Table 1 The 55 tomato plant DEGs associated with defense response to abiotic and biotic stress. DEGs were sorted by log2-fold change (log2FC). These DEGs were identified in the transcriptome analysis comparing psyllid-infested and uninfested tomato plants 3 weeks after infestation (P < 0.01). NCBI Blast searches were used to identify Gene IDs and protein products in tomatoes as well as their homologs in other species. Specifically, the expression changes in 44 genes (80%, in bold) would have resulted in improvements to plant defense pathways. These DEGs were related to defense against insect damage, microbial infection, programmed cell death, salt stress, and drought. Simultaneously, 11 DEGs, especially those related to the hypersensitive response, underwent expression changes that would have resulted in impairments to plant defense pathways

Solyc12g055920.1

CBL4

AT5G24270

-1.33

calcineurin B protein 4

Calcium sensor that regulates intracellular Na+ and K+ homeostasis and salt tolerance; Activates the plasma membrane Na+/H+ antiporter SOS1

Decreased potassium and calcium stress response; Decreased hypotonic salinity response

Halfter, Ursula, et al. "The Arabidopsis SOS2 protein kinase physically interacts with and is activated by the calcium-binding protein SOS3." Proceedings of the National Academy of Sciences 97.7 (2000): 3735-3740.

Solyc10g076700.1

STR10

AT3G08920

-0.90

rhodanese domain-containing protein 10

Involved in response to cold stress

Decreased reponse to cold stress

Bauer, Michael, and Jutta Papenbrock. "Identification and characterization of single-domain thiosulfate sulfurtransferases from Arabidopsis thaliana." FEBS letters 532.3 (2002): 427-431.

Solyc06g073260.2

CSP41B

AT1G09340

-0.81

chloroplast stem-loop binding protein of 41 kDa b, chloroplastic

Associates with pre-ribosomal particles in chloroplasts and participates in chloroplast ribosomal RNA metabolism; Required for chloroplast integrity and embryo development; Regulates the circadian system; Regulates heteroglycans and monosaccharide mobilization

Impaired chloroplast organization; Impaired circadian rhythm; Decreased defense response to bacteria and wounding; Decreased galactose catabolism; Decreased monosaccharide metabolism; Decreased transcription and translation; Decreased response to cold and drought; Decreased rRNA processing

Raab, Sabine, et al. "ABA-responsive RNA-binding proteins are involved in chloroplast and stromule function in Arabidopsis seedlings." Planta 224.4 (2006): 900-914.

Solyc01g103760.2

N/a

AT1G71900

-0.71

magnesium transporter NIPA4

Divalent cation transporter; Negative regulator of antiviral defense response

Decreased magnesium ion transport; Increased antiviral defense response

Gao, Hua, et al. "Arabidopsis ENOR3 regulates RNAi-mediated antiviral defense." Journal of Genetics and Genomics 45.1 (2018): 33-40.

Solyc02g093230.2

CCOAOMT1

AT4G34050

-0.69

caffeoyl-CoA O-methyltransferase

Methylates caffeoyl-CoA to feruloyl-CoA and 5-hydroxyferuloyl-CoA; Plays a role in the synthesis of feruloylated polysaccharides; Reinforces the plant cell wall; Regulates response to wounding or pathogen challenge

Decreased lignin biosynthesis; Decreased response to wounding or pathogen challenge

Civardi, L., J. Rigau, and P. Puigdomenech. "Nucleotide Sequence of two cDNAs coding for Caffeoyl-coenzyme A O-Methyltransferase (CCoAOMT) and study of their expression in Zea mays." Plant Physiol 120.4 (1999): 1.

Solyc07g032640.1

PSBO1

AT5G66570

-0.66

oxygen-evolving enhancer protein 1-1, chloroplastic

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

Decreased defense response to bacteria; Decreased photoinhibition; Decreased photosynthesis; Decreased photosystem II assembly and stabilization; Decreased regulation of protein dephosphorylation

Murakami, Reiko, et al. "Characterization of an Arabidopsis thaliana mutant with impaired psbO, one of two genes encoding extrinsic 33-kDa proteins in photosystem II." FEBS letters 523.1-3 (2002): 138-142.

