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Table 5 Top 10 genes differentially expressed in each of the time periods from T7 to T21 in the bark (B) and needles (N) following bark stripping (S) or methyl jasmonate (MJ) treatment of two-year old Pinus radiata plants The Scion transcript code, predicted gene name and predicted functions of the known genes are indicated. Some genes were represented by more than one transcript (isoforms—different Scion P. radiata transcript codes that represent one gene in column 1) and multiple copies of an isoform as indicated by the numbers in the parentheses, for example +(2) = two copies of an isoforms relating to the gene were identified, where + = up-regulation, − = down-regulation. The superscript followingnumbers in the parentheses following the gene names represent the core function of the gene among the 11 broad categories listed in the table footnote. For example for the Peptide transporter PTR3-A-like,a the superscript a denotes that this gene was associated with primary metabolism (see footnote). However, it is recognised that some genes may fall in more than one category. 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

Scion transcript code Gene name Function T7-B-MJ T7-B-S T7-N-MJ T14-B-MJ T14-B-S T14-N-MJ T21-B-MJ T21-B-S T21-N-MJ
NZPradTrx081530_C01 Peptide transporter PTR3-A-likea Facilitates amino acid induction (Barnes et al. 1998) +         
NZPradTrx115883_C01 Granule-bound starch synthase, partiala Responsible for amylose synthesis (Miao et al. 2014)         
NZPradTrx113785_C01 GDP-D-mannose-3′,5′-epimerasea Central enzyme of the major ascorbate biosynthesis pathway in higher plants that converts GDP-d-mannose to GDP-l-galactose (Gilbert et al. 2009) +         
NZPradTrx065162_C02 Thiazole biosynthetic enzymeb Thiamine synthesis and DNA damage tolerance (Liu et al. 2015b)         
NZPradTrx083866_C01 1-aminocyclopropane-1-carboxylate oxidase 3g Production of ethylene, that functions as a mediator of responses to external stimuli, such as wounding (Houben and Van de Poel 2019) + +   + +     
NZPradTrx117447_C01 PREDICTED: transcription factor bHLH126-likef Transcription factors play a central role in a number of biological processes, producing, for example, the induction of specific genes in response to particular stimuli as well as controlling the cell type specific or developmentally regulated expression of other genes (Latchman 2008) + (2)    +(2)    +(3) +  
NZPradTrx117447_C02
NZPradTrx091619_C02
NZPradTrx113021_C04 Cytochrome P450 CYPCh Key players in plant development and defence (Xu et al. 2015) -(2)        
NZPradTrx117482_C10
NZPradTrx103647_C02 Oleoyl-acyl carrier protein thioesterase, partiala Plays an essential role in chain termination during de novo fatty acid synthesis https://www.uniprot.org/uniprot/Q42561         
NZPradTrx111880_C01 Cell wall invertasea Mediates reduced export of sucrose or enhanced import of hexoses at the site of infection (Proels and Hückelhoven 2014) [78] +     +    + (2)  
NZPradTrx132560_C01
NZPradTrx186688_C01 DNA binding protein, putativei DNA binding proteins serve two principal functions: to organize and compact the chromosomal DNA and to regulate and effect the processes of transcription, DNA replication, and DNA recombination (Travers 2001).   +      
NZPradTrx187077_C01
NZPradTrx065807_C02 PREDICTED: cleavage and polyadenylation specificity factor subunit 5-likei Component of the cleavage factor Im (CFIm) complex that functions as an activator of the pre-mRNA 3′-end cleavage and polyadenylation processing required for the maturation of pre-mRNA into functional mRNAs https://www.uniprot.org/uniprot/Q16630         
NZPradTrx095732_C01 Thaumatin-like proteind Involved in local responses of roots to colonization by non-pathogenic plant growth-promoting rhizobacteria (PGPR) fluorescent Pseudomonas spp. (Léon-Kloosterziel et al. 2005) -,+ (2)    +   + +  
NZPradTrx064724_C01
NZPradTrx108940_C08
NZPradTrx087317_C02
NZPradTrx038584_C01 Chloroplast threonine deaminase 1 precursorc Useful in isoleucine (Ile) biosynthesis and impairing digestive processes in the insect gut (Chen et al. 2007)   + +   + +   + +
NZPradTrx111230_C01 Triacylglycerol lipase, putativea Releases fatty acids from a number of different substrates (Padham et al. 2007)         
NZPradTrx084103_C02 PREDICTED: glutamate--cysteine ligase, chloroplastic-liked Seems to play an important role in controlling the expression of resistance responses like the regulation of salicylic acid (SA) and phytoalexin (camalexin) production. Involved in resistance to fungal and bacterial pathogens. https://www.uniprot.org/uniprot/P46309   +        
NZPradTrx074370_C02, NZPradTrx132647_C01 PREDICTED: lysine histidine transporter 2-likek Amino acid-proton symporter. Transporter with a broad specificity for neutral and acidic amino acids https://www.uniprot.org/uniprot/Q9LRB5   +    +   +   +(2)
