Journal: Biosafety and Health

Article Title: Molecular phylogenomic analysis reveals a single origin of monkeypox virus transmission in Guangzhou, China in June 2023

doi: 10.1016/j.bsheal.2023.08.002

Figure Lengend Snippet: Phylogenetic analysis of monkeypox (mpox) virus sequences first reported in Guangzhou, China. A) The eight local sequences (red dot) in FASTA format were aligned by the BioEdit software 7.0.9 with the reference sequences of mpox viral clade IIb downloaded from GISAID (black dot) and NCBI (NC_063383.1, green dot, selected as the outgroup). The maximum likelihood (ML) phylogenetic tree of the full-length genome sequences of mpox virus was constructed with the MEGA software 11.0.11 using the General Time Reversible model with 500 bootstrap replicates. The scale bar represents the genetic distance. Bootstrap values >75% are presented at the corresponding nodes of the tree. Abbreviations: FASTA, Fast-All; GISAID, Global Initiative on Sharing Avian Influenza Data; NCBI, National Center For Biotechnology Information. B) The analysis of amino acid mutation of the eight local sequences compared to the reference Japan|EPI ISL 17692269|2023-04-28. In most cases, the mutation sites are mixed. Only the dominant amino acid is shown. “*” represents termination codon. As for this special site, the CAG (Q) codon accounts for 29.26% of all reads, but the TAG (stop) codon accounts for 70.74%. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: We then performed the amplicon-based mpox viral full-length genome sequencing of mpox virus using a newly developed method by MGI Tech Co., Ltd. (MGI), China.

Techniques: Virus, Software, Construct, Mutagenesis

Journal: Scientific Reports

Article Title: The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology

doi: 10.1038/s41598-020-80826-9

Figure Lengend Snippet: Comparison of bacterial taxonomy classification according to two different 16S amplicon regions. ( a ) The Venn-diagram is divided into two different methods (red: V3-V4 amplicon and blue: sFL16S) and shows the number of a classified bacterial taxon at the phylum to species level. ( b ) The heatmap shows the frequency of the only identified taxa in both methods drawn by each taxonomic rank, in order. The bacterial taxon belonging to the four major phyla ( Bacteroidetes , Firmicutes , Actinobacteria , and Proteobacteria ), to the species, showing the confidence score of each taxon. The darkness of the color is proportional to the confidence score's value, as shown in the color bar.

Article Snippet: Loop Genomics recently proposed a new 16S full-length-based synthetic long-read sequencing technology (sFL16S).

Techniques: Comparison, Amplification

Journal: Scientific Reports

Article Title: The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology

doi: 10.1038/s41598-020-80826-9

Figure Lengend Snippet: Phylogenetic tree analysis based on distance matrix calculated by multiple sequence alignment (MSA). ( a ) Neighbor-joining phylogenetic tree analysis of the Bifidobacterium strains identified in both methods. The 16S reference sequences were obtained from the SILVA 138v non-redundant ribosomal RNA gene database. The pink, orange, and green boxes indicate the clustered ASVs by Bifidobacterium species. ( b ) MSA with the reference sequence for the Bifidobacterium strains and ASVs identified from V3V4 and sFL16S. The alignment analysis was performed by the IUB multiple alignment matrix with options (transition weight 0.50; delay-divergent cutoff 30%) using MEGA X software. The MSA results visualized using the NCBI Multiple Sequence Alignment Viewer 1.16.1v.

Article Snippet: Loop Genomics recently proposed a new 16S full-length-based synthetic long-read sequencing technology (sFL16S).

Techniques: Sequencing, Software

Journal: Scientific Reports

Article Title: The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology

doi: 10.1038/s41598-020-80826-9

Figure Lengend Snippet: Comparison of taxonomy matching accuracy for V3V4 and sFL16S on NCBI Bacterial Genome Database. Violin plots represent matching rates that result from taxonomy matching analysis in the NCBI Bacterial Genome Database (40 K bacterial and archaeal genomes), according to taxonomic rank (genus and species). Using the NCBI reference 16S sequence data, we conducted the BLAST search to determine the matching rate with the ASV taxonomy data in two different methods. The y-axis indicates the percentiles of the taxonomy matching rate. The violin plots are filled in red (left) and blue (right) for V3V4 and sFL16S data, respectively. The boxes indicate the mean value (black bold horizontal line), percentiles of the taxonomy matching rate distribution. The upper and low whiskers indicate the maximum and the minimum value of the taxonomy matching rate, respectively. The shaded area surrounding the boxes on each side indicate the ASV frequency of the taxonomy matching rate.

Article Snippet: Loop Genomics recently proposed a new 16S full-length-based synthetic long-read sequencing technology (sFL16S).

Techniques: Comparison, Sequencing

Journal: Scientific Reports

Article Title: The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology

doi: 10.1038/s41598-020-80826-9

Figure Lengend Snippet: Comparison of the taxon matching rate with NCBI bacterial genome database.

Article Snippet: Loop Genomics recently proposed a new 16S full-length-based synthetic long-read sequencing technology (sFL16S).

Techniques: Comparison