Solyc08g076220.2

N/a

AT1G32060

-0.64

phosphoribulokinase, chloroplastic

Involved in reductive pentose-phosphate cycle; Involved in defense response to bacteria and cold stress

Decreased defense response to bacteria; Impaired reductive pentose-phosphate cycle; Decreased response to cold stress

Kiddle, Guy, et al. "Effects of leaf ascorbate content on defense and photosynthesis gene expression in Arabidopsis thaliana." Antioxidants and Redox Signaling 5.1 (2003): 23-32.

Solyc02g091560.2

SHM1

AT4G37930

-0.53

serine hydroxymethyltransferase 1, mitochondrial

Catalyzes interconversion of serine and glycine in the photorespiratory pathway; Involved in controlling cell damage caused by abiotic stress; Regulates the hypersensitive defense response

Decreased response to tetrahydrofolate; Decreased L-serine metabolism; Decreased one-carbon metabolism; Decreased photorespiration; Decreased hypersensitive response; Decreased response to cadmium, cold, heat, and light stress; Decreased tetrahydrofolate metabolism

Moreno, Juan Ignacio, et al. "Arabidopsis SHMT1, a serine hydroxymethyltransferase that functions in the photorespiratory pathway influences resistance to biotic and abiotic stress." The Plant Journal 41.3 (2005): 451-463.

Solyc01g107660.2

SEP1

AT4G34190

-0.47

stress enhanced protein 1 protein

Involved in non-photochemical quenching; Plays a role in the thylakoid membrane in response to light stress

Decreased response to high light intensity; Decreased photosynthesis; Decreased response to wounding

Maejima, Kensaku, et al. "Degradation of class E MADS-domain transcription factors in Arabidopsis by a phytoplasmal effector, phyllogen." Plant signaling & behavior 10.8 (2015): e1042635.

Solyc05g008370.1

RPI2

AT2G01290

-0.38

ribose-5-phosphate isomerase 2

Catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate

Decreased prorammed cell death; Decreased pentose-phosphate shunt, non-oxidative branch; Decreased vegetative-to-reproductive phase transition of meristem; Decreased hypersensitive response

Xiong, Yuqing, et al. "Deficiency in a cytosolic ribose-5-phosphate isomerase causes chloroplast dysfunction, late flowering and premature cell death in Arabidopsis." Physiologia plantarum 137.3 (2009): 249-263.

Solyc05g006990.2

NPF4.6

AT1G69850

-0.29

protein NRT1/ PTR FAMILY 4.6

Low-affinity proton-dependent nitrate transporter; Involved in constitutive nitrate uptake; Involved in (+)-abscisic acid (ABA) transport; Mediates cellular ABA uptake

Decreased abscisic acid transport; Decreased nitrate assimilation; Decreased regulation of stomatal movement; Decreased response to nematode

Huang, Nien-Chen, et al. "Cloning and functional characterization of an Arabidopsis nitrate transporter gene that encodes a constitutive component of low-affinity uptake." The Plant Cell 11.8 (1999): 1381-1392.

Solyc01g094680.2

SPPL2

AT1G63690

0.25

signal peptide peptidase-like 2

Involved in pathogen defense response

Increased defense response to pathogens

Ascencio-Ibáñez, José Trinidad, et al. "Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection." Plant physiology 148.1 (2008): 436-454.

Solyc03g034200.2

RCF3

AT5G53060

0.26

RNA-binding KH domain-containing protein RCF3

Negative regulator of osmotic stress-induced gene expression; Regulates thermotolerance responses under heat stress; Forms a complex with CPL1 that modulates co-transcriptional processes; Represses stress-inducible gene expression; Involved in primary miRNA processing and pre-miRNA biogenesis; Involved in JA-mediated fungal defense

Increased heat acclimation; Increased jasmonic acid-mediated signaling; Increased mRNA processing; Increased miRNA processing; Increased regulation of defense response to fungus; Increased regulation of gene expression; Increased response to osmotic stress; Increased RNA splicing

Xiong, Liming, et al. "HOS5–a negative regulator of osmotic stress-induced gene expression in Arabidopsis thaliana." The Plant Journal 19.5 (1999): 569-578.

