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Table 6 Number of differentially expressed (DETs) transcripts (up to a maximum of top10) that were unique (non-overlapping) for each condition (time × treatment × plant part) category. The table also shows the ID of the genes assigned in this study for ease of identification in the tables, Scion transcripts code, predicted gene name and function. These transcripts were not expressed at any other time or treatment. T7, T14 and T21 represents respectively 7, 14 and 21 days after application of methyl jasmonate (MJ) and bark strip (strip) treatments in the bark (B) or needles (N). (+) = up-regulated and (−) = down-regulated. Only transcripts with predicted gene functions are included. The predicted gene functions are mostly from UniProt [77]

From: Analysis of the transcriptome of the needles and bark of Pinus radiata induced by bark stripping and methyl jasmonate

Condition No. unique DETs ID P. radiata code Gene name Predicted gene function Direction
T7-B-MJ 96 U1 NZPradTrx115883_C02 granule bound starch synthase 1a precursor Involved in the pathway starch biosynthesis https://www.uniprot.org/uniprot/P0C585
U2 NZPradTrx184661_C01 PREDICTED: putative caffeoyl-CoA O-methyltransferase At1g67980-like Involved in the reinforcement of the plant cell wall. Also involved in the responding to wounding or pathogen challenge by the increased formation of cell wall-bound ferulic acid polymers https://www.uniprot.org/uniprot/Q9C9W3
U3 NZPradTrx108036_C04 Cytochrome b reductase Required for the NADH-dependent electron transfer involved in the desaturation and hydroxylation of fatty acids and in the desaturation of sterol precursors
https://www.uniprot.org/uniprot/Q9ZNT1
U4 NZPradTrx119186_C01 DEAD-box RNA helicase Ubiquitous in RNA-mediated processes and function by coupling cycles of ATP binding and hydrolysis to changes in affinity for single-stranded RNA https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3032546/
U6 NZPradTrx060156_C02 PREDICTED: probable rhamnose biosynthetic enzyme 1 Involved with nucleotide-sugar metabolic process https://www.uniprot.org/uniprot/A0A1U7W8H4 +
U7 NZPradTrx119948_C01 PREDICTED: protein HOTHEAD-like Required to limit cellular interactions between contacting epidermal cells during floral development (Krolikowski et al. 2003) +
U8 NZPradTrx119070_C01 PREDICTED: mitochondrial-processing peptidase subunit alpha-like Substrate recognition and binding subunit of the essential mitochondrial processing protease (MPP), which cleaves the mitochondrial sequence off newly imported precursors proteins. https://www.uniprot.org/uniprot/P29677 +
U9 NZPradTrx110606_C03
NZPradTrx110606_C04
snakin Active against fungal and bacterial plant pathogens (Berrocal-Lobo et al. 2002)
U10 NZPradTrx094750_C01 PREDICTED: zinc finger CCCH domain-containing protein 20-like Known to play important roles in RNA processing as RNA-binding proteins in animals (Wang et al. 2008)
T7-B-strip 39 U11 NZPradTrx111276_C02 low molecular weight heat-shock protein Expressed in plants experiencing high-temperature stress (Hernandez and Vierling 1993)
U12 NZPradTrx109179_C02 LP3-1 Shown to be up-regulated in response to water deficit stress and to also act as transcription factors for genes likely involved in hexose transport (Lecoy and García-Gil 2020)
NZPradTrx077717_C01  
U13 NZPradTrx112152_C04 PREDICTED: L-type lectin-domain containing receptor kinase IV.1-like Involved in resistance response to the pathogenic oomycetes, promotes hydrogen peroxide production and cell death https://www.uniprot.org/uniprot/Q9LXA5 +
U14 NZPradTrx082734_C01 Casparian strip domain-like gene Recruit the lignin polymerisation machinery necessary for the deposition of Casparian strips in the endodermis https://www.ebi.ac.uk/interpro/entry/InterPro/IPR006459/
U15 NZPradTrx105759_C05 Methyl esterase 13 Involved in jasmonic and salicylic acid metabolic process https://www.uniprot.org/uniprot/F4IE65 +
U16 NZPradTrx042090_C01 Geranyl diphosphate synthase Catalyses the condensation of dimethylallyl diphosphate and isopentenyl diphosphate to geranyl diphosphate, the key precursor of monoterpene biosynthesis (Burke et al. 1999) +
U17 NZPradTrx064702_C01 Class II chitinase Involved in the defence response against pathogen and fungal infection (de A. Gerhardt et al. 1997)
U18 NZPradTrx105720_C01 Defensin Inhibits the growth of a broad range of pathogens, including bacteria, fungi and viruses (Ermakova et al. 2016; Picart et al. 2012) [75, 76].
