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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)

+