Solyc04g056280.2

CDKC-1

AT5G10270

0.26

cyclin dependent kinase C-1

Postranscriptional modifier; Involved in protein phosphorylation; Involved in leaf growth and development; Involved in defense reponse to virus

Increased leaf development; Increased phosphorylation of RNA polymerase II C-terminal domain; Increased defense response to virus

Pischke, Melissa S., et al. "A transcriptome-based characterization of habituation in plant tissue culture." Plant Physiology 140.4 (2006): 1255-1278.

Solyc05g048850.2

RH8

AT4G00660

0.27

DEAD-box ATP-dependent RNA helicase 8

ATP-dependent RNA helicase involved in mRNA turnover and mRNA decapping

Increased cytoplasmic mRNA processing body assembly and mRNA transport; Increased regulation of translation; Increased stress granule assembly; Increased viral process

Baek, Woonhee, et al. "A DEAD-box RNA helicase, RH8, is critical for regulation of ABA signalling and the drought stress response via inhibition of PP2CA activity." Plant, cell & environment 41.7 (2018): 1593-1604.

Solyc06g008970.2

XPD

AT1G03190

0.28

general transcription and DNA repair factor IIH helicase subunit XPD

Component of the general transcription and DNA repair factor IIH core comple; Plays an essential role in transcription initiation; Essential during plant growth; Negatively regulates a response to UV damage and heat stress

Increased DNA repair; Increased mitotic recombination; Increased transcription; Increased protein phosphorylation; Increased regulation of mitotic recombination; Increased response to heat, oxidative, and UV stress; Increased transcription by RNA polymerase II

Liu, Zongrang, et al. "Arabidopsis UVH6, a homolog of human XPD and yeast RAD3 DNA repair genes, functions in DNA repair and is essential for plant growth." Plant physiology 132.3 (2003): 1405-1414.

Solyc01g096290.2

RPL40A

AT2G36170

0.28

ubiquitin-60S ribosomal protein L40

Involved in protein degradation via the proteasome; Linear polymer chains formed via attachment by the initiator Met-lead during cellular signaling

Increased modification-dependent protein catabolism; Increased protein ubiquitination; Increased translation; Increased defense response to bacteria

Ditt, Renata F., et al. "The Arabidopsis thaliana transcriptome in response to Agrobacteria tumefaciens." Molecular plant-microbe interactions 19.6 (2006): 665-681.

Solyc04g082560.2

ITSN2

N/a

0.29

intersectin-2

Adapter protein that provides indirect link between the endocytic membrane and the actin assembly machinery; Regulates the formation of clathrin-coated vesicles; Involved in endocytosis of integrin beta-1 and transferrin receptor

Increased endocytosis; Increased dendrite extension; Increased regulation of Rho protein signal transduction; Increased viral process

Mettlen, Marcel, et al. "Endocytic accessory proteins are functionally distinguished by their differential effects on the maturation of clathrin-coated pits." Molecular biology of the cell 20.14 (2009): 3251-3260.

Solyc06g062350.2

RIN1

AT5G22330

0.29

ruvB-like protein 1

Core component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication, and DNA repair; Component of the NuA4 histone acetyltransferase complex involved in transcriptional activation of select genes

Increased box C/D snoRNP assembly; Increased cell differentiation; Increased chromatin remodeling; Increased flower development; Increased meristem development; Increased regulation of defense response to fungus; Increased regulation of transcription by RNA polymerase II

Heyndrickx, Ken S., and Klaas Vandepoele. "Systematic identification of functional plant modules through the integration of complementary data sources." Plant physiology 159.3 (2012): 884-901.

Solyc11g005130.1

UBN1

AT1G21610

0.30

ubinuclein-1

Required for replication-independent chromatin assembly

Increased nucleosome organization; Increased regulation of gene silencing; Increased response to salt stress

Nie, Xin, et al. "The HIRA complex that deposits the histone H3. 3 is conserved in Arabidopsis and facilitates transcriptional dynamics." Biology open 3.9 (2014): 794-802.