NZPradTrx098051_C01 PREDICTED: endo-1,3;1,4-beta-D-glucanase-likej Implicated in responses to stress, wounding, and pathogen infection (Rezzonico et al. 1998)   +        
NZPradTrx053937_C01 2-methyl-6-phytylbenzoquinone methyltranferasej One of the regulators of the composition of tocopherols-class of compounds that function as lipid soluble antioxidants that are extremely potent quenchers of singlet oxygen and free radical species (Shintani et al. 2002)         
NZPradTrx119228_C01 4-hydroxyphenyl-pyruvate dioxygenasea Plays an important role in degrading aromatic amino acids (Fritze et al. 2004)    +    +    
NZPradTrx184501_C01 PREDICTED: 50S ribosomal protein L6, chloroplastic-likei Binds directly to 23S ribosomal RNA and is located at the aminoacyl-tRNA binding site of the peptidyltransferase centre. https://www.uniprot.org/uniprot/O23049         
NZPradTrx186075_C01 PREDICTED: hexokinase-1-likea Fructose and glucose phosphorylating enzyme https://www.uniprot.org/uniprot/Q42525        
NZPradTrx105399_C03 PREDICTED: leucine-rich repeat-containing protein 40-likej Plays crucial roles in development and stress responses (Liu et al. 2017) [17, 79]         
NZPradTrx051602_C02 Sodium-bile acid cotransporter, putativek Is involved in photorespiratory metabolism (South et al. 2017)         
NZPradTrx082621_C01 Mitogen activated protein kinase 6j Involved in oxidative stress-mediated signalling cascade (such as ozone)
https://www.uniprot.org/uniprot/Q39026
   +       
NZPradTrx033779_C01 PREDICTED: pentatricopeptide repeat-containing protein At1g62670, mitochondrial-likei Binds one or several organellar transcripts, and influences their expression by altering RNA sequence, turnover, processing, or translation (Barkan and Small 2014)         
NZPradTrx184660_C01 PREDICTED: PGR5-like protein 1A, chloroplastic-likea Ferredoxin-plastoquinone reductase involved in cyclic electron flow (CEF) around photosystem I https://www.uniprot.org/uniprot/Q8H112         
NZPradTrx097586_C01 Type III chlorophyll a /b-binding proteina Functions as a light receptor, capturing and delivering excitation energy to photosystems with which it is closely associated https://www.uniprot.org/uniprot/P27523         
NZPradTrx101698_C02 PrMC3b Predicted to encode a chalcone-synthase-like protein (Walden et al. 1999)        
NZPradTrx117804_C07 PREDICTED: probable carboxylesterase 2a Carboxylesterases hydrolyse esters of short-chain fatty acids (Marshall et al. 2003)         
NZPradTrx100227_C01 PREDICTED: medium-chain-fatty-acid--CoA ligasea Catalyses the esterification, concomitant with transport, of exogenous fatty acids into metabolically active CoA thioesters for subsequent degradation or incorporation into phospholipids https://www.uniprot.org/uniprot/P38135     +      
NZPradTrx081530_C01 PREDICTED: peptide transporter PTR3-A-likea Facilitates amino acid induction (Barnes et al. 1998)     +      
NZPradTrx192941_C01 Beta-amylase Involved in starch breakdown in plants (Kaplan and Guy 2004)     +      
NZPradTrx052040_C01 PREDICTED: oleosin 16 kDa-likej May have a structural role to stabilize the lipid body during desiccation of the seed by preventing coalescence of the oil. https://www.uniprot.org/uniprot/Q42980         
NZPradTrx108711_C04 PREDICTED: putative UDP-rhamnose:rhamnosyltransferase 1-likea Involved in fatty acid metabolism (van der Sluis and Erasmus 2016)      +     
NZPradTrx112833_C08 Tify domain containing proteini Found in a variety of plant transcription factors https://pfam.xfam.org/family/PF06200      +   +   +
NZPradTrx112833_C07
NZPradTrx071306_C02 PREDICTED: transmembrane ascorbate ferrireductase 1-likej Catalyses ascorbate-dependent trans-membrane ferric-chelate reduction
https://www.uniprot.org/uniprot/Q8L856
     +     
NZPradTrx051982_C01 PREDICTED: histone H2B.2-like isoform 2i Play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability https://www.uniprot.org/uniprot/Q5QNW6         
NZPradTrx119456_C01 PR10-1.13j Involved in defence against pathogen infection and other environmental stresses (Liu et al. 2005)      +     
NZPradTrx053878_C02 Aldehyde dehydrogenasea Involved in plant metabolism and contributes to aldehyde homeostasis to eliminate toxic aldehydes (Zhao et al. 2017)       +(3)    +(3)
NZPradTrx053878_C01
NZPradTrx053878_C03
NZPradTrx087148_C01 PREDICTED: lanC-like protein 2-likeg May play a role in abscisic acid (ABA) signalling
https://www.uniprot.org/uniprot/F4IEM5
      +    
NZPradTrx115807_C06 Hydrolase, putativej Enzyme which catalyses hydrolysis reaction, i.e. the addition of the hydrogen and hydroxyl ions of water to a molecule with its consequent splitting into two or more simpler molecules.
