Biology subjects

Auvinen, P.

Publications and source records attributed to Auvinen, P..

At least 19 recordsLinked to original sources

bioRxiv2026

Contemporary hybridization and localized genomic differentiation between grey seal subspecies

Grey seals are divided into two subspecies, Halichoerus grypus grypus in the Baltic Sea and H. grypus atlantica in the North Atlantic Ocean. Historically, intense hunting caused local extinctions of grey seals across their range and promoted geographical isolation of the subspecies. However, recent population recovery and recolonization have renewed their overlap in a contact zone in Danish and Swedish waters. Here, using whole-genome sequencing data from 119 individuals, we investigate the demographic history of grey seals, the divergence of the subspecies, and genomic signatures of local adaptation and potential hybridization in the contact zone. We estimate that divergence began approximately 10,000 years ago, with gene flow ceasing 2000 years ago. We detect peaks of high genetic differentiation near genes with putative functions in osmo- and thermoregulation, consistent with salinity and temperature differences between the Baltic Sea and the North Atlantic. As evidence of the geographic isolation breaking up, we report a hybrid individual in the southwest Baltic contact zone, with Baltic maternal and Atlantic paternal ancestry, and identify a migrant of Baltic origin in the North Sea. Our study illustrates how local environmental variation and long-term hunting pressure have contributed to divergence between mammal subspecies over a short evolutionary timescale, with recent population recovery, recolonization and hybridization reshaping gene flow dynamics. Broadly, our work emphasizes the importance of studying evolutionary processes amid anthropogenic influences, including both disturbances and conservation successes, where demographic fluctuations, range shifts, altered gene flow, and adaptation to changing environments interact in complex, potentially consequential ways.

evolutionary biology↗

bioRxiv2025

Deep origins and distinct adaptations indicated for a glacial relict seal

Isolated populations of postglacial relicts are known from many regions and are typically found on mountains for terrestrial species and in lakes for aquatic species. Among the few aquatic mammalian relicts, the Saimaa ringed seal (Pusa hispida saimensis) has been landlocked in Lake Saimaa, Finland, for the last 10,000 years. Saimaa ringed seals show genetic, behavioral, and morphological differences to the other ringed seal subspecies, but the extent these differences stem from the end of the last glacial period remains unclear. Here, we demonstrate with comprehensive sampling and state-of-the-art genomic methods that the Saimaa ringed seals are much older than the lake they inhabit, having formed a separate evolutionary branch for at least 60,000 years. This deep evolutionary origin of the Saimaa ringed seals is further underscored by our ecomorphological analyses revealing adaptively distinct features in their dentition and tongue. Overall, glacial relicts, many threatened by extinction, may harbor a richer selection of evolutionary history than might be expected from their recent isolation history alone.

zoology↗

bioRxiv2024

A pangenome and pantranscriptome of hexaploid oat

Oat grain is a traditional human food rich in dietary fiber that contributes to improved human health. Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogs. Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales. In contrast to many other cereal species, genomic research in oat is still at an early stage, and surveys of structural genome diversity and gene expression variability are scarce. Here, we present annotated chromosome-scale sequence assemblies of 33 wild and domesticated oats along with an atlas of gene expression across six tissues of different developmental stages in 23 accessions. We describe the interplay of gene expression diversity across subgenomes, accessions and tissues. Gene loss in the hexaploid is accompanied by compensatory up-regulation of the remaining homeologs, but this process is constrained by subgenome divergence. Chromosomal rearrangements have significantly impacted recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D and a homeologous sequence exchange between chromosomes 2A and 2C in a semidwarf mutant has risen to prominence in Australian elite varieties. The oat pangeome will promote the adoption of genomic approaches to understanding the evolution and adaptation of domesticated oats and will accelerate their improvement.

genomics↗

bioRxiv2024

Late Quaternary climatic impact on the woodland strawberry genome: a perennial herb's tale

