Journal: Journal of Medical Physics

Article Title: Validation of American Association of Physicists in Medicine TG 43 Dosimetry Data in Commercial Treatment Planning System

doi: 10.4103/jmp.JMP_20_21

Figure Lengend Snippet: Source models presented in American Association of Physicists in Medicine Task Group-43U1S2 Report

Article Snippet: CivaTech oncology model CS10 , 103 Pd.

Techniques:

Journal: Nature Communications

Article Title: The origin and maintenance of supergenes contributing to ecological adaptation in Atlantic herring

doi: 10.1038/s41467-024-53079-7

Figure Lengend Snippet: Genome statistics for the CS10 and BS3 de novo genome assemblies in comparison with the current reference assembly

Article Snippet: The CS10 sample from the Celtic and BS3 sample from the Baltic Sea were used for optical (BioNano) mapping .

Techniques: Comparison

Journal: Nature Communications

Article Title: The origin and maintenance of supergenes contributing to ecological adaptation in Atlantic herring

doi: 10.1038/s41467-024-53079-7

Figure Lengend Snippet: The green to red color gradient in dot plots represents percent sequence identity from 80 to 100%. The models representing SVs surrounding the inversions are below the dot plots. Chr6: 400 kb sequence includes 300 kb outside inversion and 100 kb inside inversion for both proximal and distal regions. Chr12: 200 kb sequence includes 100 kb outside inversion and 100 kb inside inversion for both proximal and distal regions. Chr17: 400 kb sequence includes 300 kb outside inversion and 100 kb inside inversion for both proximal and distal regions. Chr23: 400 kb proximal. 600 kb distal sequence includes 500 kb outside inversion and 100 kb inside inversion. The plots are based on the CS10_hap1 and BS3_hap2 genome assemblies.

Article Snippet: The CS10 sample from the Celtic and BS3 sample from the Baltic Sea were used for optical (BioNano) mapping .

Techniques: Sequencing

Journal: Nature Communications

Article Title: The origin and maintenance of supergenes contributing to ecological adaptation in Atlantic herring

doi: 10.1038/s41467-024-53079-7

Figure Lengend Snippet: Inversion breakpoint coordinates on the reference assembly for chromosomes 6, 12, 17, and 23

Article Snippet: The CS10 sample from the Celtic and BS3 sample from the Baltic Sea were used for optical (BioNano) mapping .

Techniques:

Journal: The New Phytologist

Article Title: Recent advances in Cannabis sativa genomics research

doi: 10.1111/nph.17140

Figure Lengend Snippet: Statistics for the latest Cannabis sativa reference genome and transcriptome assemblies.

Article Snippet: cs10/CBDRx (GCA_900626175.2) , Female , 876 147 649 , 736 579 359 , 221 , 91 913 889 , 1052 , 1959 202 , 34 , 10 , 100× , Oxford Nanopore Technology , 25 302 protein‐coding genes , Grassa et al . ( ) .

Techniques: Cannabis, Sequencing

Journal: The New Phytologist

Article Title: Recent advances in Cannabis sativa genomics research

doi: 10.1111/nph.17140

Figure Lengend Snippet: Chromosomal nomenclatures of Cannabis sativa genome assemblies highlighting the discrepancies in chromosome numbering among the current assemblies ( https://www.ncbi.nlm.nih.gov/assembly/GCF_900626175.2#/st ; Maoz, 2020 ).

Article Snippet: cs10/CBDRx (GCA_900626175.2) , Female , 876 147 649 , 736 579 359 , 221 , 91 913 889 , 1052 , 1959 202 , 34 , 10 , 100× , Oxford Nanopore Technology , 25 302 protein‐coding genes , Grassa et al . ( ) .

Techniques: Cannabis, Sequencing

Journal: The New Phytologist

Article Title: Recent advances in Cannabis sativa genomics research

doi: 10.1111/nph.17140

Figure Lengend Snippet: Maximum‐likelihood phylogenetic tree depicting the relationship among the Cannabis sativa cannabinoid synthase genes tetrahydrocannabinolic acid synthase ( THCAS ), cannabidiolic acid synthase ( CBDAS ) and cannabichromenic acid synthase ( CBCAS ). The published nucleotide sequences of the active/functional forms of THCAS (GenBank acc. no. AB057805.1) , CBDAS (GenBank acc. no. AB292682.1) , CBCAS (GenBank acc. no. LY658671.1) and the paralogues of these genes as annotated in the cs10 v.2.0 and Jamaican Lion (female parent and male parent) assemblies (Supporting Information Tables S1, S2) were aligned against the latest C. sativa reference genome assemblies (Table ) using B last +/2.2.29 (Altschul et al ., ). Best hits corresponding to a percentage identity > 98.5%, query coverage > 75% and alignment length = query length ± 100 bp were retained (Tables S1, S2). The nucleotide sequences of these best hits were extracted from each assembly (where applicable) using bedtools v.2.26.0 (Quinlan & Hall, ). transdecoder v.3.0 was used to predict the longest open reading frame from the extracted regions ( https://transdecoder.github.io/ ). The predicted proteins along with amino acid sequences (complete CDS) of AB057805.1 (gene ID in blue), AB292682.1 (gene ID in red), LY658671.1 (gene ID in green) and the other cannabinoid synthase gene copies annotated in the cs10 v.2.0 and Jamaican Lion (female parent and male parent) genome assemblies were used for multiple sequence alignment using clustal Omega (Sievers et al ., ). The phylogenetic tree was reconstructed from these alignments using raxml v.8.12.12. with 500 bootstrap replicates under the JTT model of amino acid substitution and visualized using Interactive Tree Of Life (iTOL) (Letunic & Bork, ; Stamatakis et al ., ). The tree was rooted with the Humulus lupulus THCAS homolog (GenBank acc. no. LA634839.1). Only bootstrap values of > 70% are shown. It is worth noting that all CBCAS genes cluster with some the THCAS genes reflecting the high sequence similarity between these two cannabinoid synthase genes (Fig. ).

