Sapplemental table 2. Proteins changed in root tips of soybean under flooding stress

Protein ID / Accession number / Description / Theoretical pI/Mw / MP / Frames / Hits / Ratio / StdDev / WoLF PSORT / PSORTII / NucPred
Decreased proteins
Glyma02g43630.1 / XP_003518448.1 / TMV resistance protein N-like / 5.91 / 96875 / 2 / 1 / 2 / 0.001 / 0.001 / Nucl / plasma membran / 0.54
Glyma03g32140.1 / XP_003527283.1 / ribophorin II / 5.90 / 74807 / 2 / 3 / 3 / 0.001 / 0.002 / plastid / ER / 0.01
Glyma04g32950.1 / ACJ76773.1 / eukaryotic translation initiation factor 5A2 / 5.58 / 18530 / 2 / 1 / 2 / 0.002 / 0.003 / cyto / cyto / 0.00
Glyma08g03580.1 / XP_002514191.1 / processing peptidase alpha subunit / 5.56 / 54789 / 2 / 3 / 3 / 0.004 / 0.005 / mito / mito / 0.07
Glyma11g14950.1 / XP_003537997.1 / heat shock cognate 70 kDa protein / 5.10 / 71081 / 3 / 2 / 3 / 0.004 / 0.002 / cyto/ Nucl / ER / 0.25
Glyma09g38110.1 / ABO61030.1 / vacuolar H+-ATPase B subunit / 4.95 / 54182 / 2 / 3 / 4 / 0.007 / 0.003 / cyto / vacuole / 0.15
Glyma07g09240.1 / CAQ56034.1 / peroxiredoxin / 5.41 / 17366 / 2 / 1 / 2 / 0.009 / 0.004 / Golgi / mito/ peroxisome / 0.08
Glyma08g46020.1 / AAK07827.1 / processing peptidase beta subunit / 6.49 / 58953 / 2 / 2 / 2 / 0.011 / 0.01 / mito / mito / 0.08
Glyma07g33950.1 / ABV23277.1 / leucine-rich repeat-like protein / 9.04 / 49877 / 2 / 2 / 2 / 0.022 / 0.022 / Nucl / cyto / 0.35
Glyma10g41330.1 / AAD03392.1 / ATPase beta subunit / 5.80 / 59836 / 6 / 13 / 18 / 0.036 / 0.008 / mito / mito / 0.01
Glyma20g27280.1 / ABO47736 / alpha-tubulin / 4.96 / 49412 / 2 / 2 / 26 / 0.048 / 0.052 / ND / ND / 0.14
Glyma07g05580.1 / ABL96300.1 / granule-bound starch synthase / 6.62 / 68063 / 4 / 8 / 11 / 0.057 / 0.032 / chlo / plastid / 0.02
Glyma08g15960.1 / XP_003599013.1 / beta-glucosidase / 6.62 / 68063 / 2 / 2 / 4 / 0.071 / 0.061 / chlo / ND / 0.07
Glyma15g17320.1 / XP_002322392.1 / predicted protein [Populustrichocarpa] / 6.45 / 39727 / 4 / 1 / 4 / 0.075 / 0.048 / Nucl / ND / 0.16
Glyma07g01730.1 / NP_001236180 / acid phosphatase precursor / 8.75 / 29065 / 3 / 3 / 5 / 0.077 / 0.037 / ND / vaculole / 0.02
Glyma06g01790.1 / XP_003527283.1 / ribophorin I / 8.75 / 29065 / 2 / 1 / 2 / 0.097 / 0.111 / ER / ND / 0.03
Glyma01g03810.1 / NP_176226.3 / splicing factor PWI domain-containing protein / 5.46 / 105031 / 4 / 3 / 4 / 0.117 / 0.137 / Nucl / Nucl / 0.93
Glyma03g35080.1 / XP_003521450.1 / 60S acidic ribosomal protein P2 / 4.21 / 11304 / 2 / 1 / 4 / 0.131 / 0.145 / cyto / ND / 0.02
Glyma05g36600.1 / XP_003537997.1 / heat shock protein 70kda / 5.11 / 73389 / 2 / 2 / 2 / 0.149 / 0.083 / ER / ND / 0.11
Glyma19g41120.1 / XP_003554589 / cathepsin B-like / 5.85 / 39444 / 2 / 1 / 2 / 0.152 / 0.049 / extr / cyto / 0.00
Glyma04g13490.1 / NP_001238450.1 / uncharacterized protein / 8.15 / 21201 / 2 / 1 / 2 / 0.167 / 0.042 / Nucl / ND / 0.19
Glyma08g04370.3 / XP_003530494.1 / aldehydedehydrogenase / 6.12 / 43920 / 2 / 1 / 2 / 0.172 / 0.114 / ND / ND / 0.00
