Journal: Advanced Science

Article Title: Accounting for ALA Natural Mutations Enhances the Efficiency of Graphene Oxide Nanopriming in Bar ‐Modified Arabidopsis

doi: 10.1002/advs.202500058

Figure Lengend Snippet: Genome‐wide DNA methylation analysis in WT and GM seeds before and after GO treatments. a) Circos plots show the methylation levels across different chromosomes for WT and GM seeds before and after GO exposure. The colored sections on the outer ring represent different chromosomes. The concentric rings from outer to inner illustrate untreated samples, 0.75 mg‐C/L GO‐treated samples, and 1.5 mg‐C/L GO‐treated samples. Whole‐genome methylation levels were calculated as mean values within 100 kb windows for each chromosome. The color gradient from cyan to red indicates the methylation percentages, whereas the innermost ring represents gene density. b) Whole‐genome methylation levels in CG, CHG, and CHH contexts for WT and GM seeds after various GO exposures (sample size n = 3). Data are presented as means ± SD, with gray and red dots depicting individual data points in the WT and GM groups. Three biological replicates were included for each treatment. Independent sample two‐sided t ‐tests were performed: * indicates significant differences within the same genotype relative to the condition without GO, and # indicates significant differences between GM and WT under the same treatment. Significant differences are marked with p values. c) Differential methylation regions at promoter regions and gene bodies of key genes (Figure ) are represented by a color gradient showing Log 2 FC in methylation levels. Triangles and circles indicate CG and CHH methylation, respectively. No differential methylation was observed in the CHG context. Regions without differential methylation are blank. d) Dot plots of differential methylation for ALA metabolism‐related genes compare promoter and gene body methylation across conditions. Blue and red dots denote different comparisons, as indicated in the legend. Dots with circles indicate methylation levels with |Log 2 FC| >10.

Article Snippet: Library construction was performed using an MGIEasy whole‐genome bisulfite library preparation kit (MGI).

Techniques: Genome Wide, DNA Methylation Assay, Methylation

Journal: iScience

Article Title: Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content

doi: 10.1016/j.isci.2021.102219

Figure Lengend Snippet: The five different enzyme concentrations/ng DNA using stLFR sequencing of D. wulumuqiensis R12 (A) The barcode frequency distribution of five conditions. (B) The Supernova-assembled statistics of five conditions.

Article Snippet: Different from previous studies, in which stLFR was applied for animal or plant genomics, our method allowed the pooling and parallel sequencing of a large number of samples, which cannot be achieved by 10X Genomics read cloud sequencing technology ( ).

Techniques: Sequencing

Journal: iScience

Article Title: Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content

doi: 10.1016/j.isci.2021.102219

Figure Lengend Snippet: Statistics of three sequencing strategies assembly genomes

Article Snippet: Different from previous studies, in which stLFR was applied for animal or plant genomics, our method allowed the pooling and parallel sequencing of a large number of samples, which cannot be achieved by 10X Genomics read cloud sequencing technology ( ).

Techniques: Sequencing

Journal: iScience

Article Title: Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content

doi: 10.1016/j.isci.2021.102219

Figure Lengend Snippet: The three sequencing strategies-assembled genome statistics of the six bacterial strains The total assembly genome length (bottom), N50 length (middle), and maximum scaffold length (top) by using different algorithms are shown. The assembly algorithms of each sample from left to right are NGS draft genome, stLFR chromosome scaffolds, stLFR + ONT complete genome, ONT complete genome assembled by Canu, and Hybrid complete genome assembled by Unicycler using ONT reads and NGS reads.

Article Snippet: Different from previous studies, in which stLFR was applied for animal or plant genomics, our method allowed the pooling and parallel sequencing of a large number of samples, which cannot be achieved by 10X Genomics read cloud sequencing technology ( ).

Techniques: Sequencing

Journal: iScience

Article Title: Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content

doi: 10.1016/j.isci.2021.102219

Figure Lengend Snippet: The longest chromosome sequence comparisons for strains (A–D) (A) E. coli K-12 using stLFR-assembled genome and the third-generation sequencing-assembled genome, (B) Rufibacter sp. LB8, (C) D. wulumuqiensis R12, and (D) J. melonis M714 using stLFR-assembled genomes, stLFR + ONT-assembled genomes, ONT + NGS Unicycler-assembled genomes, and ONT Canu-assembled genomes. The outermost circle is GC heatmap, the next circle is the histogram of GC (red: G > C; blue: G < (C), and the middle circle is gene density in chromosomes. The last two circles are the COG positive/negative annotation heatmaps, and the legend is shown at the bottom.

Article Snippet: Different from previous studies, in which stLFR was applied for animal or plant genomics, our method allowed the pooling and parallel sequencing of a large number of samples, which cannot be achieved by 10X Genomics read cloud sequencing technology ( ).

Techniques: Sequencing

Journal: iScience

Article Title: Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content

doi: 10.1016/j.isci.2021.102219

Figure Lengend Snippet: The longest chromosome sequence comparison (A and B) (A) Sequences alignment viewer and (B) accuracy evaluation of stLFR genomes, stLFR + ONT genomes, Canu-assembled genomes, and NGS genomes when compared with the complete genomes assembled by Unicycler using NGS and ONT reads for the strains E. coli K-12, Rufibacter sp. LB8, D. wulumuqiensis R12, and J. melonis M714.

Article Snippet: Different from previous studies, in which stLFR was applied for animal or plant genomics, our method allowed the pooling and parallel sequencing of a large number of samples, which cannot be achieved by 10X Genomics read cloud sequencing technology ( ).

Techniques: Sequencing, Comparison