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: Frontiers in Veterinary Science

Article Title: Clinical sequencing uncovers the genomic characteristics and mutation spectrum of the 2018 African swine fever virus in Guangdong, China

doi: 10.3389/fvets.2022.978243

Figure Lengend Snippet: Depth and coverage of GZ201801_2 measured using SAMtools v1.10 after sequencing . (A) MGI platform sequencing and (B) Nanopore sequencing.

Article Snippet: In this study, a full genome sequencing of clinical samples from the first ASF outbreak in Guangdong in 2018 was performed using MGI (MGI Tech Co., Ltd., Shenzhen, China) and Nanopore sequencing platforms, followed by Sanger sequencing to verify the variations.

Techniques: Sequencing, Nanopore Sequencing

Journal: Frontiers in Veterinary Science

Article Title: Clinical sequencing uncovers the genomic characteristics and mutation spectrum of the 2018 African swine fever virus in Guangdong, China

doi: 10.3389/fvets.2022.978243

Figure Lengend Snippet: Methylation of positive and reverse strands in the genome predicted using Tombo and its corresponding depth. (A) The score of 5mC and (B) 6mA modification of positive and reverse strands. We compared the raw signal levels between sequenced samples and alternative models to obtain the statistical results of the corresponding sites, Tombo generated the correlation scores to evaluate the possibility of methylation on certain sites in the full-length viral genome. A higher score indicated that the site was more likely to undergo methylation modification. (C) Depth of Nanopore sequencing of positive and reverse strands. The top 10 methylation sites and their adjacent regions in the ASFV_GZ201801_2 that are most likely to be modified by (D) 5mC and (E) 6mA methylation also predicted using Tombo.

Article Snippet: In this study, a full genome sequencing of clinical samples from the first ASF outbreak in Guangdong in 2018 was performed using MGI (MGI Tech Co., Ltd., Shenzhen, China) and Nanopore sequencing platforms, followed by Sanger sequencing to verify the variations.

Techniques: Methylation, Modification, Generated, Nanopore 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: 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