Ahrazem, O., Rubio-Moraga, A., Argandola-Picazo, J., Castillo, R., and Gomez-Gomez, L., 2016. Intron retention and rhythmic diel pattern regulation of carotenoid cleavage dioxygenase 2 during crocetin biosynthesis in saffron. Plant Mol. Biol. 91(3), 355-374.

Ahrazem, O., Trapero, A., Gomez, M.D., Rubio-Moraga, A., and Gomez-Gomez, L., 2010. Genomic analysis and gene structure of the plant carotenoid dioxygenase 4 family: A deeper study in Crocus sativus and its allies. Genomics. 96, 239-250.

Ahrazem, O., Rubio-Moraga, A., Berman, J., Capell, T., Christou, P., Changfu, Z., and Gomez-Gomez, L., 2015. The carotenoid cleavage dioxygenase CCD2 catalysing the synthesis of crocetin in spring crocuses and saffron is a plastidial enzyme. New Phytol. 209(2), 650-663.

Almagro Armenteros, J.J., Tsirigos, K.D., Sønderby, C.K.., Petersen, T.N., Winther, O., Brunak, S., von Heijne, G., and Nielsen, H., 2019. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nature Biotechnol. 37(4), 420-423.

Artimo, P., Jonnalagedda, M., Arnold, K., Baratin, D., Csardi, G., de Castro, E., Duvaud, S., Flegel, V., Fortier, A., Gasteiger, E., Grosdidier, A., Hernandez, C., Ioannindis, V., Kuznetsov, D., Liechti, R., Moretti, S., Mostaguir, K., Redaschi, N., Rossier, G., Xenarios, I., and Stockinger, H., 2012. ExPASy: SIB bioinformatics resource portal. Nucleic Acid Res. 40(W1), W597-W603.

Auldridge, M.E., McCarty, D.R., and Klee, H.J., 2006. Plant carotenoid cleavage oxygenases and their apocarotenoid products. Plant Biol. 9(3), 315-321.

Armenteros, JJA., Tsirigos, KD., Sonderby, CK., Petersen, TN., Winther, O., Brunak, S., Von Heijne, G., and Nielsen, H., 2019. SignalP 5.0 improves signal peptide predictions using deep neural networks. Nat. Biotechnol. 37(4), 420-423.

Baba, S.A, Mohiuddin, T., Basu, S., Swarnkar, M.K., Malik, A.H., Wani1, Z.A., Abbas, N., Singh, A.K., and Ashraf, N., 2015. Comprehensive transcriptome analysis of Crocus sativus for discovery and expression of genes involved in apocarotenoid biosynthesis. BMC Genomics. 16(698), 1-14.

Babaabasi, B., 2017. Cellular and Molecular Bioinformatics. Khalili Press. [in Persian].

Balderman, S., Naim, M., and Fleischmann, P., 2005. Enzymatic carotenoid degradation and aroma formation in nectarines (Prunus persica). Food Res. Int. 38(8-9), 833-836.

Beiki, A.H., Keify, F., and Mozafari, J., 2011. Rapid genomic DNA isolation from corm of Crocus species for genetic diversity analysis. J. Med. Plant Res. 5(18), 4596-4600.

Bendtsen, J.D., Nielsen, H., Von Heijne, G., and Brunak, S., 2004. Improved prediction of signal 3.0. J. Mol. Biol. 340(4), 783-795.

Bertoni, M., Kiefer, F., Biasini, M., Bordoli, L., and Schwede, T., 2017. Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Sci. Rep. 7(1), 10480.

Bienert, S., Waterhouse, A., de Beer, T.A.P., Tauriello, G., Studer, G., Bordoli, L., and Schwede, T., 2017. The SWISS-MODEL Repository - new features and functionality. Nucleic Acid Res. 45, 313-319.

Bouvier, F., Suire, C., Mutterer, J., and Camara, B., 2003. Oxidative remodeliang of chromoplast carotenoids: identification of the carotenoid dioxygenase CsCCD and CsZCD genes involved in Crocus secondary metabolite biogenesis. Plant Cell. 15(1), 47-62.

Combet, C., Blanchet, C., Geourjon, C., and Deleage, G., 2000. NPS@: Network protein sequence analysis. Trends Biochem. Sci. 25(3), 147-150

Dehghan, M., and Tohidfar, M., 2019. Phenylpropanoid gene expression analysis in saffron using transcriptome data. J. Medic. Plant Biotechnol. 4(2), 105-118.

