Project description:Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to phenotypic diversity, its interaction with genetic variation requires further investigation. MethylC-seq from naturally-occurring Arabidopsis accessions
Project description:eQTL mapping in a F1 diversity panel generated from 111 A.thaliana natural accessions 57 F1 lines without replicates, the 5th or 6th true leaf
Project description:Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to phenotypic diversity, its interaction with genetic variation requires further investigation. Here, we report population-wide DNA sequencing of genomes, transcriptomes, and methylomes of wild Arabidopsis thaliana accessions. Single cytosine methylation polymorphisms are unlinked to genotype. However, the rate of linkage disequilibrium decay amongst differentially methylated regions targeted by RNA-directed DNA methylation is similar to the rate for single nucleotide polymorphisms. Association analyses of these RNA-directed DNA methylation regions with genetic variants identified 2,372 methylQTL, which revealed the first population estimate of genetically dependent methylation variation. Analysis of invariably methylated transposons and genes across this population indicates that loci targeted by RNA-directed DNA methylation are epigenetically reactivated during male gametogenesis, which facilitates their silencing across generations. RNA-seq from naturally-occurring Arabidopsis accessions
Project description:Comparative genomic hybridisation of Streptococcus pneumoniae isolates from a single clonal complex, in order to determine genomic diversity. Isolates were selected from a range of tissue types and serotypes in order to cover the full diversity of the clone, and also in order to try and identify tissue-specific genes
Project description:Bifidobacteria have been described as a key component of the human gut microbiota, and recently significant efforts have been made to investigate their genome contents and assess the genetic variability at inter- and intra-species level. In the current work we investigated genome diversity among representatives of bifidobacterial species, i.e., Bifidobacterium pseudocatenulatum. These analyses were performed with comparative genomic hybridization (CGH) experiments and they revealed the existence of a strictly conserved set of 685 gene families. Furthermore, CGH analyses showed that genetic regions of diversity included mobile elements and putative genomic life-style adaptation islands, such as loci that encode pili and capsular polysaccharides, and genes involved in carbohydrate metabolism. CGH analysis was performed with microarrays that were based on the genome sequences of Bifidobacteriapseudocatenulatum DSM20438 (ABXX00000000.2). A total of 39,249 probes of 35 bp in length were designed using OligoArray 2.1 software. Oligos were synthesized in triplicate on a 2 × 40-k CombiMatrix array (CombiMatrix, Mulkiteo, USA). Replicates were distributed on the chip at random, non-adjacent positions. A set of 74 negative control probes designed on phage and plant sequences was also included on the chip. Seventeen micrograms of purified genomic DNA was labeled with Cy5-ULS using the Kreatech ULS array CGH Labeling kit (Kreatech Diagnostics) according to the supplier’s instructions. Hybridization of labeled test DNA to these microarrays was performed according to CombiMatrix protocols.
Project description:Bifidobacteria have been described as a key component of the human gut microbiota, and recently significant efforts have been made to investigate their genome contents and assess the genetic variability at inter- and intra-species level. In the current work we investigated genome diversity among representatives of bifidobacterial species, i.e., Bifidobacterium adolescentis. These analyses were performed with comparative genomic hybridization (CGH) experiments and they revealed the existence of a strictly conserved set of 685 gene families. Furthermore, CGH analyses showed that genetic regions of diversity included mobile elements and putative genomic life-style adaptation islands, such as loci that encode pili and capsular polysaccharides, and genes involved in carbohydrate metabolism. CGH analysis was performed with microarrays that were based on the genome sequences of B. adolescentis ATCC15703 (NC_008618) . A total of 39,249 probes of 35 bp in length were designed using OligoArray 2.1 software. Oligos were synthesized in triplicate on a 2 × 40-k CombiMatrix array (CombiMatrix, Mulkiteo, USA). Replicates were distributed on the chip at random, non-adjacent positions. A set of 74 negative control probes designed on phage and plant sequences was also included on the chip. Seventeen micrograms of purified genomic DNA was labeled with Cy5-ULS using the Kreatech ULS array CGH Labeling kit (Kreatech Diagnostics) according to the supplier’s instructions. Hybridization of labeled test DNA to these microarrays was performed according to CombiMatrix protocols.
Project description:Epigenetic variation can impact gene transcription and may play roles in phenotypic diversity and adaptation. Here we report 1,107 high quality single-base resolution methylomes, and 1,210 transcriptomes from the 1001 Arabidopsis Genomes population. Analyses reveal strong effects of geographic origin on average DNA methylation levels, alterations of gene expression by epialleles and a highly complex genetic basis for DNA methylation. Physical genome maps for nine of the most diverse accessions revealed how transposable elements and other structural variations shaped the epigenome to allow rapid adaptation to environmental changes, with strong emphasis on disease resistance. Analysis of the cistromes and epicistromes in these accessions revealed a significant association between both methylation and nucleotide variation and the conservation of transcription factor binding sites. The Arabidopsis thaliana 1001 Epigenomes Project now provides a comprehensive resource to help further understand how epigenetic variation contributes to both molecular and phenotypes in natural populations of the most widely studied reference plant.
Project description:Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to phenotypic diversity, its interaction with genetic variation requires further investigation. Here, we report population-wide DNA sequencing of genomes, transcriptomes, and methylomes of wild Arabidopsis thaliana accessions. Single cytosine methylation polymorphisms are unlinked to genotype. However, the rate of linkage disequilibrium decay amongst differentially methylated regions targeted by RNA-directed DNA methylation is similar to the rate for single nucleotide polymorphisms. Association analyses of these RNA-directed DNA methylation regions with genetic variants identified 2,372 methylQTL, which revealed the first population estimate of genetically dependent methylation variation. Analysis of invariably methylated transposons and genes across this population indicates that loci targeted by RNA-directed DNA methylation are epigenetically reactivated during male gametogenesis, which facilitates their silencing across generations.
Project description:ZIKV strains belong to three phylogenetic lineages: East African, West African, and Asian/American. RNA virus genomes exist as populations of genetically-related sequences whose heterogeneity may impact viral fitness, evolution, and virulence. The genetic diversity of representative ZIKVs (N=7) from each lineage was examined using next generation sequencing (NGS) paired with downstream Shannon entropy calculation and single nucleotide variant (SNV) analysis. This comprehensive analysis of ZIKV genetic diversity provides insight into the genetic diversity of ZKIV and repository of SNV positions across lineages.