Journal: Nature Communications

Article Title: Evolutionary origin and population diversity of a cryptic hybrid pathogen

doi: 10.1038/s41467-024-52639-1

Figure Lengend Snippet: Genome features and ohnolog information for the parental and hybrid isolates

Article Snippet: Library preparation was conducted using the Twist Whole Genome / Metagenomics_LowpassWGS-Twist Miniprep (Twist Bioscience).

Techniques:

Journal: Nature Communications

Article Title: Evolutionary origin and population diversity of a cryptic hybrid pathogen

doi: 10.1038/s41467-024-52639-1

Figure Lengend Snippet: A Among a total of 10,078 orthologous groups of genes, 7485 are categorized as core (present in 100% of isolates; N = 22) and 2593 as accessory (present in <100% of isolates; N < 22); among these accessory genes, 1448 are softcore (present in ≥95% and <100%; N = 21), 793 are shell (5-95% of isolates; 21 > N ≥ 2), and 352 are cloud (present in less than 5% of isolates; N = 1). B Among 95 biosynthetic gene cluster families (BGCFs), 46 are categorized as core and 49 as accessory (9 are software, 25 are shell, and 15 are cloud). C The number of accessory gene families increases as the number of strains increases, suggesting additional sequencing is needed to fully capture A. latus gene content variation. N values varied between 1 and 26,393 depending on the number of strains being analyzed. D The number of accessory BGCFs substantially increases with additional isolates suggesting the gene content variation of BGCs has also yet to be captured. Notably the core genome is larger among gene families, whereas the accessory portion is larger among BGCFs. Errors bars indicate standard deviation. E Protein sequence lengths differed among gene categories wherein core and softcore genes are longer than shell and cloud genes ( N = 10,079). F As genes were less frequently observed among isolates, they were also functionally annotated less frequently. G The number of genes in BGCs differed per category wherein softcore BGCs tend to be smaller than BGCs categorized as core, shell, and cloud ( N = 2511). H Few BGCs are predicted to make known secondary metabolites. Source data are provided as Source Data files. For panels E and G , statistical comparisons were made using a Kruskal–Wallis rank sum test ( p < 0.01 for both tests); pairwise comparisons were made using the Dunn’s test. One, two, and three asterisks represents a significance threshold of 0.05, 0.01, and 0.001, respectively. In panels C – E , G , average values are depicted and error bars indicate the standard deviation from the mean.

Article Snippet: Library preparation was conducted using the Twist Whole Genome / Metagenomics_LowpassWGS-Twist Miniprep (Twist Bioscience).

Techniques: Software, Sequencing, Standard Deviation

Journal: Nature Communications

Article Title: Evolutionary origin and population diversity of a cryptic hybrid pathogen

doi: 10.1038/s41467-024-52639-1

Figure Lengend Snippet: A. latus (purple), A. spinulosporus (blue), and A. quadrilineatus (red) are indistinguishable in culture. At the genomic level, A. latus isolates have larger genome sizes and gene repertoires than other Aspergillus species and can be distinguished from its close relatives through Fluorescence-Activated Cell Sorting (or FACS) analysis of DNA content. Furthermore, amplification and sequencing of single-locus molecular markers, including taxonomically informative loci, is expected to show evidence of two distinct loci that are phylogenetically distinct in a single-locus phylogeny. At the phenotypic level, A. latus spores are larger than those of other species due to their larger genome size.

Article Snippet: Library preparation was conducted using the Twist Whole Genome / Metagenomics_LowpassWGS-Twist Miniprep (Twist Bioscience).

Techniques: Fluorescence, FACS, Amplification, Sequencing

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