| 1. |
- Bensch, Staffan, et al.
(författare)
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The genome of Haemoproteus tartakovskyi and its relationship to human malaria parasites
- 2016
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Ingår i: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 8:5, s. 73-1361
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Tidskriftsartikel (refereegranskat)abstract
- The phylogenetic relationships among hemosporidian parasites, including the origin of Plasmodium falciparum, the most virulent malaria parasite of humans, have been heavily debated for decades. Studies based on multiple-gene sequences have helped settle many of these controversial phylogenetic issues. However, denser taxon sampling and genome-wide analyses are needed to confidently resolve the evolutionay relationships among hemosporidian parasites. Genome sequences of several Plasmodium parasites are available but only for species infecting primates and rodents. To root the phylogenetic tree of Plasmodium, genomic data from related parasites of birds or reptiles are required. Here, we use a novel approach to isolate parasite DNA from microgametes and describe the first genome of a bird parasite in the sister genus to Plasmodium, Haemoproteus tartakovskyi Similar to Plasmodium parasites, H. tartakovskyi has a small genome (23.2 Mb, 5,990 genes) and a GC content (25.4%) closer to P. falciparum (19.3%) than to Plasmodium vivax (42.3%). Combined with novel transcriptome sequences of the bird parasite Plasmodium ashfordi, our phylogenomic analyses of 1,302 orthologous genes demonstrate that mammalian-infecting malaria parasites are monophyletic, thus rejecting the repeatedly proposed hypothesis that the ancestor of Laverania parasites originated from a secondary host shift from birds to humans. Genes and genomic features previously found to be shared between P. falciparum and bird malaria parasites, but absent in other mammal malaria parasites, are therefore signatures of maintained ancestral states. We foresee that the genome of H. tartakovskyi will open new directions for comparative evolutionary analyses of malarial adaptive traits.
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| 2. |
- Hellgren, Olof, et al.
(författare)
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De novo synthesis of thiamine (vitamin B1) is the ancestral state in Plasmodium parasites – evidence from avian haemosporidians
- 2018
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Ingår i: Parasitology. - 0031-1820. ; 145:8, s. 1084-1089
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Tidskriftsartikel (refereegranskat)abstract
- Parasites often have reduced genomes as their own genes become redundant when utilizing their host as a source of metabolites, thus losing their own de novo production of metabolites. Primate malaria parasites can synthesize vitamin B1 (thiamine) de novo but rodent malaria and other genome-sequenced apicomplexans cannot, as the three essential genes responsible for this pathway are absent in their genomes. The unique presence of functional thiamine synthesis genes in primate malaria parasites and their sequence similarities to bacterial orthologues, have led to speculations that this pathway was horizontally acquired from bacteria. Here we show that the genes essential for the de novo synthesis of thiamine are found also in avian Plasmodium species. Importantly, they are also present in species phylogenetically basal to all mammalian and avian Plasmodium parasites, i.e. Haemoproteus. Furthermore, we found that these genes are expressed during the blood stage of the avian malaria infection, indicating that this metabolic pathway is actively transcribed. We conclude that the ability to synthesize thiamine is widespread among haemosporidians, with a recent loss in the rodent malaria species.
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| 3. |
- Hellgren, Olof, et al.
(författare)
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De novo synthesis of thiamine (vitamin B1) is the ancestral state in Plasmodium parasites – evidence from avian haemosporidians
- 2017
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Ingår i: Parasitology. - : Cambridge University Press (CUP). - 0031-1820 .- 1469-8161. ; 145:8, s. 1084-1089
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Tidskriftsartikel (refereegranskat)abstract
- Parasites often have reduced genomes as their own genes become redundant when utilizing their host as a source of metabolites, thus losing their own de novo production of metabolites. Primate malaria parasites can synthesize vitamin B1 (thiamine) de novo but rodent malaria and other genome-sequenced apicomplexans cannot, as the three essential genes responsible for this pathway are absent in their genomes. The unique presence of functional thiamine synthesis genes in primate malaria parasites and their sequence similarities to bacterial orthologues, have led to speculations that this pathway was horizontally acquired from bacteria. Here we show that the genes essential for the de novo synthesis of thiamine are found also in avian Plasmodium species. Importantly, they are also present in species phylogenetically basal to all mammalian and avian Plasmodium parasites, i.e. Haemoproteus. Furthermore, we found that these genes are expressed during the blood stage of the avian malaria infection, indicating that this metabolic pathway is actively transcribed. We conclude that the ability to synthesize thiamine is widespread among haemosporidians, with a recent loss in the rodent malaria species.
