Supplementary. Table S1 A total of DEGs detected in this study (Gm) No. genename significance in annotation 1 At1g01020 D2 ARV1__expressed protein, similar to hypothetical protein DDB0188786 [Dictyostelium discoideum] (GB:EAL62332.1); contains InterPro domain Arv1-like protein (InterPro:IPR007290) 2 At1g01100 D2 60S acidic ribosomal protein P1 (RPP1A), similar to 60S ACIDIC RIBOSOMAL PROTEIN P1 GB:O23095 from (Arabidopsis thaliana) 3 At1g01120 D2, Dm KCS1__fatty acid elongase 3-ketoacyl-CoA synthase 1 (KCS1), nearly identical to GB:AAC99312 GI:4091810 from (Arabidopsis thaliana) 4 At1g01160 D1, D2, Dm GIF2__SSXT protein-related / transcription co-activator-related, similar to SYT/SSX4 fusion protein (GI:11127695) (Homo sapiens); supporting cDNA gi:21539891:gb:AY102640.1:; contains Pfam profile PF05030: SSXT protein (N-terminal region) 5 At1g01170 D2 ozone-responsive stress-related protein, putative, similar to stress-related ozone-induced protein AtOZI1 (GI:790583) (Arabidopsis thaliana); contains 1 predicted transmembrane domain; 6 At1g01240 D1, D2, Dm expressed protein 7 At1g01300 D2, Dm aspartyl protease family protein, contains Pfam domain, PF00026: eukaryotic aspartyl protease 8 At1g01320 D2 tetratricopeptide repeat (TPR)-containing protein, low similarity to SP:P46825 Kinesin light chain (KLC) {Loligo pealeii}; contains Pfam profile PF00515: TPR Domain 9 At1g01430 D2, Dm expressed protein, similar to hypothetical protein GB:CAB80917 GI:7267605 from (Arabidopsis thaliana) 10 At1g01470 D1, D2, Dm LEA14_LSR3__late embryogenesis abundant protein, putative / LEA protein, putative, similar to SP:P46518 Late embryogenesis abundant protein Lea14-A {Gossypium hirsutum}; contains Pfam profile PF03168: Late embryogenesis abundant protein 11 At1g01540 D2 protein kinase family protein, contains protein kinase domain, Pfam:PF00069; contains serine/threonine protein kinase domain, INTERPRO:IPR002290 12 At1g01630 D1, D2, Dm SEC14 cytosolic factor, putative / phosphoglyceride transfer protein, putative, contains Pfam PF00650 : CRAL/TRIO domain and PF03765 : CRAL/TRIO, N-terminus; similar to polyphosphoinositide binding protein Ssh2p GB:AAB94599 GI:2739046 from (Glycine max) 13 At1g01720 D1, D2, Dm ANAC002_ATAF1__no apical meristem (NAM) family protein, contains Pfam PF02365: No apical meristem (NAM) domain; similar to NAC domain protein NAM GB:AAD17313 GI:4325282 from (Arabidopsis thaliana) 14 At1g01725 D1, D2, Dm expressed protein 15 At1g01730 D1, Dm expressed protein 16 At1g01800 Dm short-chain dehydrogenase/reductase (SDR) family protein, similar to carbonyl reductase GI:1049108 from (Mus musculus) 17 At1g01820 Dm peroxisomal biogenesis factor 11 family protein / PEX11 family protein, contains Pfam PF05648: Peroxisomal biogenesis factor 11 (PEX11) 18 At1g01970 D1, Dm pentatricopeptide (PPR) repeat-containing protein, low similarity to 67 kD chloroplastic RNA- binding protein RSP67.2 (Raphanus sativus) GI:9755888; contains Pfam profile PF01535: PPR repeat 19 At1g02205 D1, D2, Dm CER1__CER1 protein, identical to maize gl1 homolog (glossy1 locus) GI:1209703 and CER1 GI:1199467 from (Arabidopsis thaliana) 20 At1g02280 D1, D2, Dm TOC33_ATTOC33_PPI1_TOC75-III__GTP-binding