Solyc02g079040.2

CBP60B

AT5G57580

0.30

calmodulin-binding protein 60 B

Transcription activator that binds DNA in a sequence-specific manner to promote the expression of target genes

Increased salicylic acid biosynthesis; Increased defense response to bacteria

Reddy, Vaka S., et al. "Genes encoding calmodulin-binding proteins in the Arabidopsis genome." Journal of Biological Chemistry 277.12 (2002): 9840-9852.

Solyc10g044910.1

N/a

AT4G06676

0.31

protein EI24 homolog

Regulator of macroautophagy

Increased macroautophagy; Increased programmed cell death

Cheng, Chia-Yi, et al. "Araport11: a complete reannotation of the Arabidopsis thaliana reference genome." The Plant Journal 89.4 (2017): 789-804.

Solyc01g104970.2

BAK1

AT4G33430

0.31

brassinosteroid insensitive 1-associated receptor kinase 1

Involved in brassinosteroid signaling response to beacterium/fungi/oomycetes; Mediates programmed cell death

Increased brassinosteroid mediated signaling pathway; Increased programmed cell death; Increased defense response to bacteria/fungus/oomycetes

Li, Jia, et al. "BAK1, an Arabidopsis LRR receptor-like protein kinase, interacts with BRI1 and modulates brassinosteroid signaling." Cell 110.2 (2002): 213-222.

Solyc10g083610.1

CTR1

AT5G03730

0.31

serine/threonine-protein kinase CTR1

Ethylene receptor related to bacterial two-component regulators; Acts as a redundant negative regulator of ethylene signaling;

Increased cellular turnover; Increased cytokinin metabolism; Increased defense response to bacteria and insect damage; Increased response to ethylene; Increased hydrogen peroxide biosynthesis; Increased phloem/xylem histogenesis; Increased regulation of seedling development; Increased regulation of stomatal opening; Increased response to abscisic acid, auxin, and gibberellin; Increased response to heat and salt stress

Chang, Caren, et al. "Arabidopsis ethylene-response gene ETR1: similarity of product to two-component regulators." Science 262.5133 (1993): 539-544.

Solyc11g013260.1

PHB3

AT5G40770

0.32

prohibitin-3, mitochondrial

Holdase/unfoldase involved in the stabilization of newly synthesized mitochondrial proteins; Necessary for mitochondrial and cell metabolism and biogenesis; Required to regulate ethylene-mediated signaling; Involved in growth maintenance; Functions in nitric oxide-mediated responses

Increased cellular turnover; Increased defense response to bacteria; Increased lateral root development; Increased mitochondrion organization; Increased response to auxin, ethylene, and nitric oxide; Increased to salt stress; Increased salicylic acid biosynthesis

Christians, Matthew J., and Paul B. Larsen. "Mutational loss of the prohibitin AtPHB3 results in an extreme constitutive ethylene response phenotype coupled with partial loss of ethylene-inducible gene expression in Arabidopsis seedlings." Journal of experimental botany 58.8 (2007): 2237-2248.

Solyc08g059660.1

SEU

AT1G43850

0.32

transcriptional corepressor SEUSS

DNA-binding adapter subunit of the SEU-LUG transcriptional corepressor of AGAMOUS during the early floral meristem development; Regulates petal shape; Controls cell division during petal development; Acts through direct or indirect regulation of PHABULOSA and YAB1 and thus regulate cellular proliferation within the developing petal blade

Increased cell differentiation; Increased response to DNA damage; Increased defense response to most external biotic stimuli; Increased embryo development ending in seed dormancy; Increased gynoecium development; Decreased transcription by RNA polymerase II; Increased response to auxin; Increased response to cycloheximide; Increased response to hypoxia, oxidative stress, and excess silver ion

Sridhar, Vaniyambadi V., et al. "Transcriptional repression of target genes by LEUNIG and SEUSS, two interacting regulatory proteins for Arabidopsis flower development." Proceedings of the National Academy of Sciences 101.31 (2004): 11494-11499.

