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1 Figure legend for supplemental tables (S1-S6). The predicted and annotated amino acid sequences for the different LEA proteins found in the available databases (378) were analyzed using MEME software (Bailey et al., 2006) to detect conserved motifs, which allowed their classification into six groups. The motif arrangement and/or the sequence homology in the motifs from some heterogeneous groups lead to subgroup divisions (LEA2, LEA3, LEA4). Although similar colors and numbers were used to indicate the motifs in the different groups, they do not imply any sequence relation among them in the different blocks. Accession numbers are indicated for each sequence depending on the database utilized to retrieve the EST or protein sequence. For ESTs (NCBI nr database), BLAST (tblastn) was performed using a protein query. Only the sequences corresponding to complete predicted proteins were used. An example of each of the nomenclature of the databases is: TC (TIGR database: gi (NCBI databse: ES frame +2 (NCBI: databse tr Q8RW12 (EMBL database: Q07187 EM1_ARATH (Uniprot database: Bailey T L, Williams N, Misleh C, Li W W (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucl Acids Res 34: W369-W373.
2 Table S1. Group 1 proteins (D-19, PF00477) Accession number Species Motif Number of mer repetitions Bryophytes CN frame +2 Tortula ruralis AW frame+3 Physcomitrella patens Pteridophytes CV frame +2 Ceratopteris richardii Q40860 Q40860_PICGL Picea glauca DN frame -3 Pinus taeda BU frame +1 Prunus dulcis BW GI Lycopersicon esculentum CA Theobroma cacao Q39095_ARATH Arabidopsis thaliana EM6 P09443 LE19_GOSHI Gossypium hirsutum D-19 P93165_SOYBN Glycine max Q41685_PHAAU Vigna radiata P93510_ROBPS Robinia pseudoacacia Q850G8_ARAHY Arachis hypogaea CX frame+1 Citrus sinensis CB GI Vitis vinifera CA GI Medicago truncatula BU frame+1 Populus tremula P17639 EMB1_DAUCA Daucus carota EMB 1 DV frame +2 Euphorbia esula 2 (2X) DV frame +3 Coffea canephora 2 (2X) CX Gossypium hirsutum 2 (2X) BU Glycine max 2 (2X) Q41684_PHAAU Vigna radiata 2 (2X) P93509_ROBPS Robinia pseudoacacia 2 (2X) Q7XBA7_QUERO Quercus robur 2 (2X) BQ Lactuca sativa 2 (4X) Q07187 EM1_ARATH Arabidopsis thaliana EM1 2 (4X) CV frame +1 Solanum tuberosum 2 (2X) O65725_BRANA Brassica napus P11573 SEEP_RAPSA Raphanus sativus P8B6 P46514 LE10_HELAN Helianthus annuus Q05190 LE19A_HORVU Hordeum vulgare B-19.1 Q9M4N9_SECCE Secale cereale P46517 EMB5_MAIZE Zea mays EMB564 P46520 EMP1_ORYSA Oryza sativa BG Sorghum bicolor Q6L5L8_BROIN Bromus inermis P04568 Triticum aestivum Q41804_MAIZE Zea mays 2 (2X) BG frame+1 Sorghum bicolor EM 1 2 (3X) Q6L5L7_BROIN Bromus inermis 2 (4X) Q05191 LE194_HORVU Hordeum vulgare B (4X)
3 Table S2. Group 2 proteins (D-11, PF00257) K-subgroup Accession number Species K Domains gi Picea abies K2 gi Pinus sylvestris K2 gi Pseudotsuga menziesii K2 tr Q9LUX4 Pyrus serotina K gi Retama raetam K gi Taraxacum officinale K gi Nicotiana tabacum K2 tr Q43668 Trollius ledebouri K2 gi Vaccinium corymbosum K2 gi Populus euramericana K3 gi Quercus robur K3 gi Vaccinium corymbosum K3 gi Quercus robur K4 gi Pistacia vera K5 gi Vaccinium corymbosum K5 gi Arabidopsis thaliana At3g50970 K6 gi Spinacia oleracea K10 gi Oryza sativa K2 tr O64939 Argopyrum elongatum K6 gi Triticum aestivum K6 gi Triticum aestivum K7 gi Hordeum vulgare K9