protein (TOC33), identical to atToc33 protein (GI:11557973) (Arabidopsis thaliana); Carboxyl-terminal end highly similar to GTP-binding protein SP:U43377, location of EST gb:AA394770 and gb:R30089; identical to cDNA for chloroplast atToc33 protein GI:11557972 21 At1g02300 D1, D2, Dm cathepsin B-like cysteine protease, putative, similar to cathepsin B-like cysteine proteinase GI:609175 from (Nicotiana rustica) 22 At1g02305 D1, D2, Dm cathepsin B-like cysteine protease, putative, similar to cathepsin B-like cysteine proteinase (Nicotiana rustica) GI:609175; contains Pfam profile PF00112: Papain family cysteine protease 23 At1g02450 D1, Dm NIMIN1__NPR1/NIM1-interacting protein 1 (NIMIN-1), identical to NIMIN-1 protein (Arabidopsis thaliana) gi:12057154:emb:CAC19844; identical to cDNA NIMIN-1 protein (nimin-1 gene)GI:12057153 24 At1g02475 D1, Dm expressed protein 25 At1g02560 D2 CLPP5_NCLPP1_NCLPP5__ATP-dependent Clp protease proteolytic subunit (ClpP1), identical to nClpP1 GB:BAA82065 GI:5360579 from (Arabidopsis thaliana); contains Pfam profile PF00574: Clp protease; contains TIGRfam profile TIGR00493: ATP-dependent Clp protease, proteolytic subunit ClpP 26 At1g02640 Dm BXL2_ATBXL2__glycosyl hydrolase family 3 protein, similar to beta-xylosidase GB:Z84377 GI:2102655 from (Aspergillus niger) 27 At1g02650 D1, Dm DNAJ heat shock N-terminal domain-containing protein, contains Pfam profile PF00226: DnaJ domain 28 At1g02730 D1 ATCSLD5_CSLD5__cellulose synthase family protein, similar to cellulose synthase catalytic subunit (gi:13925881) from Nicotiana alata, cellulose synthase-4 (gi:9622880) from Zea mays 29 At1g02740 Dm MRG family protein, member of Pfam PF05712: MRG; similar to Transcription factor-like protein MRG15 (MORF-related gene 15 protein) (MSL3-1 protein) (Protein HSPC008/HSPC061) (SP:Q9UBU8) {Homo sapiens} 30 At1g02780 D1 EMB2386__60S ribosomal protein L19 (RPL19A), similar to ribosomal protein L19 GI:36127 from (Homo sapiens) 31 At1g02850 Dm glycosyl hydrolase family 1 protein, contains Pfam PF00232 : Glycosyl hydrolase family 1 domain; TIGRFAM TIGR01233: 6-phospho-beta-galactosidase; similar to hydroxyisourate hydrolase (GI:19569603) (Glycine max) 32 At1g02930 D2, Dm ATGSTF6_ATGSTF3_ERD11_GST1_GSTF6__glutathione S-transferase, putative, similar to glutathione S-transferase GI:860955 from (Hyoscyamus muticus) 33 At1g03030 D1, Dm phosphoribulokinase/uridine kinase family protein, contains Pfam PF00485: Phosphoribulokinase / Uridine kinase family; Belongs to Interpro IPR006083 Phosphoribulokinase/uridine kinase family; similar to Uridine kinase (Uridine monophosphokinase) (SP:P27515) {Saccharomyces cerevisiae}; ESTs gb:AA585719, gb:AA728503 and gb:T22272 come from this gene 34 At1g03080 D1, D2, Dm kinase interacting family protein, similar to kinase interacting protein 1 (GI:13936326) (Petunia integrifolia) 35 At1g03290 D1, D2, Dm expressed protein, ESTs gb:H36966, gb:R65511, gb:T42324 and gb:T20569 come from this gene 36 At1g03300 D1, Dm agenet domain-containing protein, contains Pfam PF05641: Agenet domain 37 At1g03400 D2 2-oxoglutarate-dependent dioxygenase, putative, similar to 2A6 (GI:599622) and tomato ethylene synthesis regulatory