Solyc06g084040.2

DRIP2

AT2G30580

0.32

E3 ubiquitin protein ligase DRIP2

E3 ubiquitin-protein ligase that acts as a negative regulator of the response to water stress; Mediates ubiquitination and subsequent proteasomal degradation of the drought-induced transcriptional activator DREB2

Increased protein ubiquitination; Increased response to drought

Qin, Feng, et al. "Arabidopsis DREB2A-interacting proteins function as RING E3 ligases and negatively regulate plant drought stress–responsive gene expression." The plant cell 20.6 (2008): 1693-1707.

Solyc02g077320.2

SNI1

AT4G18470

0.32

SNI1 protein

Involved in DNA double-strand break repair; Negative regulator of hypersensitive response and systemic acquired resistance; Functions synergistically with NTL9/CBNAC as negative regulator of pathogen-induced PR1 expression; Suppresses defense response in the absence of pathogen challenge and is removed in response to induction

Increased response to DNA damage; Increased defense response to nematode; Increased histone H3 acetylation; Decreased defense response to pathogens; Decreased histone H3-K4 methylation; Decreased systemic acquired resistance; Increased regulation of transcription; Decreased hypersensitive response

Li, Xin, et al. "Identification and cloning of a negative regulator of systemic acquired resistance, SNI1, through a screen for suppressors of npr1-1." Cell 98.3 (1999): 329-339.

Solyc11g010950.1

ELP4

AT3G11220

0.33

elongator complex protein 4

Component of the RNA polymerase II elongator complex; Promotes organs development by modulating cell division rate; Regulates mechanisms producing carbon or importing sucrose; Involved in the repression of the abscisic acid signaling during seed germination; Required for auxin distribution or signaling; Prevents anthocyanins accumulation

Increased response to sucrose; Decreased anthocyanin metabolism; Increased cellular turnover; Increased auxin-mediated signaling; Increased regulation of carbon utilization; Increased regulation of leaf development; Increased response to oxidative stress; Increased tRNA wobble uridine modification

Nelissen, Hilde, et al. "The elongata mutants identify a functional Elongator complex in plants with a role in cell proliferation during organ growth." Proceedings of the National Academy of Sciences 102.21 (2005): 7754-7759.

Solyc11g017300.1

CSN5A

AT1G22920

0.33

COP9 signalosome complex subunit 5a

Protease subunit of the COP9 signalosome complex; Involved in photomorphogenesis and response to jasmonate; Essential regulator of the ubiquitin conjugation pathway; Involved in repression of photomorphogenesis in darkness; Required for degradation of PSIAA6

Decreased photomorphogenesis; Increased regulation of G2/M transition of mitotic cell cycle; Increased protein deneddylation; Increased red light phototransduction; Increased defense response to insects; Increased response to auxin; Increased floral organ development

Kwok, Shing F., et al. "Arabidopsis homologs of a c-Jun coactivator are present both in monomeric form and in the COP9 complex, and their abundance is differentially affected by the pleiotropic cop/det/fus mutations." The Plant Cell 10.11 (1998): 1779-1790.

Solyc04g082810.2

AHL27

AT1G20900

0.35

AT-hook motif nuclear-localized protein 27

Specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions; Negatively regulates plant innate immunity to pathogens through the down-regulation of PAMP-triggered FRK1 expression; Regulates flowering and hypocotyl elongation; Chromatin remodeling factor that negatively regulates leaf senescence

Increased chromatin organization; Increased flower development; Impaired innate immune response; Increased leaf senescence; Increased photomorphogenesis; Increased vegetative to reproductive phase transition of meristem

Lim, Pyung Ok, et al. "Overexpression of a chromatin architecture-controlling AT-hook protein extends leaf longevity and increases the post-harvest storage life of plants." The Plant Journal 52.6 (2007): 1140-1153.

