Direct GO Count (CC) 0 100 200 300 400 500 600 700 800 900 1,000 1,100 1,200 1,300 1,400 1,500 1,600 1,700 1,800 1,900 2,000 2,100 2,200 2,300 2,400 2,500 2,600 2,700 2,800 2,900 3,000 3,100 3,200 3,300 3,400 3,500 #Seqs plasma membrane cytosol nucleus mitochondrion plasmodesma integral to membrane chloroplast membrane cytoplasmic membrane-bounded vesicle plastid Golgi apparatus intracellular chloroplast stroma vacuolar membrane chloroplast envelope vacuole endoplasmic reticulum nucleolus cell wall apoplast cytoplasm plant-type cell wall chloroplast thylakoid membrane peroxisome extracellular region cytosolic ribosome cytosolic large ribosomal subunit cytosolic small ribosomal subunit CUL4-RING ubiquitin ligase complex ribosome chloroplast thylakoid anchored to plasma membrane mitochondrial inner membrane plant-type vacuole membrane endoplasmic reticulum membrane anchored to membrane microtubule thylakoid intracellular membrane-bounded organelle chloroplast thylakoid lumen mitochondrial matrix cytoplasmic part plastoglobule phragmoplast mitochondrial respiratory chain complex I stromule heterotrimeric G-protein complex nuclear envelope integral to plasma membrane microsome #GO SupportingFigure S1 – Most highly representedGOterms inthe pennycress transcriptome annotation GO terms wereassigned to each transcriptusing theBlast2GO pipeline. Themosthighly represented biologicalprocess, cellular component, and molecular function terms arerepresented. Direct GO Count (BP) 0 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 1,000 1,050 1,100 1,150 1,200 1,250 1,300 1,350 1,400 1,450 #Seqs oxidation-reduction process regulation of transcription, DNA-dependent response to salt stress response to cadmium ion response to chitin protein phosphorylation protein targeting to membrane regulation of plant-type hypersensitive response defense response to fungus defense response to bacterium response to cold response to abscisic acid stimulus positive regulation of transcription, DNA-dependent response to wounding negative regulation of defense response embryo development ending in seed dormancy systemic acquired resistance, salicylic acid mediated signaling pathway jasmonic acid mediated signaling pathway MAPK cascade response to water deprivation proteolysis response to auxin stimulus salicylic acid biosynthetic process response to nitrate nitrate transport vegetative to reproductive phase transition of meristem cellular membrane fusion protein folding regulation of hydrogen peroxide metabolic process translation glycolysis abscisic acid mediated signaling pathway response to ethylene stimulus regulation of flower development transmembrane transport response to jasmonic acid stimulus response to sucrose stimulus systemic acquired resistance negative regulation of programmed cell death Golgi organization root hair elongation endoplasmic reticulum unfolded protein response cysteine biosynthetic process response to heat protein ubiquitination response to oxidative stress response to high light intensity signal transduction response to endoplasmic reticulum stress toxin catabolic process #GODirect GO Count (MF) 0 100 200 300 400 500 600 700 800 900 1,000 1,100 1,200 1,300 1,400 1,500 1,600 1,700 1,800 1,900 2,000 2,100 2,200 2,300 2,400 2,500 2,600 #Seqs ATP binding protein binding zinc ion binding sequence-specific DNA binding transcription factor activity DNA binding nucleotide binding protein serine/threonine kinase activity RNA binding nucleic acid binding protein tyrosine kinase activity electron carrier activity metal ion binding structural constituent of ribosome heme binding sequence-specific DNA binding GTP binding copper ion binding calcium ion binding receptor activity oxidoreductase activity ubiquitin-protein ligase activity hydrolase activity 2-alkenal reductase [NAD(P)] activity carbohydrate binding calmodulin binding kinase activity catalytic activity binding protein dimerization activity oxygen binding identical protein binding protein homodimerization activity cation binding GTPase activity transferase activity ADP binding iron ion binding unfolded protein binding flavin adenine dinucleotide binding protein kinase activity methyltransferase activity protein serine/threonine phosphatase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen pyridoxal phosphate binding magnesium ion binding translation initiation factor activity monooxygenase activity carboxylesterase activity heat shock protein binding nucleoside-triphosphatase activity #GO