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: bioRxiv

Article Title: Genome wide CRISPR screen for Pasteurella multocida toxin (PMT) binding proteins reveals LDL Receptor Related Protein1 (LRP1) as crucial cellular receptor

doi: 10.1101/2022.08.04.502755

Figure Lengend Snippet: Mouse embryonic fibroblasts (MEF) stably expressing Flag-Cas9-EGFP were transduced with a lentiviral CRISPR-library. Cells were treated three times with PMT(C1165S)DTa and surviving cells grown. Genomic DNA was extracted, inserted sgRNA amplified and sequenced.

Article Snippet: We utilized a well-functioning and validate genome-wide mouse lentiviral CRISPR guide RNA library v2 (Addgene).

Techniques: Stable Transfection, Expressing, Transduction, CRISPR, Amplification

Journal: bioRxiv

Article Title: Genome wide CRISPR screen for Pasteurella multocida toxin (PMT) binding proteins reveals LDL Receptor Related Protein1 (LRP1) as crucial cellular receptor

doi: 10.1101/2022.08.04.502755

Figure Lengend Snippet: The volcano plot shows gene expression changes between cells treated with lethal PMT-DTa chimera and those only transduced with the CRISPR library. All reads were mapped locally using BWA-MEM [ ,6], then quantified with featureCounts [4], and finally fold changes between the condition were calculated by DESeq2 [7] (see galaxy history). The volcano plot was drawn with the bioinfokit toolkit [8]. Significantly enriched genes, having a positive fold change above 0.584 and a p-value lower or equal 5%, are shown in blue. The significance thresholds are marked by gray-dotted lines. The ten most significant genes are highlighted with their name. Non-significant genes are colored in gray.

Article Snippet: We utilized a well-functioning and validate genome-wide mouse lentiviral CRISPR guide RNA library v2 (Addgene).

Techniques: Gene Expression, Transduction, CRISPR