1

Supplemental Figure 1S. Alignment and phylogeny of CRY proteins.

Comparison of the amino acid sequences of the DNA-photolyase domain (a) and FAD binding domain (b) from several CRY proteins. AtCRY, SlCRY, GmCRY, OsCRY and FvCRY were from Arabidopsis thaliana, Solanum lycopersicum, Glycine max, Oryza sativa Japonica Group and Fragaria vesca, respectively. Consensus sequences are identified with gray highlighting. c. Phylogeny reconstruction of CRY proteins. A neighbor-joining tree was calculated using clustal W. Branch lengths indicate the number of substitutions per site. FaCRY1 and FaCRY2 are highlighted with open boxes. GenBank accession numbers of the amino acid sequences used include; GmCRY1, Glycine max cryptochrome 1 (NP_001235205); NsCRY1, Nicotiana sylvestris cryptochrome 1 (ABB36796); VrCRY1, Vitis riparia cryptochrome 1 (ABX80391); VvCRY1, Vitis vinifera cryptochrome 1 (ABX79355); PsCRY1, Pisum sativum cryptochrome 1 (AAO23970); SlCRY1, Solanum lycopersicum cryptochrome 1 (NP_001234667); CbCRY1, Capsella bursa-pastoris cryptochrome 1 (ACX49994); AtCRY1, Arabidopsis thaliana cryptochrome-1 (NP_567341); OsCRY1, Oryza sativa Japonica Group cryptochrome 1a (BAD17529); OmCRY1, Orobanche minor cryptochrome 1 (AAR08429); FvCRY1, Fragaria vesca CRY1 (ACV89993); FaCRY1, Fragaria ananassa cryptochrome1 (AB743569); GmCRY2, Glycine max cryptochrome2 (BAI47558); NsCRY2, Nicotiana sylvestris cryptochrome 2 (ABB36797); SlCRY2, Solanum lycopersicum cryptochrome 2 (NP_001234245); BjCRY2, Brassica juncea cryptochrome 2 (ADM47404); ArCRY2, Armoracia rusticana cryptochrome 2 (BAC67178); AtCRY2, Arabidopsis thaliana cryptochrome 2 (NP_171935); OsCRY2, Oryza sativa Indica Group (CAC82538); TaCRY2, Triticum aestivum cryptochrome 2 (ABX58030); FvCRY2, Fragaria vesca Cry2 (ACZ71184); FaCRY2, Fragaria ananassa cryptochrome 2 (AB743570).

 

CRY1

CRY2

Suppl. Fig 1S. a: DNA-photolyase domain

CRY2

Suppl. Fig 1S. b: FAD binding domain CRY1

Suppl. Fig 1S. c

Supplemental Figure 2S. Alignment and phylogeny of PHY proteins.

Comparison of the amino acid sequences of the (a) PAS, (b) GAF, and (c) PHY domains of various PHY proteins. AtPHY, SlPHY, VvPHY, OsPHY, and FvPHY were from Arabidopsis thaliana, Solanum lycopersicum, Vitis vinifera, Oryza sativa Japonica Group and Fragaria vesca, respectively. Consensus sequences are identified with gray highlighting. d. Phylogeny reconstruction of PHY proteins. A neighbor-joining tree was calculated using clustal W. Branch lengths indicate the number of substitutions per site. FaPHYA and FaPHYB are highlighted with open boxes. GenBank accession numbers of the amino acid sequences used include: VvPHYA, Vitis vinifera phytochrome A (ACC60965); VrPHYA, Vitis riparia phytochrome A (ACC60969); ArPHYA, Armoracia rusticana phytochrome A (BAA99410); AtPHYA, Arabidopsis thaliana phytochrome A (NP_172428); StPHYA, Solanum tuberosum phytochrome A (ABA46868); MgPHYA, Monotropastrum globosum phytochrome A (AAR08427); AfPHYA, Aquilegia formosa phytochrome A (ACV87353); BvPHYA, Beta vulgaris phytochrome A (ACY01932); GmPHYA, Glycine max phytochrome A (BAG72094); SbPHYA, Sorghum bicolor phytochrome A (AAR30884); OsPHYA, Oryza sativa Japonica Group phytochrome A (AAM47309); AmPHYA, Amblyopyrum muticum phytochrome A (AEA40447); HvPHYA, Hordeum vulgare subsp. vulgare phytochrome A (ABB13322); SlPHYA, Solanum lycopersicum phyA (CAA05089); FaPHYA, Fragaria ananassa phytochrome A (AB743571); VrPHYB, Vitis riparia phytochrome B (ACC60970); VvPHYB, Vitis vinifera phytochrome B (ACC60966); StPHYB, Solanum tuberosum phytochrome B (ABC72086); NpPHYB, Nicotiana plumbaginifolia phytochrome B (CAA74992); AfPHYB, Aquilegia formosa phytochrome B (ACV87354); AePHYB, Amphicarpaea edgeworthii phytochrome B (AEA41043); AtPHYB, Arabidopsis thaliana phytochrome B (ABY61307); OsPHYB, Oryza sativa Indica Group phytochrome B (CAA40795); SbPHYB, Sorghum bicolor phytochrome B (AAR30903); GmPHYB, Glycine max phytochrome B (AAA34000); SlPHYB, Solanum lycopersicum phytochrome B1 (CAA05293); FaPHYB, Fragaria ananassa phytochrome B (AB743572); CfPHY, Chara foetida phytochrome (CAA56565.1). FvPHYA and FvPHYB were obtained by blastp searches using FaPHYA and FaPHYB sequences from DATABASE: vescagenemodels2.faa (http://www.strawberrygenome.org/). Sequence numbers of FvPHYA and FvPHYB are from Fragaria vesca Phytochrome A (gene 22948) and Fragaria vesca Phytochrome B (gene 05117), respectively.

 

PHYA

PHYB

Suppl. Fig 2S. a: PER-ARNT-SIM (PAS) domain

PHYA

PHYB

Suppl. Fig 2S. b: cGMP phosphodiesterase/adenyl cyclase/FhlA (GAF) domain

PHYA

PHYB

Suppl. Fig 2S. c: phytochrome (PHY) domain

Suppl. Fig 2S. d