Supplementary Table1. Characteristics of transcript-derived fragments (TDFs) expressed during the drought stress given to almond Prunus dulcis ‘Sefied’.
E value d / Species / Accession no.c / Homology b / Accession no.a / Size (bp) / TDF#5e-84 / Prunus mume / XM008222553.1 / Probable protein phosphatase 2C 55 / LC036597 / 206 / 1
1e-17 / Prunus cerasifera / FM253563.1 / BAC insert containing Ma gene, resistant Ma1 allele, clone 76H19 / LC036598 / 257 / 2
8e-05 / Malus x domestica / XM008346102.1 / Protein misato homolog 1-like, mRNA / LC036599 / 181 / 3
2e-37 / Ricinus communis / XM002510308.1 / protein phosphatase 2c, putative, mRNA / LC036597 / 207 / 4
1e-71
4e-40 / Prunus mume
Morus alba / XM008223835.1
AB479106.1 / Urease, transcript variant X2, mRNA
ure mRNA for urease, complete cds / LC036600 / 182 / 5
0.0 / Prunus mume / XM_008241130 / serine/threonine-protein kinase AFC2 isoform X2 / LC036606 / 419 / 6
4e-11 / Malus x domestica / XM_008361362.1 / ganglioside-induced differentiation-associated protein 2-like / LC036601 / 107 / 7
------/ ------/ ------/ No significant similarity in plants / LC036602 / 292 / 8
2e-129
0.006 / Prunus mume
Prunus mume / XM_008244781.1
XM008222949.1 / CDP-diacylglycerol--inositol 3-phosphatidyltransferase 1-like
Large proline-rich protein BAG6 / LC036603 / 291 / 9
------/ ------/ ------/ ------/ ------/ 10
3e-73 / Prunus mume / XM_008223835.1 / Urease / LC036600 / 182 / 11
------/ - / ------/ No significant similarity in plants / LC036604 / 370 / 12
1e-71
3e-41 / Prunus mume
Morus alba / XM_008223835.1
AB479106.1 / Urease
ure mRNA for urease, complete cds / LC036600 / 182 / 13
3e-73
3e-41 / Prunus mume
Morus alba / XM_008223835.1
AB479106.1 / Urease
ure mRNA for urease, complete cds / LC036600 / 182 / 14*
1e-71
3e-41 / Prunus mume
Morus alba / XM_008223835.1
AB479106.1 / Urease
ure mRNA for urease, complete cds / LC036600 / 182 / 15
7e-92
2e-78 / Ricinus communis
Arabidopsis thaliana / XM002511222.1
NM114701.2 / 2-deoxyglucose-6-phosphate phosphatase, putative, mRNA
haloacid dehalogenase-like hydrolase family protein mRNA, complete cds / LC036605 / 345 / 16*
0.0
2e-113
5e-101 / Prunus mume
Ricinus communis
Mesembryanthemum crystallinum / XM_008241130.1
XM002511255.1
AF234652.1 / serine/threonine-protein kinase AFC2
afc, putative, mRNA
protein kinase MK5 mRNA, complete cds / LC036606 / 419 / 17*
0.0 / Prunus mume / XM_008241130.1 / serine/threonine-protein kinase AFC2 / LC036606 / 419 / 18
3e-27 / Theobroma cacao / XP_007042238.1 / Translation initiation factor 2, small GTP-binding protein isoform 2 / LC036607 / 370 / 19
1e-10 / Malus x domestica / XM_008361362.1 / ganglioside-induced differentiation-associated protein 2-like / LC036608 / 223 / 20
a DDBJ assigned accession no. to TDFs;b cDNA-AFLP fragments showing sequence similarity to NCBI Data base sequences using nucleotide BLAST and BLASTX (Altschul et al. 1997); chomologous GenBank accession number; d The E-value was used to indicate the significance of sequence similarity; * indicates TDFs selected for qRT-PCR.Sequencing of TDF number 10 failed.
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Supplementary Table 2. Relationships in predicted gene interaction network of drought resistance in almond.
Relation / Type of relation / Reference / Mined sentenceacid phosphatase ---| PR1 / Regulation / Andersson MX, Kourtchenko O, Dangl JL, Mackey D, Ellerström M.(2006) Phospholipase-dependent signalling during the AvrRpm1- and AvrRpt2-induced disease resistance responses in Arabidopsis thaliana.Plant J 47:947-59 / It has been reported that rice pathogenesis-related1b gene is highly induced by jasmonic acid, protein phosphatase inhibitors catharidin and endothall 67 in a light-dependent manner.
ABI2 --+> TIL1 / Regulation / Yin H, Zhang X, Liu J, Wang Y, He J, Yang T, Hong X, Yang Q, Gong Z. (2009) Epigenetic regulation, somatic homologous recombination, and abscisic acid signaling are influenced by DNA polymerase epsilon mutation in Arabidopsis.Plant Cell 21:386-402 / The dominant, abscisic acid-insensitive abi1-1 or abi2-1 mutations suppressed the abscisic acid hypersensitivity of the abo4-1 mutant.