Exploring a species paleohistory is crucial for understanding its responsiveness to climatic events, identifying drivers of adaptation, and developing effective biodiversity conservation strategies in the face of ongoing climate change. We analyzed 200 genomes of the perennial herb woodland strawberry (Fragaria vesca L.) from across Europe and investigated the population structure and demographic history of the species during past geoclimatic events. We found a clear division of populations into western and eastern genetic clusters, indicative of distinct glacial refugia and adaptations to variation in temperature seasonality. The eastern core populations were several times larger (defined as effective population size, NE) than populations in other regions, showed no evidence of inbreeding, and were resilient to several glacial maxima. However, we observed decreasing NE and higher inbreeding in populations toward range edges, particularly in the north, where these individuals went through bottlenecks during glaciations. Population divergence suggested that western and eastern Europe were colonized from separate refugia in multiple waves during the Holocene, while the largest current populations from the northern Mediterranean to southern regions of the Nordic countries formed a connected population chain with gene flow between eastern core populations and western Europe, primarily occurring through Central Europe. Similar patterns of colonization and hybridization may have occurred during past interglacial periods, contributing to the present-day population structure of woodland strawberry. We suggest that the unprecedented resolution of the species climatic history across six glacial-interglacial cycles presented here holds the promise of transforming the general understanding of species paleohistory through geoclimatically tracing ancestral haplotypes.

plant biology↗

bioRxiv2024

Effects of alcohol on the transcriptome, methylome, and metabolome of in vitro gastrulating human embryonic cells

Prenatal alcohol exposure (PAE) affects embryonic development, causing a variable fetal alcohol spectrum disorder (FASD) phenotype with neurodevelopmental disorders and birth defects. To explore the effects of PAE on gastrulation, we used an in vitro model with subchronic moderate (20 mM) and severe (70 mM) ethanol exposures during the differentiation of human embryonic stem cells into germ layer cells. We analysed genome-wide gene expression (mRNA sequencing), DNA methylation (EPIC Illumina microarrays), and metabolome (non-targeted LC-MS method) of the endodermal, mesodermal, and ectodermal cells. The largest number of ethanol-induced alterations were observed in the endodermal cells, whereas the most prominent changes were seen in the ectodermal cells. Genes of the major morphogen signaling pathways involved in gastrulation and body patterning were affected by ethanol. Many of the altered genes, such as BMP4, FGF8, SIX3, and LHX2, have been previously associated with PAE and phenotypes of FASD, like defects in heart and corpus callosum development as well as holoprosencephaly. Furthermore, methionine metabolism was altered in all germ layer cells. Our findings support the early origin of alcohol-induced developmental disorders and strengthen the role of methionine cycle in the etiology of FASD.

genetics↗

bioRxiv2024

Aerobic Adaptation and Metabolic Dynamics of Propionibacterium freudenreichii DSM 20271: Insights from Comparative Transcriptomics and Surfaceome Analysis

Propionibacterium freudenreichii (PFR) DSM 20271 is a bacterium known for its ability to thrive in diverse environments and to produce vitamin B12. Despite its anaerobic preference, recent studies have elucidated its ability to prosper in the presence of oxygen, prompting a deeper exploration of its physiology under aerobic conditions. Here, we investigated the response of DSM 20271 to aerobic growth by employing comparative transcriptomic and surfaceome analyses alongside metabolite profiling. Cultivation under controlled partial pressure of oxygen (pO2) conditions revealed significant increases in biomass formation and altered metabolite production, notably of B12 vitamin, pseudovitamin-B12, propionate and acetate, under aerobic conditions. Transcriptomic analysis identified differential expression of genes involved in lactate metabolism, TCA cycle, and electron transport chain, suggesting metabolic adjustments to aerobic environments. Moreover, surfaceome analysis unveiled growth environment-dependent changes in surface protein abundance, with implications for sensing and adaptation to atmospheric conditions. Supplementation experiments with key compounds highlighted the potential for enhancing aerobic growth, emphasizing the importance of iron and -ketoglutarate availability. Furthermore, in liquid culture, FeSO4 supplementation led to increased heme production and reduced vitamin B12 production, highlighting the impact of oxygen and iron availability on the metabolic pathways. These findings deepen our understanding of PFRs physiological responses to oxygen availability and offer insights for optimizing its growth in industrial applications. ImportanceThe study of the response of Propionibacterium freudenreichii to aerobic growth is crucial for understanding how this bacterium adapts to different environments and produces essential compounds like vitamin B12. By investigating its physiological changes under aerobic conditions, we can gain insights into its metabolic adjustments and potential for enhanced growth. These findings not only deepen our understanding of P. freudenreichii responses to oxygen availability but also offer valuable information for optimizing its growth in industrial applications. This research sheds light on the adaptive mechanisms of this bacterium, providing a foundation for further exploration and potential applications in various fields.

