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

Journal: Horticulture Research

Article Title: Alternative transcription and feedback regulation suggest that SlIDI1 is involved in tomato carotenoid synthesis in a complex way.

doi: 10.1093/hr/uhab045

Figure Lengend Snippet: Sequence analysis of oft3. a The genomic DNA structure of SlIDI1 and the deleted fragment in oft3. Black boxes and gray lines represent the exons and introns of SlIDI1, respectively. The deleted fragment encompassed 55 bp in exon 5 (underlined) and 61 bp in intron 5. b Genotyping of tomato varieties using the markers developed based on the SlIDI1 deletion mutation of oft3. One 520 bp band was amplified by PCR in five orange-fruited inbred lines (Lanes 1–5), and their corresponding F1 hybrids (Lanes 11–14) were obtained by crossing with oft3, whereas a 636 bp band was amplified in five wild-type red-fruited inbred lines (Lanes 6–10). The two bands were produced by PCR in the three F1 hybrids between oft3 and the r mutant TB0040 (Lane 15), t mutant TB0017 (Lane 16) and wild-type AC (Lane 17). c Deduced protein sequence of SlIDI1 in oft3. SlIDI1 in oft3 was deduced to produce a truncated protein (157 aa) terminated by the premature translational stop signal resulting from the deletion mutation.

Article Snippet: The full-length CDS and the upstream 1500 bp genomic sequence of SlIDI1 from AC (WT) were artificially synthesized by GenScript Biotechnology Co., Ltd. (Nanjing, China).

Techniques: Sequencing, Mutagenesis, Amplification, Produced

Journal: Horticulture Research

Article Title: Alternative transcription and feedback regulation suggest that SlIDI1 is involved in tomato carotenoid synthesis in a complex way.

doi: 10.1093/hr/uhab045

Figure Lengend Snippet: Functional complementation and knockout analysis of oft3. Functional complementation analysis was conducted in oft3 by transforming oft3 plants with SlIDI1 driven by its native promoter, and all the transformants (pIDI:IDI1 #1 ~ 12) were restored to the red-fruited phenotype, as observed in wild-type AC (left). CR-idi1 #1 was generated by knocking out SlIDI1 in wild-type AC using the CRISPR–Cas9 system. CR-idi1 #1 plants from the T1 generation that were shown to be homozygous for mutated SlIDI1 by genotyping showed an orange-fruited phenotype, similar to that of oft3 (right). Fruit color and longitudinal sections from four different ripening stages are shown. DPA: days post-anthesis.

Article Snippet: The full-length CDS and the upstream 1500 bp genomic sequence of SlIDI1 from AC (WT) were artificially synthesized by GenScript Biotechnology Co., Ltd. (Nanjing, China).

Techniques: Functional Assay, Knock-Out, Generated, CRISPR

Journal: Horticulture Research

Article Title: Alternative transcription and feedback regulation suggest that SlIDI1 is involved in tomato carotenoid synthesis in a complex way.

doi: 10.1093/hr/uhab045

Figure Lengend Snippet: Carotenoid contents of the flowers of AC (WT) and the CRISPR–Cas9-generated SlIDI1 mutant

Article Snippet: The full-length CDS and the upstream 1500 bp genomic sequence of SlIDI1 from AC (WT) were artificially synthesized by GenScript Biotechnology Co., Ltd. (Nanjing, China).

Techniques: CRISPR

Journal: Horticulture Research

Article Title: Alternative transcription and feedback regulation suggest that SlIDI1 is involved in tomato carotenoid synthesis in a complex way.

doi: 10.1093/hr/uhab045

Figure Lengend Snippet: Spatiotemporal specific expression analysis of SlIDI1 in wild-type AC by qRT–PCR. a Tissue-specific expression analysis of SlIDI1 in different tissues of wild-type AC. b Stage-specific expression analysis of SlIDI1 in the fruit, petals and stamens of wild-type AC at different ripening or maturation stages. Values are the means of four biological replicates ± SD. For stage-specific expression analysis, values were compared among different stages of each tissue, and asterisks denote significance by Student’s t-test (*P < 0.05, **P < 0.01). DPA: days post-anthesis, DBA: days before anthesis.

Article Snippet: The full-length CDS and the upstream 1500 bp genomic sequence of SlIDI1 from AC (WT) were artificially synthesized by GenScript Biotechnology Co., Ltd. (Nanjing, China).