ABI1 ---| ABI2 / Regulation / Hoth S, Morgante M, Sanchez JP, Hanafey MK, Tingey SV, Chua NH.(2002) Genome-wide gene expression profiling in Arabidopsis thaliana reveals new targets of abscisic acid and largely impaired gene regulation in the abi1-1 mutant. J Cell Sci 15:4891-900 / However, abscisic acid induction of ABI2 was abolished in abi1-1 (Fig. 4)., Two dominant abscisic acid insensitive mutants, abi1-1 and abi2-1, are impaired in phosphatase2C genes (ABI1 and ABI2).
acid phosphatase ---| PLDALPHA1 / Regulation / Novotna Z, Linek J, Hynek R, Martinec J, Potocky M,Valentova O. (2003) Plant PIP2-dependent phospholipase D activity is regulated by phosphorylation. FEBS Letters 554: 50-54 / Pre-incubation of the plasma membrane fraction with acid phosphatase resulted in concentration-dependent inhibition of PIP2-dependent PLD activity.
TIL1 ---> histone / Regulation / Yin H, Zhang X, Liu J, Wang Y, He J, Yang T, Hong X, Yang Q, Gong Z. (2009) Epigenetic regulation, somatic homologous recombination, and abscisic acid signaling are influenced by DNA polymerase epsilon mutation in Arabidopsis. Plant Cell 21:386-402 / The abo4-1 plants were early flowering with lower expression of FLOWER LOCUS C and higher expression of FLOWER LOCUS T and changed histone modifications in the two loci.
LAMMER kinase ---> AFC2 / Regulation / Isshiki M, Tsumoto A, Shimamoto K. (2006) The serine/arginine-rich protein family in rice plays important roles in constitutive and alternative splicing of pre-mRNA. The Plant Cell 18: 146-158 / We further showed that an Arabidopsis Clk/Sty protein kinase phosphorylates plant SR proteins and modulates their interaction with AFC2.
PLDALPHA1 --+> ABI1 / Regulation / Zhang, W, Qin C, Zhao J, Wang X. (2004) Phospholipase D alpha 1-derived phosphatidic acid interacts with ABI1 phosphatase 2C and regulates abscisic acid signaling. Proc Natl Acad Sci 101: 9508-9513 / These results indicate that (i) phosphatidic acid is associated with ABI1, (ii) the formation of phosphatidic acid-ABI1 complexes is promoted by abscisic acid, and (iii) the activation of PLDalpha1 produces phosphatidic acid that binds to ABI1.
acid phosphatase ---| URE / Regulation / Lee CH, Lee do K, Ali MA, Kim PJ. (2008) Effects of oyster shell on soil chemical and biological properties and cabbage productivity as a liming materials. Waste Manag (2008) 28:2702-2708 / With the exception of acid phosphomonoesterase activity, which decreased with increasing soil pH in SL but slightly increased in SiL, the activities of urease and alkali phosphomonoesterase increased markedly with increasing soil pH by shell meal application.
ABI2 ---> PP2C / Regulation / Rodriguez PL, Benning G, Grill E. (1998) ABI2, a second protein phosphatase 2C involved in abscisic acid signal transduction in Arabidopsis. FEBS Letters 421: 185–190 / The mutation that confers the abi2-1 phenotype is equivalent to the mutation previously identified in abi1-1 and the resulting Gly168Asp abi2 protein shows a reduced PP2C activity., Merlot et al. (2001)[Go] reported that ABI1 and ABI2 contribute nearly 50% of the abscisic acid-induced PP2C activity, indicating that other PP2Cs may also be involved in redundant abscisic acid signaling.
AFC2 ---> SR1 / Regulation / Ali GS, Reddy AS. (2006) ATP, phosphorylation and transcription regulate the mobility of plant splicing factors. J Cell Sci 119: 3527-3538 / We have shown previously that, in vitro, SR45 interacts with and is phosphorylated by AFC2, a LAMMER-type kinase that might regulate the mobility of SR45 and probably SR1/SRp34 (Golovkin and Reddy, 1999[Go]).
ABI3 --+> PR1 / Expression / Ahn IP, Kim S, Lee YH, Suh SC (2007) Vitamin B1-induced priming is dependent on hydrogen peroxide and the NPR1 gene in Arabidopsis. Plant Physiology 143: 838–848 / Expression of PR1 and PAL1 was augmented in thiamine- and DC3000-treated Col-0, etr1, jar1, and abi3-3 plants.
ABI3 --+> ABI2 / Expression / Suzuki M, Ketterling MG, Q-B Li, McCarty DR. (2003) Viviparous1 alters global gene expression patterns through regulation of abscisic acid signaling. Plant Physiology 132: 1664-1677 / Our finding that transcript levels of ABI1 and ABI2 are elevated in abi3-6 seeds compared with Col wild type, suggests that this pathway is also active in normal seed development.
