae) and the Opistocystinae. Relationships within Naidinae are largely well supported, but in some parts unexpected: (1) A Glade containing the largely tropical genera Dero and Branchiodrilus is sister to the rest of the subfamily, and together with a third tropical genus, Allonais, they form a basal paraphyly. All these genera show morphological adaptations to environmental hypoxia, leading to the conclusion that Naidinae originated in tropical freshwaters. (2) The genera Dero, Nais and Piguetiella are paraphyletic. (3) At least Branchiodrilus, Paranais, Chaetogaster, Nais, Stylaria appear to contain cryptic species. Morphological characters, especially those associated with chaetae, are to a great extent homoplastic within Naidinae, which certainly has contributed to the overall taxonomic confusion of this subfamily.
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| 10. |
- Erséus, Christer, 1951, et al.
(author)
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The popular model annelid Enchytraeus albidus is only one species in a complex of seashore White Worms (Clitellata, Enchytraeidae)
- 2019
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In: Organisms Diversity & Evolution. - : Springer Science and Business Media LLC. - 1439-6092 .- 1618-1077. ; 19:2, s. 105-133
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Journal article (peer-reviewed)abstract
- The white worm Enchytraeus albidus Henle, 1837 (Clitellata, Enchytraeidae) is easy to keep in laboratory cultures, and has therefore been employed as a model organism in basic and applied biological research. Its natural habitat includes terrestrial composts and wrack beds on seashores. However, the name E. albidus is currently used for a complex of morphologically similar and closely related species. We here revise the components of the E. albidus species complex based on a sample of 100 Enchytraeus specimens from 56 sites, most of which are across Europe. These samples were DNA-barcoded for the mitochon- drial COI gene. A subset of them was sequenced for the nuclear ITS2 and H3 markers. Six species were delimited with strong support by the COI and ITS2 gene trees, as well as by a multi-locus species delimitation analysis. These species are identified morphologically and described as E. albidus s. str. (with designation of a neotype); Enchytraeus moebii (Michaelsen, 1885); Enchytraeus albellus Klinth, Erséus and Rota, sp. nov., E. cf. krumbachi (Čejka, 1913), E. sp. 1 (unnamed), and Enchytraeus polatdemiri Arslan and Timm, 2018. The last-mentioned species is a soda lake specialist, whereas E. albidus s. str. is both terrestrial and marine littoral; all other species occur only in seashores. The phylogeny of this group was estimated using the multi-species coalescent model. Monophyly of the E. albidus complex was recovered. Within this complex, three groups were recovered as monophyletic, but the relationship between them is unclear. One group comprises E. albidus s. str., E. albellus, and E. moebii; the second group E. cf. krumbachi and the unnamed E. sp. 1, and the third consists of only E. polatdemiri. This study serves as a framework for genetic identification of white worms used for experimental purposes.
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