microbiology↗

bioRxiv2023

Comparison of phage and plasmid populations present in the gut microbiota of Parkinson's disease patients

The aging population worldwide is on the rise, leading to a higher number of Parkinsons disease (PD) cases each year. PD is presently the second most prevalent neurodegenerative disease, affecting an estimated 7-10 million individuals globally. This research aimed to identify mobile genetic elements in human fecal samples using a shotgun metagenomics approach. We found over 44,000 plasmid contigs and compared plasmid populations between PD patients (n = 68) and healthy controls (n = 68). Significant associations emerged between Body Mass Index (BMI) and plasmid alpha diversity. Moreover, the gene populations present on plasmids displayed marked differences in alpha and beta diversity between PD patients and healthy controls. We identified a considerable number of phage contigs that were differentially abundant in the two groups. Moreover, we improved the continuity and identification of the protein coding regions of the phage contigs by implementing alternative genetic codes. We built a classification system based on a selection of the phages differentially abundant in the groups. A machine learning approach based on phage abundances allowed a classification of the subjects into the PD or control group with an area under curve (AUC) of 0.969.

microbiology↗

bioRxiv2023

Metagenome-assembled microbial genomes from Parkinson's disease fecal samples

The human gut microbiome composition has been linked to Parkinsons disease (PD). However, knowledge of the gut microbiota on the genome level is still limited. Here we performed deep metagenomic sequencing and binning to build metagenome-assembled genomes (MAG) from 136 human fecal microbiomes (68 PD samples and 68 control samples). We constructed 952 non-redundant high-quality MAGs and compared them between PD and control groups. Among these MAGs, there were 22 different versions of Collinsella and Prevotella MAGs, indicating high variability of those genera in the human gut environment. Microdiversity analysis indicated that Ruminococcus bromii was statistically significantly (p < 0.002) more diverse on the strain level in the control samples compared to the PD samples. In addition, by clustering all genes and performing presence-absence analysis between groups, we identified several control-specific (p < 0.05) related genes, such as speF and Fe-S oxidoreductase. We also report detailed annotation of MAGs, including Clusters of Orthologous Genes (COG), Cas operon type, antiviral gene, prophage, and secondary metabolites biosynthetic gene clusters, which can be useful for providing a reference for future studies.

genomics↗

bioRxiv2023

Transcriptome analysis reveals novel regulators of the Scots pine stilbene pathway

Stilbenes are developmentally induced metabolites in Scots pine heartwood where they have important role in protecting wood from decaying fungi. The stilbene pathway is also stress inducible, and ultraviolet (UV)-C radiation was among the first discovered artificial stress activators of the pathway. Many conditions that activate the pathway are known, but the specific transcriptional regulators and the biosynthetic enzyme responsible for activating the stilbene precursor cinnamate in the pathway are unknown. Here we describe the first large-scale transcriptomic analysis of pine needles in response to UV-C exposure and treatment with translational inhibitor cycloheximide, both activating the transcription of stilbene pathway genes, to uncover the candidates for the transcriptional regulation of the pathway and the cinnamate activating CoA ligase. We show that the regulation of pine stilbene pathway has shared features with grapevine stilbene pathway. In both species, the stilbene pathway was transcriptionally activated after UV-C treatment, protein phosphatase inhibitors and plant hormones ethylene and jasmonate. The pine stilbene synthase promoter retains its inducibility when transformed in plants that normally do not synthesize stilbenes. Pine stilbene synthase promoter was able to activate the expression of a reporter gene in Arabidopsis in response to UV-C exposure and phosphatase inhibitors, but not as response to plant hormone treatment. This indicates that stilbene synthase gene regulation occurs both via ancient stress-response pathway(s) but also via species specific regulators. With transcriptomic approach we identified candidate enzymes for cinnamate acting CoA ligase and transcription factors regulating the pathway.

