Functional genomics of the Glanville fritillary butterfly

The glanville fritillary butterfly is an important ecological model species for habitat fragmentation, whose genetics was poorly understood. In order to expand the research of this butterfly species into the realm of functional genomics a lot genetic tools were developed. These tools were used to investigate the genetic basis of phenotypic traits that are important in the wild. Gene expression microarrays based on de novo assembled transcriptome were used to study expression differences between adult butterflies from newly established colonies and older colonies as well as gene expression variation among larval families reared in three thermal regimens during final larval instar. Colonization and larval development are crucially important in maintaining the metapopulation structure of glanville fritillary butterfly in the Åland. We identified gene expression differences than can explain the observed variation in the phenotypes in the natural population. We sequenced the full genome of the glanville fritillary butterfly and used this to do additional gene expression and allelic variation analysis variation from multiple populations around the baltic sea using rna sequencing (rna-seq). Flight induced gene expression changes were analyzed using butterflies from Åland islands and the small isolated Pieni Tytärsaari ("daughter island") populations in a forced flight experiment. Fragmented populations (Åland islands and Uppland) were compared to continuous populations (saaremaa and öland) in order to find common signatures of selection caused by habitat fragmentation. Together these four full-genome studies have revealed that habitat fragmentation causes selection pressure on an intricately connected set of genes and pathways that leads to a so called life history syndrome , where the butterflies that colonize new habitat patches have a distinct set of traits and associated expression differences in these traits that make them more successful in establishing new colonies.Täpläverkkoperhonen on tärkeä ekologinen mallieläin elinympäristön pirstoutumiselle. lajin genetiikka on kuitenkin viimeaikoihin saakka ollut puutteellinen. tutkimuksen laajentaminen genetiikkaan ja toiminnalliseen genomiikkaan vaati uusien geneettisten työkalujen kehittämistä ja soveltamista. Geneettiset työkalut mahdollistivat pitkään tutkittujen ekologisesti merkittävien fenotyyppisten muuttujien analysoimisen genomisella tasolla. geeni-ilmentymisen tutkimiseen kehitimme geenisirun de novo koostetusta transkriptomista. Geenisiruilla selvitimme geeni-ilmentymisen eroja aikuisista täpläverkkoperhosista, jotka olivat peräisin joko hiljattain kolonisoiduilta tai pitkää asutetuilta kedoilta. Selvitimme myös yksilön kehityksen aikana muuttuvaa geeni-ilmentymistä viimeisen toukkavaiheen aikana eri toukka-perheistä olevilla yksilöillä, jotka kasvatettiin kolmessa eri lämpökäsittelyssä. Uusien asuinympäristöjen kolonisaatio ja toukan kehitys ovat täpläverkkoperhoselle kriittisiä ahvenanmaan metapopulaation ylläpitämisessä. löysimme geeni-ilmentymiseroja, jotka voivat selittää luonnonpopulaatioissa fenotyyppitasolla havaittua vaihtelua. Seuraavana sekvensoimme täpläverkkoperhosen koko genomin ja käytimme sitä hyödyksi geeni-ilmentymisen ja alleelivariaation selvittämiseen useista itämeren täpläverkkoperhospopulaatioista, käyttäen rna sekvensointia (rna-seq). Metaboliaa mittaavassa lentokokeessa selvitimme lennon seurauksena muuntuneita geeni-ilmentymisiä Ahvenanmaan ja Pienen Tytärsaaren populaatioista. Elinympäristön pirstoutumisen vaikutusta geeni-ilmentymiseen ja alleelivariaatioon selvitimme vertaamalla kahta yhtenäisestä elinympäristöstä olevaa populaatioita (Saarenmaa ja Öölanti) kahteen pirstoutuneesta elinympäristöstä olevaan populaatioon (Ahvenanmaa ja Uplanti). Havaitsimme että elinympäristön pirstoutuminen johtaa monen ominaisuuksia samanaikaiseen valintaan, joista lentokyky edustaa yhtä osaa. Yhdessä nämä neljä genominlaajuista tutkimusta ovat paljastaneet että täpläverkkoperhosen ekologian kannalta merkittävä fenotyyppinen vaihtelu on geeni-ilmentymisen tasolla kytkeytynyt, ja on samojen säätelygeenien ja säätelyreittien ohjaama

Fight or flight? – Flight increases immune gene expression but does not help to fight an infection

Flight represents a key trait in most insects, being energetically extremely demanding, yet often necessary for foraging and reproduction. Additionally, dispersal via flight is especially important for species living in fragmented landscapes. Even though, based on life-history theory, a negative relationship may be expected between flight and immunity, a number of previous studies have indicated flight to induce an increased immune response. In this study, we assessed whether induced immunity (i.e. immune gene expression) in response to 15-min forced flight treatment impacts individual survival of bacterial infection in the Glanville fritillary butterfly (Melitaea cinxia). We were able to confirm previous findings of flight-induced immune gene expression, but still observed substantially stronger effects on both gene expression levels and life span due to bacterial infection compared to flight treatment. Even though gene expression levels of some immunity-related genes were elevated due to flight, these individuals did not show increased survival of bacterial infection, indicating that flight-induced immune activation does not completely protect them from the negative effects of bacterial infection. Finally, an interaction between flight and immune treatment indicated a potential trade-off: flight treatment increased immune gene expression in naive individuals only, whereas in infected individuals no increase in immune gene expression was induced by flight. Our results suggest that the up-regulation of immune genes upon flight is based on a general stress response rather than reflecting an adaptive response to cope with potential infections during flight or in new habitats.Peer reviewe