Demurtas, O. S., Frusciante,S., Ferrante, P., Diretto, G., Hosseinpour Azad, N., Pietrella, M., e Aprea, G., Taddei, A. R., Romano, E., Mi, J., Al-Babili, S., Frigerio, L., and Giuliano, G., 2018. Candidate enzymes for saffron crocin biosynthesis are localized in multiple cellular compartments. Plant Physiol. 177(3), 990-1006

Eftekhar Manavi S., Peyghan, R., Soltani, M., Ghorbanpour, M., Ghalyanchi and Langrodi, A., 2016. Multi-aspect molecular and structural bioinformatic study of outer membrane protein (OmpTS) of Aeromonas hydrophila common cause of infectious septicemia in fish for immunization goals. J. Animal Environ. 8(1), 165-174.

El-Gebali, S., Mistry, J., Bateman, A., Eddy, S.R., Luciani, A., Potter, S.C., Qureshi, M., Richardson, L.J., Salazar, J.A., Smart, A., Sonnhammer, E.L.L., Hirsh, L., Paladin, L., Piovesan, D., Tosatto, S.C.E., and Finn, R.D., 2019. The Pfam protein families database in 2019. Nucleic Acid Res. 48(D1), D427- D432.

Eugester, C.H., Hurlimann, H., and Leuenberger, H.J., 1969. Crocetindialdehyd und Crocetinhalbaldehyd als Blütenfarbstoffe von Jacquinia angustifolia. Helvetica Chimica Acta. 52(3), 89– 90.

Fallah Ziarani, M., Tohidfar, M., and Aminfar, Z., 2017. Bioinformatic analysis of Acyl Carier Protein (ACP) in eukaryotes and prokaryotes. Crop Biotech. 17, 15-29. [in Persian with English Summary].

Fleischmann, P., Watanabe, N., and and Winterhalter, P., 2003. Enzymatic carotenoid cleavage in star fruit (Averrhoa carambola). Phytochemistry. 63(2), 131-137.

Floss, D.S., Walter, M.H., 2009. Role of carotenoid cleavage dioxygenase 1 (CCD1) in apocarotenoid biogenesis revisited. Plant Signal. Bihav. 4(3), 172-175.

Fraser, PD., Bramley, PM. 2004. The biosynthesis and nutritional uses of carotenoids. Prog. Lipid Res. 43(3), 228-265.

Gasteiger, E., Hoogland, C., Gattiker, A., Duvaud, S., Wilkins, M.R., Appel, R.D., and Bairoch, A., 2005. Protein Identification and Analysis Tools on the ExPASy Server. The Proteomics Protocols Handbook. Humana Press, New York. P. 571-607.

Giuliano, G., Al-Babili, S., and Lintig, J., 2003. Carotenoid oxygenases: Cleave it or leave it. Plant Sci. 8(4), 145-148.

Guex, N., Peitsch, M.C., and Schwede, T., 2009. Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective. Electrophoresis. 30(S1), S162-S173

Gomez-Gomez, L., Rubio-Moraga, A., and Ahrazem, O., 2010. Understanding carotenoid metabolism in saffron stigmas: Unravelling aroma and colour formation. Func. Plant Sci. & Biotechnol. 4(2), 56-63.

Hosseinpour Azad, N., Nematzadeh, G.H., Gouliano, G., Ranjbar, G.A., Yamch, A., 2016. Identification of Apo- Carotenoids' Crocin and Crocetin Isomers in Saffron Crude Extracts by HPLC Coupled to Atmospheric Pressure Chemical Ionization and High Resolution Orbitrap Mass Spectrometry. Saffron Agron. & Technol. 4(4), 291-299. [in Persian with English Summary].

Ibdah, M., Azulay, Y., Portnoy, V., Wasserman, B., Bar, E., Meir, A., Burger, Y., Hirschberg, J., Schaffer, A.A., Katzir, N., Tadmor, Y., and Lewinsohn, E., 2006. Functional characterization of CmCCD1, a carotenoid cleavage dioxygenase from melon. Phytochemistry. 67(15), 1579–1589.