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| 4. |
- Naepflin, Kathrin, et al.
(författare)
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Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales
- 2019
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Ingår i: PeerJ. - 2167-8359. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Evolutionary genomics has recently entered a new era in the study of host-pathogen interactions. A variety of novel genomic techniques has transformed the identification, detection and classification of both hosts and pathogens, allowing a greater resolution that helps decipher their underlying dynamics and provides novel insights into their environmental context. Nevertheless, many challenges to a general understanding of host-pathogen interactions remain, in particular in the synthesis and integration of concepts and findings across a variety of systems and different spatiotemporal and ecological scales. In this perspective we aim to highlight some of the commonalities and complexities across diverse studies of host-pathogen interactions, with a focus on ecological, spatiotemporal variation, and the choice of genomic methods used. We performed a quantitative review of recent literature to investigate links, patterns and potential tradeoffs between the complexity of genomic, ecological and spatiotemporal scales undertaken in individual host-pathogen studies. We found that the majority of studies used whole genome resolution to address their research objectives across a broad range of ecological scales, especially when focusing on the pathogen side of the interaction. Nevertheless, genomic studies conducted in a complex spatiotemporal context are currently rare in the literature. Because processes of host-pathogen interactions can be understood at multiple scales, from molecular-, cellular-, and physiological-scales to the levels of populations and ecosystems, we conclude that a major obstacle for synthesis across diverse host-pathogen systems is that data are collected on widely diverging scales with different degrees of resolution. This disparity not only hampers effective infrastructural organization of the data but also data granularity and accessibility. Comprehensive metadata deposited in association with genomic data in easily accessible databases will allow greater inference across systems in the future, especially when combined with open data standards and practices. The standardization and comparability of such data will facilitate early detection of emerging infectious diseases as well as studies of the impact of anthropogenic stressors, such as climate change, on disease dynamics in humans and wildlife.
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| 5. |
- Sigeman, Hanna, et al.
(författare)
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Insights into avian incomplete dosage compensation : Sex-biased gene expression coevolves with sex chromosome degeneration in the common whitethroat
- 2018
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Ingår i: Genes. - : MDPI AG. - 2073-4425. ; 9:8
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Tidskriftsartikel (refereegranskat)abstract
- Non-recombining sex chromosomes (Y and W) accumulate deleterious mutations and degenerate. This poses a problem for the heterogametic sex (XY males; ZW females) because a single functional gene copy often implies less gene expression and a potential imbalance of crucial expression networks. Mammals counteract this by dosage compensation, resulting in equal sex chromosome expression in males and females, whereas birds show incomplete dosage compensation with significantly lower expression in females (ZW). Here, we study the evolution of Z and W sequence divergence and sex-specific gene expression in the common whitethroat (Sylvia communis), a species within the Sylvioidea clade where a neo-sex chromosome has been formed by a fusion between an autosome and the ancestral sex chromosome. In line with data from other birds, females had lower expression than males at the majority of sex-linked genes. Results from the neo-sex chromosome region showed thatWgametologs have diverged functionally to a higher extent than their Z counterparts, and that the female-to-male expression ratio correlated negatively with the degree of functional divergence of these gametologs. We find it most likely that sex-linked genes are being suppressed in females as a response to W chromosome degradation, rather than that these genes experience relaxed selection, and thus diverge more, by having low female expression. Overall, our data of this unique avian neo-sex chromosome system suggest that incomplete dosage compensation evolves, at least partly, through gradual accumulation of deleterious mutations at the W chromosome and declining female gene expression.
