Additional file 1: Figure S1. of Gene and transposable element methylation in great tit (Parus major) brain and blood

Methylation level distribution for non-CpG sites (>0 %). Figure S2. non-CpG dinucleotide methylation preferences. Figure S3. CpG methylation level distribution in genes. Figure S4. non-CpG methylation level distribution in genes. Figure S5. Average CpG methylation in different gene partitions. Figure S6. The overlap for brain differentially hypo-methylated (A) and hyper-methylated (B) gene features. Figure S7. CpG methylation in relation to gene expression in brain. Figure S8. Relative CpG methylation for CGIs divided over three genomic regional classes. Figure S9. Relationship between non-CpG methylation level and gene length. Figure S10. Average gene length for 40 groups of percentiles of non-CpG methylated genes. Figure S11. Non-CpG methylation in relation to gene expression in brain. Figure S12. CpG methylation level distribution in TEs and their 2 kb flanking regions. Figure S13. Non-CpG methylation level distribution in TEs and their 2 kb flanking region. Figure S14. CpG methylation in relation to TE expression in the brain. Figure S15. Standardized gene expression from qPCR (Fold Change) as a function of the gene expression calculated from RNA-seq. Figure S16. Whole genome bisulfite sequencing (WGBS) vs. Reduced representation bisulfite sequencing (RRBS) in blood. Table S1. Average and median gene expression in brain for genes associated with differentially methylated CGIs. Table S2. Average and median gene expression levels for upper and lower 2.5 % non-CpG methylated genes (brain). Table S3. Blast2GO gene ontology annotation. Table S4. Methylation profiles in two blood RRBS samples. Table S5. Primer information for the genes used for qPCR validation. (DOCX 1636 kb

Additional file 4: of Gene and transposable element methylation in great tit (Parus major) brain and blood

Full GO-enrichment analysis for upper and lower non-CpG methylated genes: Tables S1 to S6. (XLSX 126 kb

Additional file 2: of Gene and transposable element methylation in great tit (Parus major) brain and blood

Full GO-enrichment analysis for differentially methylated gene features: Tables S1 to S6. (XLSX 169 kb

Additional file 10: of Living apart together: crosstalk between the core and supernumerary genomes in a fungal plant pathogen

TE integration and genome coverage on three supernumerary contigs. Integration of intact TEs on supernumerary contigs 668, 561 and 550. The graphs shows in a sliding 1 kb window the fraction of bases from the reference contig that is covered by HiSeq reads of every isolate (value between 0 and 1). The upper track shows all TEs on contig 668, 561 and 550 of isolate 2516 that are >1 kb and >90 % identity to the element prototype (Additional file 5) with yellow dots. This TE landscape was used for comparison with isolates 2548, 7555 and bfb0173. Dots for these three isolates indicate elements for which there is read mapping that an element has integrated in the exact same location as the element in isolate 2516 (and is therefore ancestral). Dots that align vertically are conserved in multiple isolates. (DOCX 261 kb

DataSheet_1_A comparison of three different delivery methods for achieving CRISPR/Cas9 mediated genome editing in Cichorium intybus L..pdf

Root chicory (Cichorium intybus L. var. sativum) is used to extract inulin, a fructose polymer used as a natural sweetener and prebiotic. However, bitter tasting sesquiterpene lactones, giving chicory its known flavour, need to be removed during inulin extraction. To avoid this extraction and associated costs, recently chicory variants with a lower sesquiterpene lactone content were created by inactivating the four copies of the germacrene A synthase gene (CiGAS-S1, -S2, -S3, -L) which encode the enzyme initiating bitter sesquiterpene lactone biosynthesis in chicory. In this study, different delivery methods for CRISPR/Cas9 reagents have been compared regarding their efficiency to induce mutations in the CiGAS genes, the frequency of off-target mutations as well as their environmental and economic impacts. CRISPR/Cas9 reagents were delivered by Agrobacterium-mediated stable transformation or transient delivery by plasmid or preassembled ribonucleic complexes (RNPs) using the same sgRNA. All methods used lead to a high number of INDEL mutations within the CiGAS-S1 and CiGAS-S2 genes, which match the used sgRNA perfectly; additionally, the CiGAS-S3 and CiGAS-L genes, which have a single mismatch with the sgRNA, were mutated but with a lower mutation efficiency. While using both RNPs and plasmids delivery resulted in biallelic, heterozygous or homozygous mutations, plasmid delivery resulted in 30% of unwanted integration of plasmid fragments in the genome. Plants transformed via Agrobacteria often showed chimerism and a mixture of CiGAS genotypes. This genetic mosaic becomes more diverse when plants were grown over a prolonged period. While the genotype of the on-targets varied between the transient and stable delivery methods, no off-target activity in six identified potential off-targets with two to four mismatches was found. The environmental impacts (greenhouse gas (GHG) emissions and primary energy demand) of the methods are highly dependent on their individual electricity demand. From an economic view - like for most research and development activities - employment and value-added multiplier effects are high; particularly when compared to industrial or manufacturing processes. Considering all aspects, we conclude that using RNPs is the most suitable method for genome editing in chicory since it led to a high efficiency of editing, no off-target mutations, non-transgenic plants with no risk of unwanted integration of plasmid DNA and without needed segregation of transgenes.</p

