Table 1.
Genes encoding LOX, CYP74, AOC, and OPR isoforms of C. sativa and their predicted peptide subcellular localization.
Fig 1.
Distribution of the LOX, AOS, HPL, AOC, and OPR gene families across the C. sativa genome.
Ruler depicts chromosome length.
Fig 2.
Phylogenetic, genetic, motif, and domain analysis of the CsLOX gene family.
(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.
Fig 3.
Phylogenetic, genetic, motif, and domain analysis of the C. sativa CYP74 gene family.
(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.
Fig 4.
Phylogenetic, genetic, motif, and domain analysis of the CsAOC gene family.
(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.
Fig 5.
Phylogenetic, genetic, motif, and domain analysis of the CsOPR gene family.
(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.
Fig 6.
Oxylipin biosynthetic gene collinearity between A. thaliana, C. sativa, and S. lycopersicum.
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.
Fig 7.
Cis-acting regulatory element distribution across C. sativa oxylipin biosynthetic gene promoters.
(A) Physical distribution of motifs throughout a 1.5 kb region upstream of corresponding gene model. Gene symbols are presented on the left with grey line representing promoter regions with motif positions. Legend describes motifs associate with tissue-specific expression, environmental responses, and phytohormone inducibility. (B) Summary of cis-acting regulatory motif content. Heatmap depicts number of motifs identified in gene promoter region. The y-axis depicts C. sativa oxylipin biosynthetic genes and x-axis depicts associated condition for motif. Cell values are number of motifs identified and are colored according to legend.
Fig 8.
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.
Fig 9.
Weighted co-expression genetic network derived from the C. sativa transcriptome expression atlas.
(A) Clusters represent modules of highly connected genes containing at least one oxylipin biosynthetic gene. (B) Functional enrichment analysis of gene modules containing oxylipin biosynthetic genes: Gene Ontologies for Molecular Functions (MF), Biological Processes (BP), and Cellular Components (CC) and KEGG.
Fig 10.
Working model of C. sativa oxylipin biosynthetic enzyme isoforms and pathways involved in cannabinoid, GLV, and JA biosynthesis.
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.