4 YSK- subgroup Accession number Species Y S K Domains gi Glycine max YSK sp P21298 Raphanus sativus YSK gi Boea crassifolia YSK2 gi Codonopsis lanceolata YSK2 gi Craterostigma plantagineum YSK2 gi Craterostigma plantagineum YSK2 gi Daucus carota YSK2 gi Daucus carota YSK2 gi Fagus sylvatica YSK2 gi Hippophae rhamnoides YSK2 gi Lycopersicum esculentum YSK2 gi Quercus robur YSK2 gi Vitis riparia YSK2 gi Vitis vinifera YSK2 gi Gossypium hirsutum Y2SK gi Arabidopsis thaliana At5g66400 Y2SK2 gi Gossypium hirsutum Y2SK2 gi Nicotiana tabacum Y2SK2 gi Prunus dulcis Y2SK2 gi Solanum commersonii Y2SK2 gi Brassica juncea Y3SK2 gi Brassica napus Y3SK2 gi Helianthus debilis Y3SK2 gi Helianthus petiolaris Y3SK2 gi Tithonia rotundifolia Y3SK2 gi Helianthus annus Y4SK2 gi Cornus sericea Y24SK gi Cornus sericea Y26SK gi Cornus sericea Y13SK gi Oryza sativa YSK gi Xerophyta viscosa YSK gi Elaeis guineensis YSK2 gi Hordeum vulgare YSK2 gi Hordeum vulgare YSK2 gi Hordeum vulgare YSK2 gi Hordeum vulgare YSK2 gi Hordeum vulgare YSK2 gi Hordeum vulgare YSK2 gi Hordeum vulgare YSK2 gi Lophopyrum elongatum YSK2 gi Oryza sativa YSK2 gi Oryza sativa YSK2 gi Oryza sativa YSK2 gi Pennisetum glaucum YSK2 gi Triticum aestivum YSK2 gi Zea mays YSK2 gi Hordeum vulgare YSK3 gi Hordeum vulgare Y2SK2 gi Oryza sativa Y2SK2 gi Hordeum vulgare Y2SK3
5 SK-subgroup Accession number Species S K Domains gi Picea abies SK gi Pinus taeda SK gi Ginkgo biloba SK2 gi Pinus sylvestris SK2 gi Pinus taeda SK3 gi Picea glauca SK4 gi Pinus sylvestris SK4 gi Picea glauca SK4 gi Pinus sylvestris SK4 gi Solanum commersonii SK gi Arabidopsis thaliana At1g76180 SK2 gi Aster tripolium SK2 gi Brassica napus SK2 gi Brassica olearacea SK2 gi Plantago major SK2 gi Lavatera thuringiaca SK2 gi Nicotiana tabacum SK2 tr Q41111 Phaseolus vulgaris SK2 gi Populus euramericana SK2 gi Prunus persica SK2 gi Salvia miltiorrhiza SK2 gi Salvia miltiorrhiza SK2 gi Arabidopsis thaliana At1g20440 SK3 gi Arabidopsis thaliana At1g20450 SK3 gi Boea crassifolia SK3 gi Capsella bursa-pastoris SK3 gi Capsicum annuum SK3 gi Daucus carota SK3 gi Lupinus albus SK3 gi Solanum sogarandinum SK3 gi Betula pubescens SKn tr Q40186 Lemna gibba SK gi Zea mays SK gi Hyacinthus orientalis SK2 gi Oryza sativa SK2 gi Sorghum bicolor SK2 gi Hordeum vulgare SK3 gi Oryza sativa SK3 gi Triticum aestivum SK3
6 KS-subgroup Accession number Species K S Domains tr Q6PNN7 Ammopiptanthus mongolicus KS tr Q850G3 Arachis hypogaea KS tr Q8W267 Carica papaya KS gi Medicago sativa KS gi Medicago sativa KS gi Poncirus trifoliata KS tr Q8RW12 Ricinus communis KS gi Solanum sogarandinum KS gi Vaccinium corymbosum KS gi Citrus sinensis K2S gi Citrus x paradisi K2S AB Citrus unshiu K2S gi Citrus unshiu K3S gi Poncirus trifoliata K3S gi Hordeum vulgare KS YK-subgroup Accession number Species Y K Domains Bryophytes gi Physcomitrella patens Y11K gi Lactuca sativa YK gi Prunus dulcis YK4 gi Prunus persica YK8 gi Betula pubescens Y2K gi Cicer pinnatifidum Y2K gi Glycine max Y2K gi Glycine max Y2K gi Vigna unguiculata Y2K gi Pisum sativum Y2K2 gi Pisum sativum Y2K2 gi Pisum sativum Y2K2 gi Medicago sativa Y2K4