Correction: The Genomes of the Fungal Plant Pathogens <i>Cladosporium fulvum</i> and <i>Dothistroma septosporum</i> Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry

<p>Correction: The Genomes of the Fungal Plant Pathogens <i>Cladosporium fulvum</i> and <i>Dothistroma septosporum</i> Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry</p

Syntenic and non-syntenic regions between <i>C. fulvum</i> and <i>D. septosporum</i> are unevenly distributed over the <i>C. fulvum</i> scaffolds.

a<p>Number of repeat regions on syntenic vs. non-syntenic scaffolds.</p>b<p>A syntenic scaffold is one that contains at least a single syntenic block, but may not be syntenic along its entire length. Total syntenic scaffold size (37.4-Mb) is therefore larger than total syntenic size in whole genome (22.3-Mb).</p>c<p>Summed repeat length on syntenic <i>versus</i> non-syntenic scaffolds.</p

Arrangement of predicted dothistromin genes in <i>Dothistroma septosporum</i> and <i>Cladosporium fulvum</i>.

<p>A) Predicted dothistromin genes within the labeled clusters (left to right) are: <i>Ver1, DotC</i> (<i>Ver1</i> cluster); <i>PksA, CypX, AvfA, MoxY</i> (<i>PksA</i> cluster); <i>AflR, AflJ</i> (<i>AflR/J</i> cluster); <i>OrdB</i>, <i>AvnA, HexB, HexA, HypC, VbsA</i> (<i>VbsA</i> cluster); <i>Nor1, AdhA, VerB</i> (<i>Nor1</i> cluster). Positions of mini-clusters are approximate and they are not drawn to scale. Dothistromin genes within the published <i>D. septosporum PksA</i> and <i>VbsA</i> clusters <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003088#pgen.1003088-Bradshaw3" target="_blank">[36]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003088#pgen.1003088-Zhang1" target="_blank">[38]</a> and the newly discovered <i>AflR/J</i> and <i>Nor-1</i> clusters are found in the same order and orientation in <i>C. fulvum</i>. B) Expression of dothistromin biosynthetic genes (<i>Ver1, PksA, VbsA</i>) and regulatory gene (<i>AflR</i>) was determined in <i>D. septosporum</i> by quantitative PCR. Mean expression and standard deviations are shown for at least 3 biological replicates relative to β-tubulin expression. In <i>D. septosporum</i> all genes but <i>DsVbsA</i> are expressed more highly <i>in planta</i> (late-stage sporulating lesions from a forest sample) than in culture (PDB or B5 media) as highlighted by the dashed-grey line. C) Expression of <i>C. fulvum</i> genes is shown as for (B), revealing that expression is not higher during tomato infection than in culture (dashed-grey line). Note the different scales for expression, which reveal a much lower level of transcription both <i>in planta</i> and in PDB medium compared to <i>D. septosporum</i>.</p

Repetitive regions flanking known effectors of <i>Cladosporium fulvum</i>.

<p>Scaffolds harboring sequenced <i>C. fulvum</i> effector genes with flanking repeats. Repeat regions longer than 200-bp are shown, with different types indicated in different color code. Red arrows depict the effector genes and sizes are in kb. The sizes of scaffolds range from 8 to 213-kb but some are shortened to fit the figure due to differences in size.</p

Organization of repeats and pathogenicity-related genes in the <i>Dothistroma septosporum</i> genome.

<p>The fourteen chromosomes from the <i>D. septosporum</i> genome assembly are shown as GC (dark grey line) and AT (pale grey line) content (%) plots made from a 500-bp sliding window using Geneious (<a href="http://www.geneious.com" target="_blank">www.geneious.com</a>). All chromosomes have telomere sequence at both ends except chromosomes 2, 11 and 14 which have telomere sequences only at the left end as shown in the figure. Chromosome 1 has been split into two parts in the figure (L, R) because of its length, and the GC/AT content scale is shown beside the right arm of this chromosome. The positions of putative <i>Avr</i> and <i>Ecp</i> effector, secondary metabolite, dothistromin biosynthesis, and mating type genes are shown above the GC/AT content plot, while the positions of repeats (>200-bp) are shown below the plot. Color-coding of the gene and repeat types is indicated in the legend. Most chromosomes have repeat clusters at one or two sites that coincide with regions of high AT content. The chromosome sizes are to scale, as indicated by the vertical pale grey lines, with the values (in kb) shown at the bottom; neither the genes nor the repeats are drawn to scale.</p