Table 3 Top most expressed transcripts (identified by the percentage number of transcripts represented) in the constitutive transcriptome of the bark and the needles as assessed at T0 (sampled before treatment), indicating their identification number, Scion transcript code, gene name and predicted function. Some transcripts were represented by different copies of the transcripts (isoforms—- represented by different transcript codes in each row) and the percentages of transcripts represented by each isoform are indicated. Each isoform has a superscript linking it to its corresponding percentage number of transcripts identified. Ba = first isoform identified in the bark for the gene, Na = first isoform one identified in the needles etc. The transcripts were not significantly differentially expressed between the bark and the needles. Some transcripts were selected in both plant parts

1

NZPradTrx107583_C02 ^{Ba, Na}

Light-harvesting chlorophyll a/b-binding polypeptide (Lhcb2) mRNA

Absorb sunlight and transfer the excitation energy to the core complexes of PSII in order to drive photosynthetic electron transport (Liu et al. 2013) [70, 71]

1.46 ^Ba,0.28 ^Bb, 0.25 ^Bc

1.99^Na, 0.95 ^Nb, 1.07 ^Nc, 0.51 ^Nd, 0.51 ^Ne, 0.33 ^Nf,

NZPradTrx050124_C01 ^{Bb, Nb}

NZPradTrx118940_C01 ^{Bc, Nc}

NZPradTrx107583_C01 ^Nd

NZPradTrx107583_C03 ^Ne

NZPradTrx050061_C01 ^Nf

2

NZPradTrx100458_C02 ^Ba

Dehydrin 7

Involved in dehydration stress (Stival Sena et al. 2018) [72]

1.38 ^Ba, 0.60 ^Bb

NZPradTrx100458_C03 ^Bb

3

NZPradTrx112612_C02 ^{Ba, Na}

Metallothionein 3

Play important roles in metal homeostasis and protection against heavy metal toxicity (Nevrtalova et al. 2014) [73]

0.82 ^Ba,0.29 ^Bb

0.58 ^Nc,1.75^Na, 0.66 ^Nb

NZPradTrx085990_C02 ^Bb

NZPradTrx094970_C01 ^Nb

NZPradTrx094970_C02 ^Nc

4

NZPradTrx052720_C01 ^Ba

Chalcone synthase

Plays crucial roles in phenolic biosynthesis (Dixon and Paiva 1995) [74]

0.70 ^Ba, 0.37^Bb, 0.35 ^Bc,0.27 ^Bd, 0.26 ^Be

0.30 ^Na

NZPradTrx115271_C03 ^Bb

NZPradTrx078806_C01 ^{Bc, Na}

NZPradTrx115271_C02 ^Bd

NZPradTrx115271_C05 ^Be

5

NZPradTrx050994_C02 ^Ba

Defensin

Inhibit the growth of a broad range of pathogens, including bacteria, fungi and viruses (Ermakova et al. 2016; Picart et al. 2012) [75, 76].

0.61 ^Ba, 0.53 ^Bb

NZPradTrx050994_C01 ^Bb

6

NZPradTrx076819_C01

TCTP-like protein

Implicated in important cellular processes, such as cell growth, cell cycle progression, malignant transformation and in the protection of cells against various stress conditions and apoptosis (Bommer and Thiele 2004)

0.42

7

NZPradTrx062252_C01 ^Ba, NZPradTrx107621_C01 ^Bb

Nonspecific lipid transfer protein

Play important roles in resistance to biotic and abiotic stress. Have the ability to bind or transfer various types of hydrophobic molecules in vitro, such as fatty acids, fatty acyl-CoA, phospholipids, glycolipids and cutin monomers (Liu et al. 2015a)

0.27 ^Ba, 0.26 ^Bb

8

NZPradTrx116410_C12

Pathogenesis-related protein 10

Show biological activities related to disease resistance (Liu and Ekramoddoullah 2006)

0.26

9

NZPradTrx077717_C01

LP3-1

Implicated in water-stress

https://www.uniprot.org/uniprot/Q5G154

0.24

10

NZPradTrx100333_C02

ASR protein

Involved in sugar and abscisic acid signalling (Çakir et al. 2003)

0.25

0.24

11

NZPradTrx098632_C01

Translation elongation factor-1 alpha

Catalyses the transfer of aminoacylated-tRNAs (Sasikumar et al. 2012)

12

NZPradTrx098233_C03 ^Na

Ribulose bisphosphate carboxylase/oxygenase (RuBisCO)

Catalyses carboxylation of RuBP in the first step of the Calvin cycle of photosynthesis (Tabita 1999)

1.57 ^Na, 0.59 ^Nb, 0.53 ^Nc, 0.36 ^Nd, 0.30 ^Ne, 0.22 ^Nf

NZPradTrx064995_C01 ^Nb

NZPradTrx064875_C01 ^Nc

NZPradTrx098233_C01 ^Nd

NZPradTrx098233_C05 ^Ne

NZPradTrx064875_C02 ^Nf

13

NZPradTrx098207_C02 ^Na

Cysteine proteinase inhibitor CPI-3

Involved in plant development and defence, especially in the regulation of stress responses (Li et al. 2015)

0.77 ^Na, 0.27 ^Nb

NZPradTrx098207_C01 ^Nb

14

NZPradTrx105813_C01

PREDICTED: probable fructose-bisphosphate aldolase 2, chloroplastic-like

Plays a key role in glycolysis and gluconeogenesis https://www.uniprot.org/uniprot/Q944G9

0.37

15

NZPradTrx111299_C01 ^Na

PREDICTED: oxygen-evolving enhancer protein 1, chloroplastic-like isoform 2

Stabilizes the manganese cluster which is the primary site of water splitting

https://www.uniprot.org/uniprot/P23321

0.35 ^Na, 0.32 ^Nb

NZPradTrx100425_C01 ^Nb

16

NZPradTrx065162_C02

Thiazole biosynthetic enzyme

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

0.34

17

NZPradTrx184720_C01

PSI-D1 precursor

PsaD can form complexes with ferredoxin and ferredoxin-oxidoreductase in photosystem I (PS I) reaction centre.

https://www.uniprot.org/uniprot/Q9S7H1

0.22