A comprehensive epigenomic analysis of phenotypically distinguishable, genetically identical female and male Daphnia pulex

Background Daphnia species reproduce by cyclic parthenogenesis involving both sexual and asexual reproduction. The sex of the offspring is environmentally determined and mediated via endocrine signalling by the mother. Interestingly, male and female Daphnia can be genetically identical, yet display large differences in behaviour, morphology, lifespan and metabolic activity. Our goal was to integrate multiple omics datasets, including gene expression, splicing, histone modification and DNA methylation data generated from genetically identical female and male Daphnia pulex under controlled laboratory settings with the aim of achieving a better understanding of the underlying epigenetic factors that may contribute to the phenotypic differences observed between the two genders. Results In this study we demonstrate that gene expression level is positively correlated with increased DNA methylation, and histone H3 trimethylation at lysine 4 (H3K4me3) at predicted promoter regions. Conversely, elevated histone H3 trimethylation at lysine 27 (H3K27me3), distributed across the entire transcript length, is negatively correlated with gene expression level. Interestingly, male Daphnia are dominated with epigenetic modifications that globally promote elevated gene expression, while female Daphnia are dominated with epigenetic modifications that reduce gene expression globally. For examples, CpG methylation (positively correlated with gene expression level) is significantly higher in almost all differentially methylated sites in male compared to female Daphnia. Furthermore, H3K4me3 modifications are higher in male compared to female Daphnia in more than 3/4 of the differentially regulated promoters. On the other hand, H3K27me3 is higher in female compared to male Daphnia in more than 5/6 of differentially modified sites. However, both sexes demonstrate roughly equal number of genes that are up-regulated in one gender compared to the other sex. Since, gene expression analyses typically assume that most genes are expressed at equal level among samples and different conditions, and thus cannot detect global changes affecting most genes. Conclusions The epigenetic differences between male and female in Daphnia pulex are vast and dominated by changes that promote elevated gene expression in male Daphnia. Furthermore, the differences observed in both gene expression changes and epigenetic modifications between the genders relate to pathways that are physiologically relevant to the observed phenotypic differences.Peer reviewe

Characterisation of the dynamic nature of lipids throughout the lifespan of genetically identical female and male Daphnia magna

Lipids play a significant role in regulation of health and disease. To enhance our understanding of the role of lipids in regulation of lifespan and healthspan additional studies are required. Here, UHPLC-MS/MS lipidomics was used to measure dynamic changes in lipid composition as a function of age and gender in genetically identical male and female Daphnia magna with different average lifespans. We demonstrate statistically significant age-related changes in triglycerides (TG), diglycerides (DG), phosphatidylcholine, phosphatidylethanolamine, ceramide and sphingomyelin lipid groups, for example, in males, 17.04% of TG lipid species decline with age whilst 37.86% increase in relative intensity with age. In females, 23.16% decrease and 25.31% increase in relative intensity with age. Most interestingly, the rate and direction of change can differ between genetically identical female and male Daphnia magna, which could be the cause and/or the consequence of the different average lifespans between the two genetically identical genders. This study provides a benchmark dataset to understand how lipids alter as a function of age in genetically identical female and male species with different average lifespan and ageing rate.Peer reviewe

Pattern of DNA methylation in daphnia : evolutionary perspective

DNA methylation is an evolutionary ancient epigenetic modification that is phylogenetically widespread. Comparative studies of the methylome across a diverse range of non-conventional and conventional model organisms is expected to help reveal how the landscape of DNA methylation and its functions have evolved. Here, we explore the DNA methylation profile of two species of the crustacean Daphnia using whole genome bisulfite sequencing. We then compare our data with the methylomes of two insects and two mammals to achieve a better understanding of the function of DNA methylation in Daphnia. Using RNA-sequencing data for all six species, we investigate the correlation between DNA methylation and gene expression. DNA methylation in Daphnia is mainly enriched within the coding regions of genes, with the highest methylation levels observed at exons 2-4. In contrast, vertebrate genomes are globally methylated, and increase towards the highest methylation levels observed at exon 2, and maintained across the rest of the gene body. Although DNA methylation patterns differ among all species, their methylation profiles share a bimodal distribution across the genomes. Genes with low levels of CpG methylation and gene expression are mainly enriched for species specific genes. In contrast, genes associated with high methylated CpG sites are highly transcribed and evolutionary conserved across all species. Finally, the positive correlation between internal exons and gene expression potentially points to an evolutionary conserved mechanism, whereas the negative regulation of gene expression via methylation of promoters and exon 1 is potentially a secondary mechanism that has been evolved in vertebrates

Inter-organellar and systemic responses to impaired mitochondrial matrix protein import in skeletal muscle