Techniques: Expressing, Quantitative RT-PCR

Journal: Horticulture Research

Article Title: Alternative transcription and feedback regulation suggest that SlIDI1 is involved in tomato carotenoid synthesis in a complex way.

doi: 10.1093/hr/uhab045

Figure Lengend Snippet: Alternative transcripts of SlIDI1 identified by RACE-PCR. a RACE-PCR products amplified from the leaves, fruit, petals and anthers of wild-type AC. For 5’ RACE-PCR (left), two identical short products were amplified from leaves and fruit. For 3’ RACE-PCR (right), one short product was amplified from fruit. b Schematic representation of the structures of DNA, the full-length cDNA of SlIDI1 (SlIDI1-L) and two short RACE-PCR products (SlIDI1–5’S and SlIDI1–3’S) identified by 5’ RACE-PCR and 3’ RACE-PCR. SlIDI1-L: long transcripts with the longest 5’-UTR (44 bp) and 3’-UTR (338 bp). Exons and introns are represented by boxes and lines. The 5′ and 3’ UTR are represented by gray boxes. The two specific primers used for 5’-RACE and 3’-RACE (5’RACE-GSP and 3’RACE-GSP) are represented by red boxes. In alternative transcription-generated SlIDI1–5’S, a 274 bp deletion occurred in the CDS region, including exon 1 and part of exon 2. In alternative-splicing-generated SlIDI1–3’S, 254 bp of exon 6 was replaced by 165 bp of intron 5 (white box). c Aligned sequences of the full-length cDNA of SlIDI1 (SlIDI1-L) and two short RACE-PCR products (SlIDI1–5’S and SlIDI1–3’S). The putative initiation codons and stop codons are indicated in red. The retained 165 bp of intron 5 in SlIDI1–3’S is boxed. d Aligned protein sequences deduced from SlIDI1-L, SlIDI1–5’S and SlIDI1–3’S. SlIDI1 is 294 amino acids in length. The putative CTP and type 1 peroxisome targeting sequence (PTS1) are underlined.

Article Snippet: The full-length CDS and the upstream 1500 bp genomic sequence of SlIDI1 from AC (WT) were artificially synthesized by GenScript Biotechnology Co., Ltd. (Nanjing, China).

Techniques: Amplification, Generated, Alternative Splicing, Sequencing

Journal: Horticulture Research

Article Title: Alternative transcription and feedback regulation suggest that SlIDI1 is involved in tomato carotenoid synthesis in a complex way.

doi: 10.1093/hr/uhab045

Figure Lengend Snippet: Subcellular location of SlIDI1. 35S:SlIDI1-EGFP, with the full-length SlIDI1 CDS, and 35S:SlIDI1t-EGFP, with a truncated SlIDI1 CDS lacking the 59-amino acid extension sequence at the N-terminus, were agroinfiltrated into tobacco leaves, and the agroinfiltrated leaf epidermal cells were examined under a confocal microscope. 35S:EGFP served as the vector control

Article Snippet: The full-length CDS and the upstream 1500 bp genomic sequence of SlIDI1 from AC (WT) were artificially synthesized by GenScript Biotechnology Co., Ltd. (Nanjing, China).

Techniques: Sequencing, Microscopy, Plasmid Preparation, Control

Journal: Horticulture Research

Article Title: Alternative transcription and feedback regulation suggest that SlIDI1 is involved in tomato carotenoid synthesis in a complex way.

doi: 10.1093/hr/uhab045

Figure Lengend Snippet: Expression analysis of SlBCH1 and SlBCH2 by qRT–PCR in the fruit of the SlIDI1 mutant at four ripening stages. a and b Expression analysis of SlBCH1 and SlBCH2 in two wild-type (WT-1 and WT-2) and two oft3 genotyped individuals (oft3–1 and oft3–2) from the segregating BC1F2 population. c and d Expression analysis of SlBCH1 and SlBCH2 in the CRISPR–Cas9-generated SlIDI1 mutant CR-idi1 #1 compared with its parental line AC. Values are the means of four biological replicates ± SD and were compared between genotypes at the same ripening stage. Asterisks denote significance by Student’s t-test (*P < 0.05, **P < 0.01). DPA: days post-anthesis.

Article Snippet: The full-length CDS and the upstream 1500 bp genomic sequence of SlIDI1 from AC (WT) were artificially synthesized by GenScript Biotechnology Co., Ltd. (Nanjing, China).

Techniques: Expressing, Quantitative RT-PCR, Mutagenesis, CRISPR, Generated