https://www.uniprot.org/keywords/KW-0378
      +    +
NZPradTrx112951_C03 Embryo-abundant proteinj May act as a cytoplasm protectant during desiccation. https://www.uniprot.org/uniprot/P46520       +    
NZPradTrx097637_C01 PREDICTED: leucoanthocyanidin dioxygenase-likeb Involved in anthocyanin and protoanthocyanidin biosynthesis by catalysing the oxidation of leucoanthocyanidins into anthocyanidins https://www.uniprot.org/uniprot/Q96323       +    
NZPradTrx112166_C01 Peroxidase-like protein, partialj Response to oxidative stress https://www.uniprot.org/uniprot/Q24925       +    +
NZPradTrx082621_C01 Mitogen activated protein kinase 6g Plays key role in the transduction of environmental and developmental signals through phosphorylation of downstream signalling targets (Jagodzik et al. 2018)       +    
NZPradTrx110107_C07 PREDICTED: transcription factor aborted microspores-like Required for male fertility and pollen differentiation, especially during the post-meiotic transcriptional regulation of microspore development within the developing anther https://www.uniprot.org/uniprot/Q9ZVX2        +   
NZPradTrx112236_C02 Laccaseb Involved in phenolic metabolism and functioning of cell wall (Ranocha et al. 2002)        +   
NZPradTrx089433_C01 Lipoxygenase 2b Essential for formation of green leaf volatiles and five-carbon volatiles (Mochizuki et al. 2016)        +   
NZPradTrx109272_C04 Malic enzyme, putativea Catalyses the oxidative decarboxylation of malate to form pyruvate, a reaction important in a number of metabolic pathways (Zhang et al. 2016)        
NZPradTrx107808_C01 Putative flavoprotein-containing polyamine oxidase, partialb Involved in drought stress response and flavonoid biosynthesis (Kamada-Nobusada et al. 2008)        +   
NZPradTrx049513_C01 Putative proline-rich arabinogalactan protein 4e Contributes to the strengthening of cell walls of quickly growing organs (Hijazi et al. 2014)         +  
NZPradTrx049513_C02
NZPradTrx079868_C01 PREDICTED: (RS)-norcoclaurine 6-O-methyltransferase-likeb Involved in the biosynthesis of (S)-coclaurine, the common precursor of all benzylisoquinoline alkaloids. https://www.uniprot.org/uniprot/Q6WUC1         
NZPradTrx054832_C01 Aquaporin-like proteink Involved in transport of water and other small neutral molecules across cellular biological membranes (Kapilan et al. 2018)         +  
NZPradTrx069597_C01 Acetyl-CoA carboxylase BCCP subunita Catalyses the first committed step of fatty acid synthesis, the carboxylation of acetyl-CoA to malonyl-CoA (Sasaki and Nagano 2004)         
NZPradTrx117954_C05 E-alpha-bisabolene synthaseb Involved in defensive oleoresin formation in conifers in response to insect attack or other injury. Involved in sesquiterpene (C15) olefins biosynthesis https://www.uniprot.org/uniprot/O81086         +  
NZPradTrx087252_C01 TPA: putative GID1-like gibberellin receptorg Involved in gibberellin signalling (Sun 2011)          +
NZPradTrx074370_C01 Putative proline transporterk Mediates the amino acid proline and glycine betaine transport https://www.uniprot.org/uniprot/P92961          +(2)
NZPradTrx112166_C01
NZPradTrx113904_C06/ NZPradTrx101343_C01 PREDICTED: clavaminate synthase-like protein At3g21360-likej Associated with metal ion binding and oxido-reductase activity
https://www.uniprot.org/uniprot/Q9LIG0
         +
  1. aprimary metabolism
  2. bsecondary metabolism
  3. cdigestive inhibitors
  4. dpathogenesis-related (PR) protein families
  5. egenes involved with physical strengthening of the cell-wall
  6. ftranscription factors
  7. gphytohormones and signalling molecules
  8. hgeneral catalysts
  9. imolecules involved in transcription
  10. jmolecules involved in broad biotic and abiotic stress responses
  11. kbroad function genes