plant biology↗

bioRxiv2022

Fragmented habitat compensates for the adverse effects of genetic bottleneck

In the face of human-caused biodiversity crisis, understanding the theoretical basis of conservation efforts of endangered species and populations has become increasingly important. According to population genetics theory, population subdivision helps organisms retain genetic diversity, crucial for adaptation in a changing environment. Habitat shape is thought to be important for generating and maintaining population subdivision, but empirical cases are needed to test this assumption. We studied Saimaa ringed seals, landlocked in a labyrinthine lake and recovering from a drastic bottleneck, by whole-genome sequencing 105 individuals and additional individuals from three other ringed seal subspecies. We analyzed the distribution of variation and genetic relatedness among the individuals in relation to the habitat shape. Despite a severe history of a genetic bottleneck with prevalent homozygosity in Saimaa ringed seals, we found evidence for population structure mirroring the subregions of the lake. Highlighting the significance of habitat connectivity in conservation biology and the power of genomic tools in understanding its impact, genome-wide analyses showed that the subpopulations had retained unique variation and largely complementary patterns of homozygosity. Integration of genetic analyses in conservation decisions gives hope to Saimaa ringed seals and other endangered species in fragmented habitats.

evolutionary biology↗

bioRxiv2022

The transcription factor network of E. coli steers global responses to shifts in RNAP concentration

The robustness and sensitivity of gene networks to environmental changes is critical for cell survival. How gene networks produce specific, chronologically ordered responses to genome-wide perturbations, while robustly maintaining homeostasis, remains an open question. We analysed if short- and mid-term genome-wide responses to shifts in RNA polymerase (RNAP) concentration are influenced by the known topology and logic of the transcription factor network (TFN) of Escherichia coli. We found that, at the gene cohort level, the magnitude of the single-gene, mid-term transcriptional responses to changes in RNAP concentration can be explained by the absolute difference between the genes numbers of activating and repressing input transcription factors (TFs). Interestingly, this difference is strongly positively correlated with the number of input TFs of the gene. Meanwhile, short-term responses showed only weak influence from the TFN. Our results suggest that the global topological traits of the TFN of E. coli shape which gene cohorts respond to genome-wide stresses.

systems biology↗

bioRxiv2021

Convergent evolution of mevalonate pathway in Inonotus obliquus and Betula pendula.

Inonotus obliquus, Chaga mushroom, is a fungal species from Hymenochaetaceae family (Basidiomycota) which has been widely used for traditional medicine in Europe and Asia. Here, chaga genome was sequenced using Pacbio sequencing into a 50.7Mbp assembly consisting of 301 primary contigs with an N50 value of 375 kbp. Genome evolution analyses revealed a lineage-specific whole genome duplication event and an expansion of Cytochrome P450 superfamily. Fungal biosynthetic clusters were enriched for tandemly duplicated genes, suggesting that biosynthetic pathway evolution has proceeded through small-scale duplications. Metabolomic fingerprinting confirmed a highly complex terpene biosynthesis chemistry when compared against related fungal species lacking the genome duplication event.

evolutionary biology↗

bioRxiv2021

A Taphrina strain infecting the model plant Arabidopsis thaliana.

Yeasts are important plant-associated organisms that can modulate host immunity to either promote or prevent disease. Mechanisms of plant-yeast interactions, specifically of yeast perception by the plant innate immune system, remain unknown. Progress has been hindered by the scarcity of yeast species associated with the model plant Arabidopsis thaliana (Arabidopsis). We have previously isolated Taphrina strain M11 from wild Arabidopsis in the field. Taphrina are poorly studied dimorphic yeast-like fungi that are plant pathogens, often producing plant hormones and causing tumour-like and leaf deformation symptoms on their hosts. Here we characterize the interaction of M11 with Arabidopsis. Infection of Arabidopsis with the birch pathogen T. betulina, used as a non-host control, shows early HR, enhanced ROS accumulation, and limitation of growth, demonstrating that Arabidopsis had immunity against non-adapted yeasts. M11 triggered limited cell death, an attenuated ROS response, and grew in planta, as well as subtle but clear leaf deformation symptoms, demonstrating it is pathogenic. Hormone responsive promoter-reporter analysis demonstrated activation of cytokinin signalling during infection. Mutant infection assays indicate jasmonate and ethylene were required for immunity against M11. Analysis of the Taphrina M11 genome was used to mine evidence for yeast specific PAMPs which may underlie host immune responses against yeast-like fungi.