U19 NZPradTrx119059_C01 Annexin p33 Central regulator or effector of plant growth and stress signalling (Mortimer et al. 2008)
U20 NZPradTrx118949_C01 Peroxiredoxin Guardian against oxidative stress and modulator of peroxide signalling (Perkins et al. 2015)
T7-N-MJ 751 U21 NZPradTrx110565_C01 UDP-sulfoquinovose synthase Involved in the biosynthesis of sulfolipids found in thylakoid membranes. Converts UDP-glucose and sulfite to the sulfolipid head group precursor UDP-sulfoquinovose https://www.uniprot.org/uniprot/O48917
U22 NZPradTrx064995_C02 Chloroplast ribulose bisphosphate carboxylase/oxygenase activase alpha1, partial Catalyses carboxylation of RuBP in the first step of the Calvin cycle of photosynthesis (Tabita 1999)
U23 NZPradTrx088104_C02 RNA polymerase sigma factor rpoD, putative Initiation factor that promotes the attachment of RNA polymerase to specific initiation sites https://www.uniprot.org/uniprot/P00579
U24 NZPradTrx081803_C01 PREDICTED: mitochondrial carnitine/acylcarnitine carrier-like protein-like Mediates the transport of acylcarnitines of different length across the mitochondrial inner membrane from the cytosol to the mitochondrial matrix for their oxidation by the mitochondrial fatty acid-oxidation pathway https://www.uniprot.org/uniprot/O43772
U25 NZPradTrx086144_C02 Chloroplast omega-6 fatty acid desaturase Introduces the second double bond in the biosynthesis of 16:3 and 18:3 fatty acids, important constituents of plant membranes. It is thought to use ferredoxin as an electron donor and to act on fatty acids esterified to galactolipids, sulfolipids and phosphatidylglycerol https://www.uniprot.org/uniprot/P46312
U26 NZPradTrx065194_C01 Glutamate--ammonia ligase Key enzyme of ammonium assimilation and recycling in plants where it catalyses the synthesis of glutamine from ammonium and glutamate (Lothier et al. 2011)
U27 NZPradTrx077590_C01 PREDICTED: ATP synthase gamma chain, chloroplastic-like Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is believed to be important in regulating ATPase activity and the flow of protons through the CF0 complex https://www.uniprot.org/uniprot/Q01908
U28 NZPradTrx064646_C01 PREDICTED: photosystem I reaction center subunit XI, chloroplastic-like Involved in photosynthesis https://www.uniprot.org/uniprot/Q41385
U29 NZPradTrx115121_C05 glutathione peroxidase-like protein, partial Protects cells from phospholipid hydroperoxides and nonphospholipid peroxides during oxidative stress https://www.uniprot.org/uniprot/P36014 +
U30 NZPradTrx186664_C01 F353614_1 senescence-associated protein SPA15 May be involved in the regulation of leaf senescence
https://www.uniprot.org/uniprot/Q65XF2
T14-B-MJ 18 U31 NZPradTrx192941_C01 Beta-amylase Involved in starch breakdown in plants (Kaplan and Guy 2004) +
U32 NZPradTrx076831_C01 UV-B receptor 1 Involved in response to UV-B (Loyola et al. 2016) +
U33 NZPradTrx044917_C01 Putative cyclophilin Involved in various physiological processes including transcriptional regulation, organogenesis, photosynthetic and hormone signalling pathways, stress adaptation and defence responses (Barbosa dos Santos and Park 2019)
U34 NZPradTrx119079_C01 Xyloglucan endotransglucosylase/hydrolase 13 Cleaves xyloglucan polymers, an essential constituent of the primary cell wall, and thereby participates in cell wall construction of growing tissues. https://www.uniprot.org/uniprot/Q9FKL8
U35 NZPradTrx037564_C01 PREDICTED: bidirectional sugar transporter SWEET3-like Mediates both low-affinity uptake and efflux of sugar across the plasma membrane https://www.uniprot.org/uniprot/Q6NQN5
U36 NZPradTrx118938_C01 Glycine-rich RNA-binding protein Plays a role in RNA transcription or processing during stress. Binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. https://www.uniprot.org/uniprot/Q03250
U37 NZPradTrx109658_C01 Probable aquaporin Involved in transport of water and other small neutral molecules across cellular biological membranes (Kapilan et al. 2018)
U38 NZPradTrx094541_C02 PREDICTED: methionine gamma-lyase-like Involved in amino acid catabolism (Ravanel et al. 1998) +
T14-B-strip 12 U39 NZPradTrx119456_C01 PR10-1.13 Involved in defence against pathogen infection and other environmental stresses (Liu et al. 2005) +
U40 NZPradTrx098320_C05 PREDICTED: LOB domain-containing protein 1-like Controls the proximal-distal patterning in petals and the adaxial-abaxial determination of leaves. Involved in the repression of the homeobox gene BP https://www.uniprot.org/uniprot/Q9FKZ3-1 +
U41 NZPradTrx073494_C01 TPA: putative ARF GTPase-activating domain family protein Have potential roles in cell migration, central to normal physiology in embryogenesis, the inflammatory response and wound healing (Campa and Randazzo 2008)
