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]

NZPradTrx081530_C01

Peptide transporter PTR3-A-like^a

Facilitates amino acid induction (Barnes et al. 1998)

+

NZPradTrx115883_C01

Granule-bound starch synthase, partial^a

Responsible for amylose synthesis (Miao et al. 2014)

–

NZPradTrx113785_C01

GDP-D-mannose-3′,5′-epimerase^a

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 enzyme^b

Thiamine synthesis and DNA damage tolerance (Liu et al. 2015b)

–

NZPradTrx083866_C01

1-aminocyclopropane-1-carboxylate oxidase 3^g

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-like^f

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 CYPC^h

Key players in plant development and defence (Xu et al. 2015)

-(2)

–

NZPradTrx117482_C10

NZPradTrx103647_C02

Oleoyl-acyl carrier protein thioesterase, partial^a

Plays an essential role in chain termination during de novo fatty acid synthesis https://www.uniprot.org/uniprot/Q42561

–

NZPradTrx111880_C01

Cell wall invertase^a

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 protein^d

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 precursor^c

Useful in isoleucine (Ile) biosynthesis and impairing digestive processes in the insect gut (Chen et al. 2007)

+

+

+

+

+

+

NZPradTrx111230_C01

Triacylglycerol lipase, putative^a

Releases fatty acids from a number of different substrates (Padham et al. 2007)

–

NZPradTrx084103_C02

PREDICTED: glutamate--cysteine ligase, chloroplastic-like^d

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-like^k

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-like^j

Implicated in responses to stress, wounding, and pathogen infection (Rezzonico et al. 1998)

+

NZPradTrx053937_C01

2-methyl-6-phytylbenzoquinone methyltranferase^j

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 dioxygenase^a

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-like^a

Fructose and glucose phosphorylating enzyme https://www.uniprot.org/uniprot/Q42525

–

–

NZPradTrx105399_C03

PREDICTED: leucine-rich repeat-containing protein 40-like^j

Plays crucial roles in development and stress responses (Liu et al. 2017) [17, 79]

–

NZPradTrx051602_C02

Sodium-bile acid cotransporter, putative^k

Is involved in photorespiratory metabolism (South et al. 2017)

–

NZPradTrx082621_C01

Mitogen activated protein kinase 6^j

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-like^a

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 protein^a

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

PrMC3^b

Predicted to encode a chalcone-synthase-like protein (Walden et al. 1999)

–

–

NZPradTrx117804_C07

PREDICTED: probable carboxylesterase 2^a

Carboxylesterases hydrolyse esters of short-chain fatty acids (Marshall et al. 2003)

–

NZPradTrx100227_C01

PREDICTED: medium-chain-fatty-acid--CoA ligase^a

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-like^a

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-like^j

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-like^a

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-like^j

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

PR10-1.13^j

Involved in defence against pathogen infection and other environmental stresses (Liu et al. 2005)

+

NZPradTrx053878_C02

Aldehyde dehydrogenase^a

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-like^g

May play a role in abscisic acid (ABA) signalling

https://www.uniprot.org/uniprot/F4IEM5

+

NZPradTrx115807_C06

Hydrolase, putative^j

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 protein^j

May act as a cytoplasm protectant during desiccation. https://www.uniprot.org/uniprot/P46520

+

NZPradTrx097637_C01

PREDICTED: leucoanthocyanidin dioxygenase-like^b

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, partial^j

Response to oxidative stress https://www.uniprot.org/uniprot/Q24925

+

+

NZPradTrx082621_C01

Mitogen activated protein kinase 6^g

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

Laccase^b

Involved in phenolic metabolism and functioning of cell wall (Ranocha et al. 2002)

+

NZPradTrx089433_C01

Lipoxygenase 2^b

Essential for formation of green leaf volatiles and five-carbon volatiles (Mochizuki et al. 2016)

+

NZPradTrx109272_C04

Malic enzyme, putative^a

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, partial^b

Involved in drought stress response and flavonoid biosynthesis (Kamada-Nobusada et al. 2008)

+

NZPradTrx049513_C01

Putative proline-rich arabinogalactan protein 4^e

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-like^b

Involved in the biosynthesis of (S)-coclaurine, the common precursor of all benzylisoquinoline alkaloids. https://www.uniprot.org/uniprot/Q6WUC1

–

NZPradTrx054832_C01

Aquaporin-like protein^k

Involved in transport of water and other small neutral molecules across cellular biological membranes (Kapilan et al. 2018)

+

NZPradTrx069597_C01

Acetyl-CoA carboxylase BCCP subunit^a

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 synthase^b

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 receptor^g

Involved in gibberellin signalling (Sun 2011)

+

NZPradTrx074370_C01

Putative proline transporter^k

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-like^j

Associated with metal ion binding and oxido-reductase activity

https://www.uniprot.org/uniprot/Q9LIG0

+