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| 6. |
- Videvall, Elin, et al.
(författare)
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Butterfly monitoring using systematically placed transects in contrasting climatic regions - Exploring an established spatial design for sampling
- 2016
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Ingår i: Nature Conservation. - : Pensoft Publishers. - 1314-6947 .- 1314-3301. ; 14, s. 41-62
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Tidskriftsartikel (refereegranskat)abstract
- Butterfly monitoring schemes are recording programs initiated to monitor nationwide butterfly abundance and distribution patterns, often with help from volunteers. The method generates high-resolution data, but may be associated with a degree of habitat sampling bias if volunteers prefer to survey areas perceived to be high-quality butterfly habitats. This can result in habitats becoming underrepresented in the data set, leading to less information about the butterfly populations there. In the present study, we investigate the possibility of applying a spatial design used by the Swedish Bird Survey for nationwide, gridbased sampling, with a goal to get butterfly monitoring data covering a representative sample of different habitats. We surveyed four 2×2 km sampling squares, split into 100 m segments, in the southernmost region of Sweden (Scania) and four in the northernmost region (Norrbotten). The grid-based transects were compared with volunteer-selected transects in a G IS analysis using a refined Swedish version of CORINE land cover data to see how well these two transect designs represent true habitat coverage. A total of 53 km transect was monitored, resulting in 490 individuals and 29 different species recorded. We found that transect cover correlated significantly with overall land cover using both monitoring methods, though standardised transects outperformed volunteer-selected transects in habitat representation in Scania, but not in Norrbotten. Butterflies were found to aggregate significantly in specific habitats, but with contrasting results for the two geographically different regions. Grasslands in both regions generated a high number of recorded butterflies, although so did clear-cut and residential areas in Norrbotten as well. The highest number of individuals recorded per transect was found in bogs in Scania. This study emphasises the value of complementing free site selection monitoring schemes with spatially representative schemes such as the Swedish Bird Survey, and sheds some light on general habitat preferences for Swedish butterflies in two contrasting climatic regions. Copyright Elin Videvall et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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| 7. |
- Videvall, Elin, et al.
(författare)
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Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes
- 2017
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Ingår i: mSystems. - 2379-5077. ; 2:6
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Tidskriftsartikel (refereegranskat)abstract
- The gut microbiome of animals is emerging as an important factor influencing ecological and evolutionary processes. A major bottleneck in obtaining microbiome data from large numbers of samples is the time-consuming laboratory procedures required, specifically the isolation of DNA and generation of amplicon libraries. Recently, direct PCR kits have been developed that circumvent conventional DNA extraction steps, thereby streamlining the laboratory process by reducing preparation time and costs. However, the reliability and efficacy of direct PCR for measuring host microbiomes have not yet been investigated other than in humans with 454 sequencing. Here, we conduct a comprehensive evaluation of the microbial communities obtained with direct PCR and the widely used Mo Bio PowerSoil DNA extraction kit in five distinct gut sample types (ileum, cecum, colon, feces, and cloaca) from 20 juvenile ostriches, using 16S rRNA Illumina MiSeq sequencing. We found that direct PCR was highly comparable over a range of measures to the DNA extraction method in cecal, colon, and fecal samples. However, the two methods significantly differed in samples with comparably low bacterial biomass: cloacal and especially ileal samples. We also sequenced 100 replicate sample pairs to evaluate repeatability during both extraction and PCR stages and found that both methods were highly consistent for cecal, colon, and fecal samples (rs > 0.7) but had low repeatability for cloacal (rs = 0.39) and ileal (rs = -0.24) samples. This study indicates that direct PCR provides a fast, cheap, and reliable alternative to conventional DNA extraction methods for retrieving 16S rRNA data, which can aid future gut microbiome studies. IMPORTANCE The microbial communities of animals can have large impacts on their hosts, and the number of studies using high-throughput sequencing to measure gut microbiomes is rapidly increasing. However, the library preparation procedure in microbiome research is both costly and time-consuming, especially for large numbers of samples. We investigated a cheaper and faster direct PCR method designed to bypass the DNA isolation steps during 16S rRNA library preparation and compared it with a standard DNA extraction method. We used both techniques on five different gut sample types collected from 20 juvenile ostriches and sequenced samples with Illumina MiSeq. The methods were highly comparable and highly repeatable in three sample types with high microbial biomass (cecum, colon, and feces), but larger differences and low repeatability were found in the microbiomes obtained from the ileum and cloaca. These results will help microbiome researchers assess library preparation procedures and plan their studies accordingly.