protein E8 (SP:P10967); similar to ESTs emb:Z34690, gb:T04168, gb:H37738, gb:T76913, gb:T43801, amd gb:T21964 38 At1g03475 D1, Dm LIN2__coproporphyrinogen III oxidase, putative / coproporphyrinogenase, putative / coprogen oxidase, putative, similar to coproporphyrinogen III oxidase, chloroplast (precursor) from Glycine max (SP:P35055), Nicotiana tabacum (SP:Q42946), Hordeum vulgare (SP:Q42840), ESTs gb:AA586260 and dbj:D48620; contains Pfam domain coproporphyrinogen III oxidase, aerobic (PF01218) 39 At1g03490 D2 ANAC006__no apical meristem (NAM) family protein, contains Pfam PF02365: No apical meristem (NAM) domain; 40 At1g03630 D1, Dm POR_TFC C__protochlorophyllide reductase C, chloroplast / PCR C / NADPH-protochlorophyllide oxidoreductase C (PORC), identical to SP:O48741 protochlorophyllide reductase C, chloroplast precursor (EC 1.3.1.33) (PCR C) (NADPH-protochlorophyllide oxidoreductase C) (POR C) (Arabidopsis thaliana) 41 At1g03790 D1, D2, Dm zinc finger (CCCH-type) family protein, contains Pfam domain, PF00642: Zinc finger C-x8-C-x5- C-x3-H type (and similar) 42 At1g03870 D1, D2, Dm FLA9__fasciclin-like arabinogalactan-protein (FLA9), identical to gi_13377784_gb_AAK20861 43 At1g03880 D2 CRU2_CRB__12S seed storage protein (CRB), identical to 12S seed storage protein, gi:808937 (SP:P15456) (Plant Mol Biol 11:805-820 (1988)); contains Pfam profile PF00190 Cupin and Prosite 11-S plant seed storage proteins signature PS00305 44 At1g03900 D1, Dm ATNAP4__expressed protein 45 At1g03910 D1, D2, Dm expressed protein, low similarity to cactin (Drosophila melanogaster) GI:7673675; expression supported by MPSS 46 At1g04040 D1, D2, Dm acid phosphatase class B family protein, similar to SP:P15490 STEM 28 kDa glycoprotein precursor (Vegetative storage protein A) {Glycine max}, acid phosphatase (Glycine max) GI:3341443; contains Pfam profile PF03767: HAD superfamily (subfamily IIIB) phosphatase; supporting cDNA gi:13926197:gb:AF370572.1:AF370572 47 At1g04120 D1, D2, Dm ATMRP5_MRP5__ABC transporter family protein, Strong similarity to MRP-like ABC transporter gb:U92650 from A. thaliana and canalicular multi-drug resistance protein gb:L49379 from Rattus norvegicus 48 At1g04170 D2, Dm EIF2 GAMMA__eukaryotic translation initiation factor 2 subunit 3, putative / eIF2S3, putative / eIF-2-gamma, putative, similar to gb:U37354 from S. pombe. ESTs gb:T41979, gb:N37284 and gb:N37529 come from this gene 49 At1g04190 D2 tetratricopeptide repeat (TPR)-containing protein, low similarity to protein antigen LmSTI1 (Leishmania major) GI:1698880; contains Pfam profile PF00515 TPR Domain; EST gb:Z47802 and gb:Z48402 come from this gene 50 At1g04220 D1, D2, Dm beta-ketoacyl-CoA synthase, putative, Strong similarity to beta-keto-Coa synthase gb:U37088 from Simmondsia chinensis, GI:4091810 51 At1g04240 D1 SHY2_IAA3__auxin-responsive protein / indoleacetic acid-induced protein 3 (IAA3), identical to SP:Q38822 Auxin-responsive protein IAA3 (Indoleacetic acid-induced protein 3) {Arabidopsis thaliana}; EST gb:T04296 comes from this gene 52 At1g04270 D1, D2, Dm RPS15__40S ribosomal protein S15 (RPS15A), Strong similarity to Oryza 40S ribosomal protein S15. ESTs gb:R29788,gb:ATTS0365