Project description:Genetic variation is regarded as a prerequisite for evolution. Theoretical models suggest epigenetic information inherited independently of DNA sequence can also enable evolution. However, whether epigenetic inheritance mediates phenotypic evolution in natural populations is unknown. Here we show that natural epigenetic DNA methylation variation in gene bodies regulates genes expression, and thereby influences the natural variation of complex traits in Arabidopsis thaliana. Notably, the effects of methylation variation on phenotypic diversity and gene expression variance are comparable with those of DNA sequence polymorphism. We also identify methylation epialleles in numerous genes associated with environmental conditions in native habitats, suggesting that intragenic methylation facilitates adaptation to fluctuating environments. Our results demonstrate that methylation variation fundamentally shapes phenotypic diversity in natural populations and provides an epigenetic basis for adaptive Darwinian evolution independent of genetic polymorphism.
Project description:RNASeq of roots from two genotypes of Arabidopsis thaliana plants, Col-0 and myb36-2 grown axenically or with a 41 member bacterial Synthetic Community (SynCom) to explore the interaction between the root diffusion barriers and the root microbiome.
Project description:Root branching in response to changes in nitrogen status in the soil, is a dramatic example of the plant’s remarkable developmental plasticity. In recent work we investigated the genetic architecture of developmental plasticity, combining phenoclustering and genome-wide association studies in 96 Arabidopsis thaliana ecotypes with expression profiling in 7 ecotypes, to characterise natural variation in root architectural plasticity at the phenotypic, genetic, and transcriptional levels. This series contains the microarray expression data for 7 ecotypes that represent a range of root branching strategies. We used microarrays to detail the global programme of gene expression involved in the plants response to nitrogen in the root and identified distinct classes of up- and down-regulated genes in the seven different Arabidopsis ecotypes during this process.
Project description:Roots of Arabidopsis thaliana do not engage in symbiotic association with mycorrhizal fungi but host taxonomically diverse fungal communities that influence health and disease states. We sequenced the genomes of 41 isolates representative of the A. thaliana root mycobiota for comparative analysis with 79 other plant-associated fungi. We report that root mycobiota members evolved from ancestors having diverse lifestyles and retained diverse repertoires of plant cell wall-degrading enzymes (PCWDEs) and effector-like small secreted proteins. We identified a set of 84 gene families predicting best endophytism, including families encoding PCWDEs acting on xylan (GH10) and cellulose (AA9). These genes also belong to a core transcriptional response induced by phylogenetically-distant mycobiota members in A. thaliana roots. Recolonization experiments with individual fungi indicated that strains with detrimental effects in mono-association with the host not only colonize roots more aggressively than those with beneficial activities but also dominate in natural root samples. We identified and validated the pectin degrading enzyme family PL1_7 as a key component linking aggressiveness of endophytic colonization to plant health.
Project description:Identifying when and where environmental change induces molecular responses in natural populations is an important goal in contemporary ecology as it can aid in identifying molecular signatures of populations experiencing stressful conditions and potentially inform if species are approaching the limits of their tolerance niches. Achieving this goal is hampered by our understanding of the influence of environmental variation on the molecular systems of most ecologically relevant species as the pathways underlying fitness-affecting plastic responses have primarily been studied in model organisms under controlled laboratory conditions. To start overcoming this limitation, we establish relationships between protein abundance patterns and the abiotic environment. Profiling the proteomes of 24 natural populations of the putatively cold-adapted species Crunoecia irrorata and subsequently relating these profiles to natural variations in their abiotic freshwater spring habitats shows that protein abundances and networks respond to variation according to the functional roles these proteins have. We provide evidence that geographic and environmental distances affect protein abundances and identifications and that baseline abundances can be determined and used as information rather than noise in comparative field studies. Taking this naturally induced variation into account is a prerequisite if we are to identify the effects environmental change has on natural populations.
Project description:The identification of processes activated by specific microbes during microbiota colonization of plant roots has been hampered by technical constraints in metatranscriptomics. These include lack of reference genomes, high representation of host or microbial rRNA sequences in datasets, or difficulty to experimentally validate gene functions. Here, we recolonized germ-free Arabidopsis thaliana with a synthetic, yet representative root microbiota comprising 106 genome-sequenced bacterial and fungal isolates. We used multi-kingdom rRNA depletion, deep RNA-sequencing and read mapping against reference microbial genomes to analyse the in-planta metatranscriptome of abundant colonizers. We identified over 3,000 microbial genes that were differentially regulated at the soil-root interface. Translation and energy production processes were consistently activated in planta, and their induction correlated with bacterial strains’ abundance in roots. Finally, we used targeted mutagenesis to show that several genes consistently induced by multiple bacteria are required for root colonization in one of the abundant bacterial strains (a genetically tractable Rhodanobacter). Our results indicate that microbiota members activate strain-specific processes but also common gene sets to colonize plant roots.