Article Snippet: cs10/CBDRx (GCA_900626175.2) , Female , 876 147 649 , 736 579 359 , 221 , 91 913 889 , 1052 , 1959 202 , 34 , 10 , 100× , Oxford Nanopore Technology , 25 302 protein‐coding genes , Grassa et al . ( ) .

Techniques: Cannabis, Functional Assay, Sequencing

Journal: The New Phytologist

Article Title: Recent advances in Cannabis sativa genomics research

doi: 10.1111/nph.17140

Figure Lengend Snippet: Dotplots showing the syntenic relationship between genomes of three Cannabis sativa cultivars. Pairwise genome alignments for (a) PK v.5.0 (GenBank acc. no. GCA_000230575.5) and FN v.2.0 (GenBank acc. no. GCA_003417725.2), (b) cs10 v.2.0 (GenBank acc. no. GCA_900626175.2) and PK v.5.0 and (c) cs10 v.2.0 and FN v.2.0 were performed using M inimap2 and the alignments were visualized using d‐genies (Cabanettes & Klopp, ; Li, ) (Supporting Information Table S3). Breaks in the alignment could be due to the presence of structural variants or the less contiguous nature of the PK and FN assemblies. The difference in chromosome orientation between the assemblies also can be seen. Only chromosome‐level alignments are shown. PK, Purple Kush; FN, Finola.

Article Snippet: cs10/CBDRx (GCA_900626175.2) , Female , 876 147 649 , 736 579 359 , 221 , 91 913 889 , 1052 , 1959 202 , 34 , 10 , 100× , Oxford Nanopore Technology , 25 302 protein‐coding genes , Grassa et al . ( ) .

Techniques: Cannabis

Journal: The New Phytologist

Article Title: Recent advances in Cannabis sativa genomics research

doi: 10.1111/nph.17140

Figure Lengend Snippet: Cannabinoid synthase gene expression in relation to cannabinoid content and composition in nine high cannabinoid yielding cannabis cultivars (data taken from Zager et al ., ). (a) Tetrahydrocannabinolic acid : cannabidiolic acid (THCA : CBDA) ratio and (b) cannabinoid contents of the cultivars. The lower panel in (b) shows a zoomed‐in view of cannabinoid content (% DW) in the range 0–0.5%. (c) Trichome‐specific expression patterns of 13 cannabinoid synthase genes from cs10 v.1.0 genome assembly (GenBank acc. no. GCA_900626175.1) in these cultivars. Positions on chromosomes represent one or more cannabinoid synthase locus. The reference CBDAS (LOC115697762) and inactive THCAS (LOC115697880) loci are underlined. LOC115697762 bears 100% nucleotide identity with the functional CBDAS identified by Taura et al . (GenBank acc. no. AB292682.1), whereas LOC115697880 is 99% identical to CBCAS (GenBank acc. no. LY658671.1) at the nucleotide level (Taura et al ., ). Of the 13 loci, two (LOC115698060 and LOC115697886) are pseudogenic inactive THCAS copies containing in‐frame stop codons, whereas the remaining 11 genes produce full‐length CDS. Trichome enriched RNA‐seq reads previously reported by Zager et al . were accessed from the NCBI Sequence Read Archive (SRA project no. PRJNA498707; Zager et al ., ). The reads were mapped to the Cannabis sativa cs10 v.1.0 genome assembly (using H isat2 v.2.1.0 and sorted by genomic location using samtools v.1.9 Li et al ., ; Kim et al ., ). stringtie v.1.3.5 was used to assemble RNA‐Seq alignments into potential transcripts and to calculate gene abundances (TPM) (Supporting Information Table S6; Pertea et al ., ). Chromosome numbers have been changed to community standard nomenclature in accordance with cs10 v.2.0. (GenBank acc. no. GCA_900626174.2.). Cannabis sativa var. cs10 is associated with a high CBD chemotype. BB, Black Berry Kush; BL, Black Lime; CC, Cherry Chem; CT, Canna Tsu; MT, Mama Thai; SD, Sour Diesel; TP, Terple; TPM, Transcripts per million; VF, Valley Fire; WC, White Cookies. Error bars represent ± 1 SD of the mean metabolite content of each cultivar ( n = 3).

Article Snippet: cs10/CBDRx (GCA_900626175.2) , Female , 876 147 649 , 736 579 359 , 221 , 91 913 889 , 1052 , 1959 202 , 34 , 10 , 100× , Oxford Nanopore Technology , 25 302 protein‐coding genes , Grassa et al . ( ) .

Techniques: Gene Expression, Cannabis, Expressing, Functional Assay, RNA Sequencing, Sequencing