Solyc01g087170.2

N/a

AT2G41900

0.35

zinc finger CCCH domain-containing protein 30

Involved in response to salt stress

Increased response to salt stress

Sun, Jiaqiang, et al. "The CCCH-type zinc finger proteins AtSZF1 and AtSZF2 regulate salt stress responses in Arabidopsis." Plant and Cell Physiology 48.8 (2007): 1148-1158.

Solyc02g069310.2

NPR3

AT5G45110

0.36

regulatory protein NPR3

Substrate-specific adapter of an E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins; Regulates basal defense response to pathogens

Increased defense response to bacteria and fungus; Increased protein ubiquitination; Increased jasmonic acid mediated signaling; Increased systemic acquired resistance

Zhang, Yuelin, et al. "Negative regulation of defense responses in Arabidopsis by two NPR1 paralogs." The Plant Journal 48.5 (2006): 647-656.

Solyc05g021100.2

SWAP70

AT2G30880

0.36

switch-associated protein 70

Involved in intracellular signal transduction; Mediates defense response to bacteria

Increased defense response to bacteria; Increased intracellular signal transduction

Van Leeuwen, Wessel, et al. "Learning the lipid language of plant signalling." Trends in plant science 9.8 (2004): 378-384.

Solyc07g005880.2

RFC1

AT5G22010

0.37

replication factor C subunit 1

Broad regulator of transcriptional gene silencing, DNA replication, DNA repair, and the hypersensitive response; Required for DNA double-strand break repair and recombination; Important for lagging strand synthesis

Increased response to DNA damage; Increased DNA replication; Increased cellular turnover; Increased chromatin silencing; Increased H3-K9 methylation; Increased reproduction; Increased response to abscisic acid

Xia, S. T., et al. "Arabidopsis replication factor C subunit 1 plays an important role in embryogenesis." Zhi wu sheng li yu fen zi sheng wu xue xue bao= Journal of plant physiology and molecular biology 33.3 (2007): 179-187.

Solyc01g096390.2

NRPE1

AT2G40030

0.37

DNA-directed RNA polymerase V subunit 1

DNA-dependent RNA polymerase; Catalytic component of RNA polymerase V involved in RNA-directed DNA methylation-dependent silencing of endogenous repeated sequences; Essential component of siRNA production

Increased response to fungus; Increased DNA methylation; Increased posttranscriptional gene silencing; Increased transcription by RNA polymerase III

Pontier, Dominique, et al. "Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis." Genes & development 19.17 (2005): 2030-2040.

Solyc01g081330.2

ATJ1

AT1G28210

0.40

chaperone protein dnaJ 1, mitochondrial

Plays a continuous role in plant development; Involved in the structural organization of cellular compartments under heat stress

Increased chaperone protein refolding; Increased response to heat

Park, Min Young, et al. "The Arabidopsis J protein AtJ1 is essential for seedling growth, flowering time control and ABA response." Plant and Cell Physiology 55.12 (2014): 2152-2163.

Solyc02g021760.2

CPSF30

AT1G30460

0.40

30-kDa cleavage and polyadenylation specificity factor 30

Component of the cleavage and polyadenylation specificity factor complex that plays a key role in pre-mRNA 3'-end formation and poly(A) addition; Involved in post-transcriptional control of oxidative stress responses; Regulates salicylic acid production

Increased mRNA polyadenylation; Increased hypersensitive response; Increased salicylic acid mediated signaling pathway; Increased response to oxidative stress; Increased RNA processing

Delaney, Kimberly J., et al. "Calmodulin interacts with and regulates the RNA-binding activity of an Arabidopsis polyadenylation factor subunit." Plant physiology 140.4 (2006): 1507-1521.

Solyc08g082480.2

PI4KG4

AT2G46500

0.40

phosphatidylinositol 4-kinase gamma 4

Phosphorylation of phosphatidylinositol to PI4P is the first committed step in the generation of phosphatidylinositol 4,5-bisphosphate

Increased regulation of flower development;Increased response to abscisic acid; Increased response to salt

Ma, Shisong, et al. "Loss of TIP1; 1 aquaporin in Arabidopsis leads to cell and plant death." The Plant Journal 40.6 (2004): 845-859.