Glyma07g00430.1 / ABU87506.1 / V-H(+)-ATPase subunit A / 5.35 / 68779 / 2 / 1 / 2 / 0.208 / 0.229 / chlo / vacuole/ ER / 0.15
Glyma09g03500.1 / BAA94965.1 / epsilon2-COP / 5.30 / 32279 / 4 / 5 / 5 / 0.218 / 0.013 / Nucl / Nucl / 0.21
Glyma17g02260.1 / CAE47488.1 / copper amino oxidase / 6.21 / 75823 / 6 / 10 / 13 / 0.292 / 0.034 / extr / cell wall / 0.23
Glyma12g04400.1 / XP_002511213.1 / nucleolar protein nop56 / 8.40 / 62578 / 3 / 2 / 6 / 0.311 / 0.247 / cyto/ Nucl / Nucl / 0.60
Glyma18g05210.1 / NP_001159374 / beta-catenin / 5.53 / 85471 / 2 / 2 / 9 / 0.311 / 0.247 / cyto/ Nucl / Nucl / 0.38
Glyma16g05450.1 / NP_001237304.1 / phosphate carrier protein / 8.88 / 42996 / 2 / 3 / 5 / 0.349 / 0.037 / ND / mito / 0.09
Glyma17g10660.1 / XP_003549665.1 / protein IQ-DOMAIN 31-like / 9.49 / 64992 / 2 / 2 / 4 / 0.349 / 0.084 / Nucl / Nucl / 0.75
Glyma13g23420.1 / XP_002532501.1 / 116 kD U5 small nuclear ribonucleoprotein component / 5.08 / 109947 / 3 / 4 / 7 / 0.382 / 0.04 / Nucl / Nucl / 0.80
Glyma02g42560.1 / AAC49294.1 / clathrin heavy chain / 5.26 / 193321 / 2 / 3 / 3 / 0.433 / 0.154 / Nucl / Nucl / 0.28
Increased proteins
Glyma05g34070.1 / ACV72060.1 / RACK1 / 7.62 / 35663 / 2 / 3 / 4 / 1.878 / 0.567 / Nucl / Nucl / 0.13
Glyma16g04240.1 / AAQ08403.1 / methioninesynthase / 5.93 / 84282 / 2 / 2 / 2 / 4.645 / 4.329 / chlo / cyto/ mito / 0.08
Glyma01g03650.1 / BAB90396.1 / ADP-ribosylation factor / 6.43 / 21741 / 2 / 3 / 3 / 4.808 / 4.706 / Golgi / Golgi / 0.01
Glyma07g00540.1 / XP_002525010.1 / d-3-phosphoglycerate dehydrogenase / 7.61 / 66219 / 2 / 2 / 2 / 11.97 / 10.538 / chlo / proplastid / 0.05
Glyma04g36860.1 / ABC75834.1 / glyceraldehyde-3-phosphate dehydrogenase / 6.72 / 36770 / 2 / 2 / 2 / 22.71 / 31.323 / cyto / cyto / 0.00
Glyma17g15640.1 / XP_003549943 / expansin-like B1 / 9.35 / 27497 / 2 / 2 / 4 / 30.23 / 8.355 / chlo / ND / 0.03
Glyma12g16510.1 / XP_002282514.1 / hypothetical protein [Vitisvinifera] / 5.33 / 107818 / 2 / 1 / 2 / 37.18 / 5.03 / Nucl / Nucl / 0.24
Glyma05g25370.1 / CAI99392.1 / polygalacturonase inhibiting protein / 8.63 / 36867 / 2 / 5 / 5 / 187 / 105.08 / Ext / apoplast/ vacuole / 0.23

Protein ID, according to the phytosome databases; Accession number, accession number according to the NCBI database; Localization predicted by WoLF PSORT, PSORTII, and NucPred; Cyto, cytosol; Nucl, nuclear; Ext, extracellular; mito, mitochondria. For results from NucPred, the consensus score is basically the fraction of predictors which vote ‘nuclear’. For a discrete prediction, the user has to decide on a score threshold (preferably 0.8). Sequences which score greater than or equal to this threshold are predicted to spend time in the nucleus.

In identification of a differentially expressed proteins, the minimum requirements for the identification of a protein were more than 2 matched peptides (MP) and the fold change of proteins in flooding treated samples against control samples with more or less than 1.8 times with significant difference (P<0.05).

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