plant biology↗

bioRxiv2020

Improved chromosome level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) based on SMRT Sequencing and linkage map.

The Glanville fritillary (Melitaea cinxia) butterfly is a long-term model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome level assembly of the butterflys genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses. The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO, indicates that the genome contains 93 - 95% of the BUSCO genes in complete and single copies. We predicted 14,830 gene models using the MAKER pipeline and manually curated 1,232 of these gene models. The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome and genetics studies on this species.

genomics↗

bioRxiv2020

Genetic screen to saturate guard cell signaling network reveals a role of GDP-L-fucose metabolism in stomatal closure

Guard cells regulate plant gas exchange by controlling the aperture of stomatal pores. The process of stomatal closure involves a multi-input signaling network that governs the activity of ion channels, which in turn regulate guard cell turgor pressure and volume. Here we describe a forward genetic screen to identify novel components involved in stomatal movements. Through an ozone-sensitivity approach combined with whole-rosette gas exchange analysis, 130 mutants of established stomatal regulators and 76 novel mutants impaired in stomatal closure were identified. One of the novel mutants was mapped to MURUS1 (MUR1), the first enzyme in de novo GDP-L-fucose biosynthesis. Defects in synthesis or import of GDP-L-Fuc into the Golgi apparatus resulted in impaired stomatal closure to multiple stimuli. Stomatal phenotypes observed in mur1 were independent from the canonical guard cell signaling and instead could be related to altered mechanical properties of guard cell walls. Impaired fucosylation of xyloglucan, N-linked glycans and arabinogalactan proteins did not explain the aberrant function of mur1 stomata, however our data suggest that the stomatal phenotypes observed in mur1 can at least partially be attributed to defective dimerization of rhamnogalactouronan-II. In addition to providing the genetic framework for future studies on guard cell signaling, our work emphasizes the impact of fucose metabolism on stomatal movement.

plant biology↗

bioRxiv2020

Dual-light photodynamic therapy administered daily provides a sustained antibacterial effect on biofilm and prevents Streptococcus mutans adaptation

IntroductionAntibacterial photodynamic therapy (aPDT) and antibacterial blue light (aBL) are emerging treatment methods auxiliary to mechanical debridement for periodontitis. APDT provided with a near infrared (NIR) light in conjunction with an indocyanine green (ICG) photosensitizer has shown efficacy in several dental in-office-treatment protocols. In this study, we tested Streptococcus mutans biofilm sensitivity to either single-light (aPDT or aBL) or dual-light aPDT (simultaneous aPDT and aBL) exposure. Materials and MethodsBiofilm was cultured by pipeting diluted Streptococcus mutans suspension with growth medium on the bottom of well plates. Either a single-light aPDT (810-nm aPDT or 405-nm aBL) or a dual-light aPDT (simultaneous 810-nm aPDT and 405nm aBL) was applied, in both cases together with the ICG photosensitizer, while keeping the total light energy constant at 100J/cm2. Single-dose light exposures were given after one-day, four-day or fourteen-day biofilm incubations. Also, a repeated daily dose of the same light energy was applied during biofilm incubations on four-day and fourteen-day biofilms. Finally, antibacterial action of the dual-light aPDT with different relative ratios of 810 nm and 405 nm of light energy was examined on the single-day and four-day protocols. Biofilms were scraped, diluted into ratios between 1:1 to 1:100 000, and plated. After re-incubation, colony-forming units (CFUs) were counted, and confocal 3D biofilm imaging was performed. ResultsOn a one-day biofilm, dual-light aPDT was significantly more efficient than single-light aBL or aPDT, although all modalities were bactericidal. On a four-day maturated biofilm, a single exposure of aPDT or dual-light aPDT was more efficient than aBL, resulting in a four logarithmic scale reduction in bacterial counts. Surprisingly, when the same amount of aPDT was repeated with a daily dosing on a four-day or a fourteen-day biofilm, bacterial viability improved significantly. A similar but milder response of improved bacterial viability was seen after repetitive aBL application. The viability improvement was eliminated when dual-light aPDT was applied. By changing the relative light energy ratios in dual-light aPDT, a relative increase in aBL improved the antibacterial action of dual-light aPDT when the biofilm was older. ConclusionWhen aPDT is administered repeatedly to S. mutans biofilm, a single wavelength-based aBL or aPDT leads to a significant biofilm adaptation and increased S. mutans viability. The combined use of aBL light in synchrony with aPDT arrests the adaptation and provides significantly improved and sustained antibacterial efficacy.