Solyc12g099010.1

GFS12

AT5G18525

0.40

protein GFS12

Suppresses BCHC1, which is a negative regulator of storage vacuole trafficking and plant effector-triggered immunity

Increased defense response to bacteria; Increased protein targeting to vacuoles

Teh, Ooi-kock, et al. "BEACH-domain proteins act together in a cascade to mediate vacuolar protein trafficking and disease resistance in Arabidopsis." Molecular plant 8.3 (2015): 389-398.

Solyc08g005270.2

RCD1

AT1G32230

0.41

inactive poly [ADP-ribose] polymerase RCD1

Regulates hormonal responses during developmental; Required for embryogenesis, vegetative and reproductive development, and abiotic stress responses

Increased defense response to bacteria; Increased embryo development; Increased ethylene-activated signaling pathway; Increased jasmonic acid-mediated signaling; Increased lateral root morphogenesis; Increased programmed cell death; Increased response to drought, osmotic, ozone, and oxide stress

Ahlfors, Reetta, et al. "Arabidopsis RADICAL-INDUCED CELL DEATH1 belongs to the WWE protein–protein interaction domain protein family and modulates abscisic acid, ethylene, and methyl jasmonate responses." The Plant Cell 16.7 (2004): 1925-1937.

Solyc01g111610.2

BRG3

AT3G12920

0.42

probable BOI-related E3 ubiquitin-protein ligase 3

E3 ubiquitin-protein ligase

Increased defense response; Increased proteasome-mediated ubiquitin-dependent protein catabolic process; Increased programmed cell death

Park, Jeongmoo, et al. "DELLA proteins and their interacting RING Finger proteins repress gibberellin responses by binding to the promoters of a subset of gibberellin-responsive genes in Arabidopsis." The Plant Cell 25.3 (2013): 927-943.

Solyc03g025940.1

N/a

AT3G48880

0.42

F-box/LRR-repeat protein

Involved in endogenous messenger response to Gram-negative bacteria

Increased RNA signaling; Increased defense response to Gram-negative bacteria

Thieme, Christoph J., et al. "Endogenous Arabidopsis messenger RNAs transported to distant tissues." Nature Plants 1.4 (2015): 15025.

Solyc03g121470.2

PLDALPHA4

AT1G55180

0.43

phospholipase D alpha 4

Hydrolyzes glycerol-phospholipids at the terminal phosphodiesteric bond to generate phosphatidic acids; Promotes growth and plays a role in nitrogen signaling

Increased multidimensional cell division; Increased response to nitrogen, phosphate, and potassium starvation; Increased phospholipid catabolism; Increased nitrogen utilization; Increased post-embryonic development; Increased response to osmotic stress; Increased root development

Hong, Yueyun, et al. "Phospholipase Dε and phosphatidic acid enhance Arabidopsis nitrogen signaling and growth." The Plant Journal 58.3 (2009): 376-387.

Solyc06g083510.2

PBL25

AT3G24790

0.44

serine/threonine-protein kinase PBL25

Involved in protein phosphorylation signaling during germination and plant defense

Increased defense response; Increased protein phosphorylation; Increased reproduction

Wang, Yi, et al. "Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis." Plant physiology 148.3 (2008): 1201-1211.

Solyc01g111600.2

HIPP26

AT4G38580

0.45

heavy metal-associated isoprenylated plant protein 26

Heavy-metal-binding protein; Binds lead, cadmium and copper; Involved in heavy-metal transport; Involved in cadmium transport and play a role in cadmium detoxification

Increased acclimation during heat response; Increased metal ion transport; Increased response to cadmium stress

Gao, Wei, et al. "Arabidopsis thaliana acyl-CoA-binding protein ACBP2 interacts with heavy-metal-binding farnesylated protein AtFP6." New Phytologist 181.1 (2009): 89-102.

Solyc05g052850.2

MYB1

AT3G09230

0.54

transcription factor MYB1

Mediates salicylic acid signaling in response to salt stress

Increased response to salicylic acid; Increased response to salt stress

Wang, Ting, et al. "Salt-related MYB1 coordinates abscisic acid biosynthesis and signaling during salt stress in Arabidopsis." Plant physiology 169.2 (2015): 1027-1041.