U42 NZPradTrx103835_C01 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of terpenoid compounds https://www.uniprot.org/uniprot/P62617 +
U43 NZPradTrx102746_C02 S6 ribosomal protein Key downstream effector of the target of rapamycin (TOR) kinase pathway that regulates various biological processes, including translation, synthesis of ribosomal proteins, and transcription of rRNA (Kim et al. 2014) +
U44 NZPradTrx094959_C01 Pathogenesis-related protein 10 Involved in a cell wall rigidification to signal transduction and antimicrobial activity (Liu and Ekramoddoullah 2006) +
U45 NZPradTrx096309_C03 Dirigent-like protein Predominant roles in defence responses, secondary metabolism, and fiber biosynthesis (Li et al. 2017) +
U46 NZPradTrx105315_C01 PREDICTED: uncharacterized LOC101219508  
U47 NZPradTrx077043_C01 FAD/NAD(P)-binding oxidoreductase domain-containing protein Catalyses a wide variety of redox reactions with many different substrates (Sellés Vidal et al. 2018)
U48 NZPradTrx110593_C01 PREDICTED: chaperonin CPN60-2, mitochondrial-like Implicated in mitochondrial protein import and macromolecular assembly. May facilitate the correct folding of imported proteins. May also prevent misfolding and promote the refolding and proper assembly of unfolded polypeptides generated under stress conditions in the mitochondrial matrix. https://www.uniprot.org/uniprot/Q05046 +
T14-N-MJ 30 U49 NZPradTrx118421_C03 Caffeic acid O-methyltransferase Catalyses the conversion of caffeic acid to ferulic acid and of 5-hydroxyferulic acid to sinapic acid. The resulting products may subsequently be converted to the corresponding alcohols that are incorporated into lignins https://www.uniprot.org/uniprot/Q06509 +
U50 NZPradTrx079649_C05 Geranyl diphosphate synthase Catalyses the condensation of dimethylallyl diphosphate and isopentenyl diphosphate to geranyl diphosphate, the key precursor of monoterpene biosynthesis (Burke et al. 1999) +
NZPradTrx079649_C03  
NZPradTrx079649_C02  
U51 NZPradTrx122822_C01 PREDICTED: F-box protein GID2-like Essential component of the SCF-type E3 ligase complex, SCF(GID2), a complex that positively regulates the gibberellin signalling pathway https://www.uniprot.org/uniprot/Q9STX3 +
U52 NZPradTrx083848_C01 Chlorophyllase The first enzyme involved in chlorophyll (Chl) degradation and catalyses the hydrolysis of ester bond to yield chlorophyllide and phytol (Tsuchiya et al. 1999) +
U53 NZPradTrx103321_C01 Phenylalanine ammonia-lyase Phenylalanine aminomutase that catalyses the rearrangement of L-phenylalanine to R-beta-phenylalanine. Catalyses the first committed step in the biosynthesis of the side chain of the alkaloid taxol (paclitaxel) https://www.uniprot.org/uniprot/Q68G84 +
U54 NZPradTrx071573_C01 Starch synthase isoform II Contributes to the extension of glucan chains in the synthesis of starch (Edwards et al. 1999) +
U55 NZPradTrx105898_C01 Glutamate-1-semialdehyde 2,1-aminomutase Essential enzyme in the pathway that leads to the synthesis of chlorophyll and other tetrapyrroles in plants and some bacteria (Tyacke et al. 1995)
U56 NZPradTrx182827_C01 PREDICTED: LRR receptor-like serine/threonine-protein kinase FLS2-like Constitutes the pattern-recognition receptor (PPR) that determines the specific perception of flagellin (flg22), a potent elicitor of the defence response to pathogen-associated molecular patterns (PAMPs) https://www.uniprot.org/uniprot/Q9FL28 +
U57 NZPradTrx184681_C01 FK506 binding-like protein Involved in diverse cellular functions including protein folding, cellular signalling, apoptosis and transcription (Tong and Jiang 2016) +
U58 NZPradTrx094486_C01 Putative UDP-glucose:flavonoid glucosyltransferase Enhances the solubility of anthocyanins (Chen et al. 2011) +
T21-B-MJ 4 U59 NZPradTrx083714_C01 PREDICTED: protein GLUTAMINE DUMPER 1-like Involved in the regulation of amino acid metabolism, in the salicylic acid (SA) pathway and in the geminivirus-host interaction
https://www.uniprot.org/uniprot/O81775
+
U60 NZPradTrx053990_C01 PREDICTED: cytochrome P450 71A1-like Involved in the metabolism of compounds associated with the development of flavour in the ripening fruit process, possibly by acting as trans-cinnamic acid 4-hydrolase https://www.uniprot.org/uniprot/P24465 +
U61 NZPradTrx105443_C01 GMP synthase [glutamine-hydrolyzing] subunit A, putative Involved in de novo biosynthesis of guanosine nucleotides https://www.brenda-enzymes.org/enzyme.php?ecno=6.3.5.2 +
U62 NZPradTrx112236_C01 Laccase Involved in phenolic metabolism and functioning of cell wall (Ranocha et al. 2002) +
T21-B-S 13 U63 NZPradTrx087634_C02 Properoxidase Involved in lignification, cell elongation, stress defence and seed germination (Shigeto and Tsutsumi 2016) +
U64 NZPradTrx103699_C01 Oxidoreductase, 2OG-Fe(II) oxygenase family protein Involved in defence against pathogens (Van Damme et al. 2008) +