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: Genome Research

Article Title: Unraveling the hidden complexity of cancer through long-read sequencing

doi: 10.1101/gr.280041.124

Figure Lengend Snippet: Summary of software tools for analyzing long reads in cancer

Article Snippet: A more specific study comparing optical maps of breast cancer cell line SKBR3 with long-read whole-genome sequencing (LR-WGS) found that 74% of insertions and 80% of deletions detected with Bionano can be confirmed with PacBio and ONT, but lower concordance for inversions and duplications ( ).

Techniques: Software, Variant Assay, Sequencing, Methylation, DNA Methylation Assay, RNA modification

Journal: Viruses

Article Title: Isolation and Characterization of Contemporary Bovine Coronavirus Strains

doi: 10.3390/v16060965

Figure Lengend Snippet: Sample information and RT-qPCR results 1 .

Article Snippet: The whole genome sequence (WGS) of the BC18 strain was obtained using conventional PCR with multiple primers (shown in ) followed by Sanger sequencing at the Comprehensive Cancer Center of The Ohio State University or Oxford nanopore sequencing at Plasmidsaurus ( https://www.plasmidsaurus.com/ , accessed on 25 April 2024).

Techniques:

Journal: Viruses

Article Title: Isolation and Characterization of Contemporary Bovine Coronavirus Strains

doi: 10.3390/v16060965

Figure Lengend Snippet: Analysis of the S protein amino acid variations between four pairs of respiratory strains and enteric strains (each pair of samples was from the same animal. E: strains from enteric samples, R: strain from respiratory samples).

Article Snippet: The whole genome sequence (WGS) of the BC18 strain was obtained using conventional PCR with multiple primers (shown in ) followed by Sanger sequencing at the Comprehensive Cancer Center of The Ohio State University or Oxford nanopore sequencing at Plasmidsaurus ( https://www.plasmidsaurus.com/ , accessed on 25 April 2024).

Techniques:

Journal: Viruses

Article Title: Isolation and Characterization of Contemporary Bovine Coronavirus Strains

doi: 10.3390/v16060965

Figure Lengend Snippet: The 3D structural analyses of the predicted S protein trimers of BCoV strains using protein structure prediction software online ( https://swissmodel.expasy.org/ , accessed on 25 April 2024). The surface model used BC8 and LUN strains as templates and the stick model used all corresponding strains to predict. The location of amino acid residue 617 in the predicted S protein trimer is shown in blue and red in the detailed stick model for Iso 617 in the BC8-E strain and yellow for Thr 617 in the BC18-R strain ( A ). The location of amino acid residue 960 in the predicted S protein trimer is shown in orange, the detailed stick model for Pro 960 in the BC8-E strain is shown in brown, and Leu 960 in the BC18-R strain is shown in purple ( B ). The location of amino acid residue 1180 in the predicted S protein trimer is shown in white, the detailed stick model for Asp 1180 in the BC8-E, AH65-E, ENT-E, and AH187-E strains is shown in black, and Gly 1180 in the AH65-R, LUN-R, and AH187-R strains is shown in a warm pink color ( C ).

Article Snippet: The whole genome sequence (WGS) of the BC18 strain was obtained using conventional PCR with multiple primers (shown in ) followed by Sanger sequencing at the Comprehensive Cancer Center of The Ohio State University or Oxford nanopore sequencing at Plasmidsaurus ( https://www.plasmidsaurus.com/ , accessed on 25 April 2024).

Techniques: Software, Residue