7 Table S3. Group 3 proteins (D-7/D-29, PF02987) Subgroup 3A (D-7) Accession number Species Motifs Number of mer repetitions Q40929_PSEMZ Pseudotsuga menziesii (4X) gb DN frame +3 Pinus taeda (2X), 5 (2X) gb DR frame +1 Picea glauca 1 2 Bryophytes gb CN Tor8981 frame +1 Tortula ruralis 1 5 (3X) dbj BJ frame -2 Physcomitrella patens 4 1 Pteridophytes gb CV frame +1 Ceratopteris richardii 2 3(2X), 5 (3X) P13939 LEAD7_GOSHI Gossypium hirsutum (5X) Q5G1J3_9BRAS Isatus tinctoria (2X), 3 (7X), 4 (2X) Q9LW12_ARATH Arabidopsis thaliana (2X), 3 (7X), 4 (2X) gb CX frame +3 Citrus sinensis (3X) Q9XET0_SOYBN Glycine max (4X) gb CA frame +1 Phaseolus coccineus (5X) gb BU frame +1 Populus tremula (2X) emb AJ frame +1 Antirrhinum majus (2X), 5 (2X) gb BU frame +2 Prunus dulcis (1X), 5 (1X) gb DV frame +2 Coffea canephora (3X) O49816 LEA1_CICAR Cicer arietinum (3X), 5 (2X) gb EE frame +2 Arachis hypogaea (4X) gb DV frame +1 Nicotiana tabacum (3X) 442 LEAD3_DAUCA Daucus carota (2X), 5 (2X) dbj BW frame +2 Lycopersicon esculentum (4X) gb CA frame +3 Saccharum officinarum (7X) Q42376 LEA3_MAIZE Zea mays (8X) gb DV frame +3 Agrostis capillaris (2X), 5 (2X) Q94JF2_ORYSA Oryza sativa (3X), 5 (4X) P14928 LEA1_HORVU Hordeum vulgare (2X), 5 (6X) Q8GV49_WHEAT Triticum aestivum (2X), 5 (8X) gb DT frame +2 Festuca arundinacea (2X), 3 (2X), 5 (4X) Q6L5M0_BROIN Bromus inermis (2X), 5 (3X)
8 Subgroup 3B (D-29) Accession number Species Motifs Number of mer repetitions Liverworts Q41154_9MARC Riccia fluitans 2 1 (4X) P13940 LEA29_GOSHI Gossypium hirsutum (3X) gb DY frame +3 Prunus persica (2X) gb CX frame +3 Citrus sinensis (2X) gb CV frame +2 Juglans regia (2X), 5 (2X) Q06431_BETVE Betula verrucosa 1 (13X), 4 (5X) gb EG frame +2 Ricinus communis 1 (6X), 4 (4X) gb EG frame +2 Arachis hypogaea (2X), 3 (9X), 5 (2X) Q2N1E0_PHAVU Phaseolus vulgaris (3X), 3 (2X), 4 (3X) gb EV frame +3 Medicago truncatula (8X) Q41060_PEA Pisum sativum (2X) Q9ZTY1_SOYBN Glycine max 1 (5X), 4 (3X) Q9SPJ6_SOYBN Glycine max 2 3 (3X) Q39871_SOYBN Glycine max 1 (8X), 4 (7X) Q39873_SOYBN Glycine max (2X), 3 (22X) gb EB frame +1 Nicotiana tabacum 2 1 (4X), 4 (7X) gb EL frame +3 Helianthus tuberosus (8X), 5 (2X) gb EC frame +3 Vitis vinifera 2 1 (6X), 4 (5X) gb DW frame +3 Lactuca serriola (4X), 5 (2X) Q9ZPQ7_ARATH Arabidopsis thaliana 5 2 Q6NKU0_ARATH Arabidopsis thaliana 2 2 (12X) Q6NQH7_ARATH Arabidopsis thaliana 2 1 (3X) Q84W82_ARATH Arabidopsis thaliana 5 5 (5X) Q96246_ARATH Arabidopsis thaliana 1 (9X), 4 (9X) Q9LF88_ARATH Arabidopsis thaliana 1 (11X), 4 (10X) Q9ZPW6_ARATH Arabidopsis thaliana (24X) P13934 LEA76_BRANA Brassica napus P20075 LEAD8_DAUCA Daucus carota 1 (13X), 4 (12X) gb DV Zea mays 1 (3X), 4 (6X) Q03968 LEA3_WHEAT Triticum aestivum Q43478_HORVU Hordeum vulgare gb BE frame +3 Hordeum vulgare 5 2 Q6KA29_ORYSA Oryza sativa (4X) Q8S7U3_ORYSA Oryza sativa (7X) Q7XPL4_ORYSA Oryza sativa 1(2X) Q1JRJ4_SPOST Sporobolus stapfianus (3X)
9 Table S4. Group 4 proteins (D-113, PF03760) Subgroup 4A Accession number Species Motif DR frame +3 Picea glauca DN frame +2 Pinus taeda DT frame +2 Pinus taeda Q40928 Q40928_PSEMZ Pseudotsuga menziesii Q00747 LE25_LYCES Lycopersicon esculentum AJ frame +3 Antirrhinum majus BU frame+2 Sesamum indicum Q3YMR0 Q3YMR0_CRAPL Craterostigma plantagineum ES frame +2 Arachis hypogaea CD Frame +2 Pisum sativum BM Frame +2 Thellungiella halophila gb CA frame+3 Capsicum annuum P46515 LEA11_HELAN Helianthus annus CD frame -1 Zea mays CF frame +2 Sorghum bicolor BQ frame +2 Hordeum vulgare Q5Z771 Q5Z771_ORYSA Oryza sativa Q8H683 Q8H683_ORYSA Oryza sativa CV frame +3 Triticum aestivum DT frame +2 Festuca arundinacea DV frame +3 Agrostis stolonifera