microbiology↗

bioRxiv2019

Gut microbiome signatures of risk and prodromal markers of Parkinson's disease

ObjectivesAlterations of the gut microbiome in Parkinsons disease (PD) have been repeatedly demonstrated. However, little is known about whether such alterations precede disease onset and how they may be related to risk and prodromal markers of PD. We investigated associations of these features with gut microbiome composition. MethodsEstablished risk and prodromal markers of PD as well as factors related to diet/lifestyle, bowel function and medication were studied in relation to bacterial -/{beta}-diversity, enterotypes, and taxonomic composition in stool samples of 666 elderly TREND study participants. ResultsAmong risk and prodromal markers, physical inactivity, constipation and age showed associations with - and {beta}-diversity, and for both measures subthreshold parkinsonism and physical inactivity showed interaction effects. Moreover, male sex, possible REM-sleep behavior disorder (RBD), smoking as well as body-mass-index, antidiabetic and urate-lowering medication were associated with {beta}-diversity. Physical inactivity and constipation severity were increased in individuals with the Firmicutes-enriched enterotype. Subthreshold parkinsonism was least frequently observed in individuals with the Prevotella-enriched enterotype. Differentially abundant taxa were linked to constipation, physical inactivity, possible RBD, and subthreshold parkinsonism. Substantia nigra hyperechogenicity, olfactory loss, depression, orthostatic hypotension, urinary/erectile dysfunction, PD family history and the overall prodromal PD probability showed no significant microbiome associations. InterpretationSeveral risk and prodromal markers of PD are associated with changes in gut microbiome composition. However, the impact of the gut microbiome on PD risk and potential microbiome-dependent subtypes in the prodrome of PD need further investigation based on prospective clinical and (multi)omics data in incident PD cases.

neuroscience↗

bioRxiv2019

A novel phyllosphere resident Protomyces species that interacts with the Arabidopsis immune system.

We describe the genome contents of six Protomyces spp. that are pathogenic within the typical host range of the genus and a novel Protomyces strain (SC29) that was previously isolated from the phylloplane of wild Arabidopsis thaliana (Arabidopsis), an atypical or possible alternate host. Genome-wide phylogenetic analysis defined SC29 as a distinct Protomyces sp. Analysis of gene family expansions, gene retention, and gene loss patterns among these Protomyces spp. lead us to hypothesize that SC29 may have undergone a host jump. The role of phyllosphere residency in the lifecycle of Protomyces spp. was previously unknown. Genomic changes in SC29 and all other Protomyces spp. were consistent with adaptations to the plant phylloplane. As predicted by our analysis of its mating locus, SC29 did not cause disease on Arabidopsis as a single strain, but could persist in its phylloplane, while the closely related P. inouyei does not. SC29 treated Arabidopsis exhibited enhanced immunity against Botrytis cinerea infection, associated with activation of MAPK3/6, camalexin, and SA-signalling pathways. We conclude that SC29 is a novel Protomyces sp. able to survive in the Arabidopsis phylloplane and that phylloplane residency is an important element in the lifecycle of Protomyces spp.

microbiology↗