78 research outputs found

    Sample datasets for E. coli C-1 genome assembly tutorial

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    <p>The dataset contains three files:</p> <ol> <li>Illumina_f.fq - forward reads from MiSeq run</li> <li>Illumina_r_fq - reverse reads from MiSeq run</li> <li>minion_2d.fq - Oxford Nanopore 2d reads</li> </ol> <p>Sequencing was done on genomic DNA of E. coli strain C-1 obtained from Yale Stock Center.</p

    Fig 8 -

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    Heatmaps showing expression of oxylipin biosynthetic genes from the C. sativa gene expression atlas (A) or female trichomes of diverse marijuana lines (B). Cells values are rounded TPM values and are colored according to the legend.</p

    Working model of <i>C</i>. <i>sativa</i> oxylipin biosynthetic enzyme isoforms and pathways involved in cannabinoid, GLV, and JA biosynthesis.

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    Abbreviations: [enzymes]: allene oxide cyclase (AOC), allene oxide synthase (AOS), 2-alkynal reductase (2-AR), hydroperoxide lyase (HPL), lipoxygenase (LOX), methylerythritol 4-phosphate pathway (MEP), 12-oxo-phytodienoic reductase (OPR); [metabolites]: (9Z, 11E, 13S, 15Z)-12,13-epoxy-9,11,15-octadecatrienoic acid (12,13-EOT), (9Z, 11E, 13S)-13-hydroperoxy-9,11-octadecadienoic acid (13-HPOD), (9Z, 11E, 13S, 15Z)-13-hydroperoxy-9,11,15-octadecatrienoic acid (13-HPOT), cannabigerolic acid (CBGA), linoleic acid (C18:2), α-linolenic acid (C18:3), jasmonic acid (JA), 12-oxo-phytodienoic acid (12-OPDA), 3-oxo-2-(2′[Z]-pentenyl)-cyclopentane-1-octanoic acid (OPC8:0). The gray box indicates uncertainty in subcellular localization.</p

    Oxylipin biosynthetic gene collinearity between <i>A</i>. <i>thaliana</i>, <i>C</i>. <i>sativa</i>, and <i>S</i>. <i>lycopersicum</i>.

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    The grey lines represent collinear genetic blocks between the genomes of A. thaliana and C. sativa and between C. sativa and S. lycospersicum. Bars represent chromosomes and the black, blue, and orange lines represent the collinear pairs of LOX, CYP74, and AOC gene families, respectively.</p

    Phylogenetic, genetic, motif, and domain analysis of the CsAOC gene family.

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    (A) Cladogram of peptide sequences and conserved domains. (B) Distribution of conserved peptide sequence motifs. Colors are described in legend; x-axis represents length of peptides in amino acids. (C) Diagram of genetic structure. Blue bars, orange bars, and gray lines represent untranslated regions, exons, and introns, respectively; x-axis represents length of gene in nucleotides. (D) Polar cladogram depicting evolutionary relationship with gene families of selected species. Node labels show confidence values from 1000 bootstrap replications.</p

    Expression of oxylipin biosynthetic genes across four developmental stages in <i>C</i>. <i>sativa</i> flowers and trichomes.

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    Expression of oxylipin biosynthetic genes across four developmental stages in C. sativa flowers and trichomes.</p

    Regions of duplicated LOX genes on <i>C</i>. <i>sativa</i> Chromosomes 2 and 9.

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    Regions of duplicated LOX genes on C. sativa Chromosomes 2 and 9.</p
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