10 Subgroup 4B (D-113) Accession number Species Motif AU frame +3 Cryptomeria japonica Bryophytes PP R frame +1 Physcomitrella patens Q96273 Q96273_ARATH Arabidopsis thaliana At2g35300 Q39138 Q39138_ARATH Arabidopsis thaliana At1g32560 P09441 LEA13_GOSHI Gossypium hirsutum CX frame +3 Brassica napus Q9XES9 Q9XES9_SOYBN Glycine max gb BF Medicago truncatula DV frame +2 Euphorbia esula TC62712 frame +3 Vitis vinifera DV frame +3 Nicotiana tabacum CV frame +3 Petunia hybrida BJ frame -2 Ipomoea nil CX frame -1 Citrus sinensis Q96272_ARATH Arabidopsis thaliana At5g06760 Q56UQ3_BRANA Brassica napus Q1XAU0 Q1XAU0_SISIR Sisymbrium irio Q541U1_SOYBN Glycine max EC frame +3 Phaseolus vulgaris CA frame +2 Medicago truncatula Q6Z0I0 Q6Z0I0_ORYSA Oryza sativa Q7XLZ7 Q7XLZ7_ORYSA Oryza sativa CA frame +3 Saccharum officinarum
11 Table S5. Group 6 proteins (PvLEA18, PF10714) Accession number Species Motif gi TC67570 gi gi gi gi gi gi gi gi gi gi gi gi gi gi gi gi gi gi gi TC75991 gi gi TC88530 gi TC33577 gi TC gi gi gi TC TC gi TC Picea glauca Pinus taeda Pinus taeda Antirrhinum majus Arabidopsis thaliana At2g23110 Arabidopsis thaliana At2g23120 Arabidopsis thaliana At2g33690 Beta vulgaris Brassica napus Brassica napus Brassica napus Citrus sinensis Euphorbia esula Fragaria vesca Gerbera hybrida Glycine max Gossypium hirsutum Juglans regia Lactuca virosa Lycopersicon esculentum Phaseolus vulgaris Populus tremula Populus tremula Populus tremula Solanum tuberosum Thellungiella salsuginea Vitis vinifera Lycoris longituba Hordeum vulgare Oryza sativa (japonica cultivar-group) Oryza sativa (indica cultivar-group) Saccharum officinarum Triticum aestivum Triticum aestivum Triticum turgidum Zea mays
12 Table S6. Group 7 proteins (ASR, PF02496) Accession number Species Motif gi Cycas rumphii gi Ginkgo biloba gi Pinus taeda gi Pinus taeda gi Pseudotsuga menziesii var. menziesii gi Pseudotsuga menziesii var. menziesii gi Pinus taeda gi Pinus taeda gi Pseudotsuga menziesii var. menziesii gi Calystegia soldanella gi Capsicum annuum gi Coffea canephora gi Eucalyptus gunnii gi Glycine max gi Hevea brasiliensis gi Ipomoea nil gi Lycopersicon esculentum var. cerasiforme ASR1 gi Lycopersicon esculentum var. cerasiforme ASR2 gi Lycopersicon esculentum var. cerasiforme ASR3 gi Lycopersicon esculentum var. cerasiforme ASR4 gi Medicago sativa gi Mesembryanthemum crystallinum gi Musa acuminata gi Nicotiana tabacum gi Populus trichocarpa x Populus deltoides gi Prunus armeniaca gi Prunus persica gi Rosa hybrid cultivar gi Salicornia brachiata gi Solanum tuberosum gi Solanum tuberosum gi Vitis pseudoreticulata gi Vitis vinifera gi Vitis vinifera gi Lilium longiflorum gi Saccharum officinarum gi Oryza sativa (indica cultivar-group) gi Oryza sativa (indica cultivar-group) gi Oryza sativa (japonica cultivar-group) gi Oryza sativa (japonica cultivar-group) gi Oryza sativa (japonica cultivar-group) gi Oryza sativa (japonica cultivar-group) 2X gi Oryza sativa (japonica cultivar-group) gi Oryza sativa (japonica cultivar-group) gi Oryza sativa (japonica cultivar-group) gi Polygonatum sibiricum gi Triticum aestivum gi Zea mays gi Zingiber officinale
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