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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

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

ID number Scion transcript code (or isoforms) Gene name Predicted gene function Percentages of transcripts (out of 6312)
Bark Needles
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 1.99Na, 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,1.75Na, 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, 0.37Bb, 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
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   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
  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.