Solyc10g085000.1

BSK5

AT5G59010

0.55

serine/threonine-protein kinase BSK5

Positive regulator of brassinosteroid signaling; Involved in abiotic stress tolerance; Required for abscisic acid-mediated response to drought and salt stress

Increased brassinosteroid-mediated signaling; Increased response to abscisic acid; Increased response to cold; Increased response to salt stress

Tang, Wenqiang, et al. "BSKs mediate signal transduction from the receptor kinase BRI1 in Arabidopsis." Science 321.5888 (2008): 557-560.

Solyc02g077270.2

NCL

AT1G53210

0.66

sodium/calcium exchanger NCL1

Participates in the maintenance of calcium homeostasis; Plays roles in auxin response, diurnal rhythm, and flowering time; Involved in response to salt stress

Improved calcium ion homeostasis; Increased calcium ion transmembrane transport; Increased response to salt stress

Wang, Peng, et al. "A Na+/Ca2+ exchanger-like protein (AtNCL) involved in salt stress in Arabidopsis." Journal of Biological Chemistry 287.53 (2012): 44062-44070.

Solyc02g090490.2

PLP3

AT4G37050

0.70

patatin-like protein 3

Catalyzes the hydrolysis of the neutral lipids monogalactosyldiacylglycerol, digalactosyldiacylglycerol, and phosphatidylglycerol; Plays a role in root development

Increased defense response; Increased lipid catabolism; Increased response to abscisic acid

Rietz, Steffen, et al. "Roles of Arabidopsis patatin-related phospholipases a in root development are related to auxin responses and phosphate deficiency." Molecular Plant 3.3 (2010): 524-538.

Solyc11g069530.1

EDR2

AT4G19040

0.71

protein ENHANCED DISEASE RESISTANCE 2

Negative regulator of the salicylic acid-mediated resistance to pathogen that limits initiation of cell death and the establishment of the hypersensitive response; Prevents ethylene-induced senescence

Increased ethylene-activated signaling pathway; Decreased leaf senescence; Increased hypersensitive response; Increased defense response to fungus; Increased response to ethylene; Increased response to salicylic acid

Tang, Dingzhong, et al. "Regulation of plant defense responses in Arabidopsis by EDR2, a PH and START domain-containing protein." The Plant Journal 44.2 (2005): 245-257.

Solyc03g083350.2

PI4KG3

AT5G24240

0.72

phosphatidylinositol 4-kinase gamma 3

Phosphorylation of phosphatidylinositol to PI4P is the first committed step in the generation of phosphatidylinositol 4,5-bisphosphate

Increased regulation of flower development; Increased response to abscisic acid; Increased response to salt

Ma, Shisong, et al. "Loss of TIP1; 1 aquaporin in Arabidopsis leads to cell and plant death." The Plant Journal 40.6 (2004): 845-859.

Solyc01g096320.2

ATHB-12

AT3G61890

1.31

homeobox-leucine zipper protein ATHB-12

Transcription activator that acts as growth regulators in response to drought

Increased development; Increased transcription; Increased response to abscisic acid; Increased response to virus; Increased response to drought and osmotic stress

Olsson, Anna, Peter Engström, and Eva Söderman. "The homeobox genes ATHB12 and ATHB7encode potential regulators of growth in response to water deficit in Arabidopsis." Plant molecular biology 55.5 (2004): 663-677.

Solyc01g088520.2

DRP1E

AT3G60190

1.48

dynamin-related protein 1E

Microtubule-associated force-producing protein of tubulo-vesicular network; Plays a major role in plasma membrane maintenance and cell wall integrity; Integral for plant growth and development

Increased cellular turnover; Increased response to fungus; Increased mitochondrial fission; Increased response to cadmium stress; Increased vesicle-mediated transport

Kang, Byung-Ho, et al. "The Arabidopsis cell plate-associated dynamin-like protein, ADL1Ap, is required for multiple stages of plant growth and development." Plant Physiology 126.1 (2001): 47-68.