Effective protein import from cytosol is critical for mitochondrial functions and metabolic regulation. We describe here the mammalian muscle-specific and systemic consequences to disrupted mitochondrial matrix protein import by targeted deletion of the mitochondrial HSP70 co-chaperone GRPEL1. Muscle-specific loss of GRPEL1 caused rapid muscle atrophy, accompanied by shut down of oxidative phosphorylation and mitochondrial fatty acid oxidation, and excessive triggering of proteotoxic stress responses. Transcriptome analysis identified new responders to mitochondrial protein import toxicity, such as the neurological disease-linked intermembrane space protein CHCHD10. Besides communication with ER and nucleus, we identified crosstalk of distressed mitochondria with peroxisomes, in particular the induction of peroxisomal Acyl-CoA oxidase 2 (ACOX2), which we propose as an ATF4-regulated peroxisomal marker of integrated stress response. Metabolic profiling indicated fatty acid enrichment in muscle, a shift in TCA cycle intermediates in serum and muscle, and dysregulated bile acids. Our results demonstrate the fundamental importance of GRPEL1 and provide a robust model for detecting mammalian inter-organellar and systemic responses to impaired mitochondrial matrix protein import and folding.Peer reviewe

The meristem-associated endosymbiont Methylorubrum extorquens DSM13060 reprograms development and stress responses of pine seedlings

Microbes living in plant tissues-endophytes-are mainly studied in crop plants where they typically colonize the root apoplast. Trees-a large carbon source with a high capacity for photosynthesis-provide a variety of niches for endophytic colonization. We have earlier identified a new type of plant-endophyte interaction in buds of adult Scots pine, where Methylorubrum species live inside the meristematic cells. The endosymbiont Methylorubrum extorquens DSM13060 significantly increases needle and root growth of pine seedlings without producing plant hormones, but by aggregating around host nuclei. Here, we studied gene expression and metabolites of the pine host induced by M. extorquens DSM13060 infection. Malic acid was produced by pine to potentially boost M. extorquens colonization and interaction. Based on gene expression, the endosymbiont activated the auxin- and ethylene (ET)-associated hormonal pathways through induction of CUL1 and HYL1, and suppressed salicylic and abscisic acid signaling of pine. Infection by the endosymbiont had an effect on pine meristem and leaf development through activation of GLP1-7 and ALE2, and suppressed flowering, root hair and lateral root formation by downregulation of AGL8, plantacyanin, GASA7, COW1 and RALFL34. Despite of systemic infection of pine seedlings by the endosymbiont, the pine genes CUL1, ETR2, ERF3, HYL, GLP1-7 and CYP71 were highly expressed in the shoot apical meristem, rarely in needles and not in stem or root tissues. Low expression of MERI5, CLH2, EULS3 and high quantities of ononitol suggest that endosymbiont promotes viability and protects pine seedlings against abiotic stress. Our results indicate that the endosymbiont positively affects host development and stress tolerance through mechanisms previously unknown for endophytic bacteria, manipulation of plant hormone signaling pathways, downregulation of senescence and cell death-associated genes and induction of ononitol biosynthesis.Peer reviewe

Serum Creatine, Not Neurofilament Light, Is Elevated in CHCHD10-Linked Spinal Muscular Atrophy

ObjectiveTo characterize serum biomarkers in mitochondrial CHCHD10-linked spinal muscular atrophy Jokela (SMAJ) type for disease monitoring and for the understanding of pathogenic mechanisms. MethodsWe collected serum samples from a cohort of 49 patients with SMAJ, all carriers of the heterozygous c.197G>T p.G66V variant in CHCHD10. As controls, we used age- and sex-matched serum samples obtained from Helsinki Biobank. Creatine kinase and creatinine were measured by standard methods. Neurofilament light (NfL) and glial fibrillary acidic protein (GFAP) were measured with single molecule array (Simoa), fibroblast growth factor 21 (FGF-21), and growth differentiation factor 15 (GDF-15) with an enzyme-linked immunosorbent assay. For non-targeted plasma metabolite profiling, samples were analyzed with liquid chromatography high-resolution mass spectrometry. Disease severity was evaluated retrospectively by calculating a symptom-based score. ResultsAxon degeneration marker, NfL, was unexpectedly not altered in the serum of patients with SMAJ, whereas astrocytic activation marker, GFAP, was slightly decreased. Creatine kinase was elevated in most patients, particularly men. We identified six metabolites that were significantly altered in serum of patients with SMAJ in comparison to controls: increased creatine and pyruvate, and decreased creatinine, taurine, N-acetyl-carnosine, and succinate. Creatine correlated with disease severity. Altered pyruvate and succinate indicated a metabolic response to mitochondrial dysfunction; however, lactate or mitochondrial myopathy markers FGF-21 or GDF-15 was not changed. ConclusionsBiomarkers of muscle mass and damage are altered in SMAJ serum, indicating a role for skeletal muscle in disease pathogenesis in addition to neurogenic damage. Despite the minimal mitochondrial pathology in skeletal muscle, signs of a metabolic shift can be detected.Peer reviewe