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| 8. |
- Videvall, Elin, et al.
(författare)
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Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes
- 2017
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Ingår i: mSystems. - : American Society for Microbiology. - 2379-5077. ; 2:6
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Tidskriftsartikel (refereegranskat)abstract
- The microbial communities of animals can have large impacts on their hosts, and the number of studies using high-throughput sequencing to measure gut microbiomes is rapidly increasing. However, the library preparation procedure in microbiome research is both costly and time-consuming, especially for large numbers of samples. We investigated a cheaper and faster direct PCR method designed to bypass the DNA isolation steps during 16S rRNA library preparation and compared it with a standard DNA extraction method. We used both techniques on five different gut sample types collected from 20 juvenile ostriches and sequenced samples with Illumina MiSeq. The methods were highly comparable and highly repeatable in three sample types with high microbial biomass (cecum, colon, and feces), but larger differences and low repeatability were found in the microbiomes obtained from the ileum and cloaca. These results will help microbiome researchers assess library preparation procedures and plan their studies accordingly.
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| 9. |
- Videvall, Elin
(författare)
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Evolutionary genomics of host-microbe interactions
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The microbes living inside hosts have highly important consequences for host health and fitness. From the host’s perspective, some microbes exhibit mutualistic tendencies, others parasitic, and some commensal, but this is context-dependent and opportunistic lifestyles are widespread in nature. Our knowledge of how hosts interact molecularly with different microbes is, however, poor, and little research has been done on non-model organisms from a genomic and community-wide perspective. In this PhD thesis, I investigate host-microbe interactions from multiple angles, and utilize high-throughput sequencing techniques to paint a broad, overarching picture of the relationship between hosts and microbes. My PhD comprised two related projects, 1) host-microbiome interactions and 2) host-parasite interactions. In the former, I have evaluated how to best sample and measure the gut microbiomes of avian hosts (Paper I and II). Different sections of the ostrich gastrointestinal tract were characterized and shown to harbour divergent microbial communities (Paper I, II, and IV). I have further demonstrated that the gut microbiome of juvenile ostriches is colonized in a successional manner and gradually develops over time (Paper III), and is strongly linked to growth and mortality (Paper III and IV). In the second project I described the avian transcriptome response to malaria infection over time and to parasites with different virulence (Paper V and VI). Birds with malaria infection experience a range of transcriptional changes that involves for example the immune system, stress response, cell death regulation, and regulatory genes. To evaluate the molecular response of the malaria parasite, I assembled the blood transcriptome of Plasmodium ashfordi and showed that parasite gene expression is host-specific (Paper VII). This transcriptome was subsequently used, together with a genome assembly of Haemoproteus tartakovskyi, to construct a phylogeny of haemosporidian parasites which showed strong support for a monophyletic clade of mammalian malaria parasites (Paper VIII). Finally, the assembled transcriptome and genome were utilized to identify thiamine biosynthesis enzymes in avian Plasmodium (Paper IX), and to demonstrate that the avian Plasmodium parasites exhibit the most AT-rich genes of eukaryotes (Paper X). In summary, this work offers new insights into host-microbiome and host-parasite interactions, and enables a greater understanding of the multifaceted relationship between hosts and their microbes.
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| 10. |
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