PLDALPHA1 ---> RAB18 / Expression / Hallouin M, Ghelis T, Brault M, Bardat F, Cornel D, Miginiac E, Rona JP, Sotta B, Jeannette E. (2002) Plasmalemma abscisic acid perception leads to RAB18 expression via phospholipase D activation in Arabidopsis suspension cells.Plant Physiol 130: 265-72 / Using a transphosphatidylation reaction, we show that Abscisic acid plasmalemma perception results in a transient stimulation of phospholipase D (PLD) activity, which is necessary for RAB18 expression., In a previous study, we demonstrated that the stimulation of phospholipase D (PLD) activity and plasma membrane anion currents by abscisic acid were both required for RAB18 expression in Arabidopsis thaliana suspension cells.
ABI2 --+> RAB18 / Expression / Zhang Y, Yang C, Li Y, Zheng N, Chen H, Zhao Q, Gao T, Guo H, Xie Q. (2007) SDIR1 is a RING finger E3 ligase that positively regulates stress-responsive abscisic acid signaling in Arabidopsis. Plant Cell 19: 1912-1929 / The expression pattern of RAB18 is dramatically reduced in both abi1-1 and abi2-1 mutants and in sdir1-1 shows reduction patterns similar to those in RD22.
PLDALPHA1 ---- PP2C / Binding / Mishra G, Zhang W, Deng F, Zhao J, Wang X. (2006) A bifurcating pathway directs abscisic acid effects on stomatal closure and opening in Arabidopsis.Science (2006) 312: 264-266 / PLDa1 and phosphatidic acid interact with PP2C to signal abscisic acid-promoted stomatal closure, whereas PLDa1 and phosphatidic acid interact with the Ga-subunit to mediate abscisic acid inhibition of stomatal opening.
ABI1 ---- PLDALPHA1 / Binding / Mishra G, Zhang W, Deng F, Zhao J, Wang X. (2006) A bifurcating pathway directs abscisic acid effects on stomatal closure and opening in Arabidopsis.Science (2006) 312: 264-266 / In addition, recent studies have indicated that phospholipase D (PLD) acts as a positive regulator for abscisic acid-mediated stomatal movement through the lipid metabolite phosphatidic acid , binds to ABI1, and inhibits its activity.
AFC2 ---- SR45 / Binding / Golovkin M, Reddy AS (1999) An SC35-like protein and a novel serine/arginine-rich protein interact with Arabidopsis U1-70K protein. J Bio Chem 274: 36428–36438 / SR45 interacts with U1-snRNP 70K protein, an SC35-like SR protein (SR33) and a LAMMER-type kinase (AFC2) (Golovkin and Reddy, 1999[Go])., There is also evidence showing that Arabidopsis SR45 interacted with another SR protein, SCL33, a subunit of U1 snRNP (U1-70 K) and kinase AFC2 in vitro.
SRZ-22 ---> AFC2 / ProtModification / Golovkin M, Reddy AS (1999) An SC35-like protein and a novel serine/arginine-rich protein interact with Arabidopsis U1-70K protein. J Bio Chem 274: 36428–36438 / B, interaction of phosphorylated and nonphosphorylated SRZ22 protein with nonphosphorylated and autophosphorylated AFC2 kinase.
AFC2 ---> SRZ-22 / ProtModification / Golovkin M, Reddy AS (1999) An SC35-like protein and a novel serine/arginine-rich protein interact with Arabidopsis U1-70K protein. J Bio Chem 274: 36428–36438 / A Clk/Sty protein kinase (AFC-2) from Arabidopsis phosphorylated four SR proteins (SR33, SR45, SRZ21, and SRZ22).
AFC2 ---> SR45 / ProtModification 20 / Golovkin M, Reddy AS (1999) An SC35-like protein and a novel serine/arginine-rich protein interact with Arabidopsis U1-70K protein. J Bio Chem 274: 36428–36438 / A Clk/Sty protein kinase (AFC-2) from Arabidopsis phosphorylated four SR proteins (SR33, SR45, SRZ21, and SRZ22).
AFC2 ---> SR33 / ProtModification / Golovkin M, Reddy AS (1999) An SC35-like protein and a novel serine/arginine-rich protein interact with Arabidopsis U1-70K protein. J Bio Chem 274: 36428–36438 / A Clk/Sty protein kinase (AFC-2) from Arabidopsis phosphorylated four SR proteins (SR33, SR45, SRZ21, and SRZ22).
AFC2 ---> histone / ProtModification / Golovkin M, Reddy AS (1999) An SC35-like protein and a novel serine/arginine-rich protein interact with Arabidopsis U1-70K protein. J Bio Chem 274: 36428–36438 / AFC2 kinase showed autophosphorylation (lane 4, indicated by open arrowhead) and phosphorylated histone (lane 5, indicated by an arrow), whereas AFC1 did not show autophosphorylation.
AFC2 ---> RSZP21 / ProtModification / Golovkin M, Reddy AS (1999) An SC35-like protein and a novel serine/arginine-rich protein interact with Arabidopsis U1-70K protein. J Bio Chem 274: 36428–36438 / A Clk/Sty protein kinase (AFC-2) from Arabidopsis phosphorylated four SR proteins (SR33, SR45, SRZ21, and SRZ22).
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