Kato, M., Matsumoto, H., Ikoma, Y., Okuda, H., and Yano, M., 2006. The role of carotenoid cleavage dioxygenases in the regulation of carotenoid profiles during maturation in citrus fruit. J. Exp. Bot. 57(10), 2153–2164.

Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E.L., 2001. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol. 305(3), 567-580.

Kyte, J., and Doolittle, R.F., 1982. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157(1), 105–32. 

Liao, H., Byeon, I., and Tsai, M., 1999. Structure and function of a new phosphopeptide-binding domain containing the FHA2 of rad53. J. Mol. Biol. 294(4), 1041-1049.

Maniatis, T., Fritsch, E., and Sambrook, F., 1995. Molecular cloning. A laboratory Manual. Cold Spring Harbor Laboratory, New York.

Mathieu, S., Terrier, N., Procureur, J., Bigey, F., and Gunata, Z., 2005. A Carotenoid Cleavage Dioxygenase from Vitis vinifera L.: Functional characterization and expression during grape berry development in relation to C₁₃-norisoprenoid accumulation. J. Exp. Bot. 56(420), 2721–2731.

Messing, S.A., Gabelli, S.B., Echeverria, I., Vogel, T.J., Guan, J.C., Cai Tan, B., Klee, H.J., McCarty, R.D., and Amzel, L.M., 2010. Structural insights into maize viviparous14, a key enzyme in the biosynthesis of the phytohormone abscisic acid. Plant Cell. 22(9), 2970-2980.

Mirhoseini, S.Z., Pezeshkian, Z., and Ghovvati, S., 2016. Phylogenetic and in silico analysis of interferon Beta-1b Protein. J. Mazandaran Univ. MedicSci. 26(145), 70-82. [in Persian with English Summary].

Nassaj Hoseini, S.M., and Shamsbakhsh, M., 2010. Phylogenetic Analysis Methods. Haghshenass publication, Rasht, Iran. [in Persian].

Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, DM., Meng, E.C., and Ferrin, T.E., 2004. UCSF Chimera-avisualization system for exploratory research and analysis. J. Comput. Chem. 25(13), 1605-1612.

Pfister, S., Meyer, P., Steck, A., and Pfander, H., 1996. Isolation and Structure Elucidation of Carotenoid−Glycosyl Esters in Gardenia Fruits (Gardenia jasminoides Ellis) and Saffron (Crocus sativus Linne). J. Agric. & Food Chem. 44(9), 2612-2615.

Rubio, A., Rambla, J.L., Santaella, M., Gomez, D., Orzaez, D., Granell, A., Gomez-Gpmez, L. 2008. Cytosolic and Plastoglobule-targeted Carotenoid Dioxygenases from Crocus sativus Are Both Involved in β-Ionone Release. J. Biol. Chem. 283(36): 24816–24825.

Rubio, A., Rambla, J.L., Ahrazem, O., Granell, A., and Gomez-Gomez, L., 2009. Metabolic and target transcript analysis during Crocus sativus stigma Development. Phytochemistry. 70(8), 1009-1016.

Rubio-Moraga, A., Rambla, J.L., Fernández-de-Carmen, A., Trapero-Mozos, A., Ahrazem, O., Orzáez, D., Granell, A., and Gómez-Gómez, L., 2014. New target carotenoids for CCD4 enzymes are revealed with the characterization of a novel stress-induced carotenoid cleavage dioxygenase gene from Crocus sativus. Plant Mol. Biol. 86(4-5), 555-569.

Simkin, A.J., Underwood, B.A., Auldridge, M., Loucas, H.M., Shibuya, K., Schmelz, E., Clark, D.G., and Klee, H.J., 2004. Circadian regulation of the PhCCD1 carotenoid cleavage dioxygenase controls emission of beta-ionone, a fragrance volatile of petunia flowers. Plant Physiol. 136(3), 3504-3514.

Simkin, A.J., Moreau, H., Kuntz, M., Pagny, G., Lin, C., Tanksley, S., and McCarthy, J., 2008. An investigation of carotenoid biosynthesis in Coffea canephora and Coffea Arabica. J. Plant Physiol. 165(10), 1087-1106.

Sui, X., Kiser, P.D., Lintig, J.V., and Palczewski, K., 2013. Structural basis of carotenoid cleavage: From bacteria to mammals. Arch. Biochem. Biophys. 539(2), 203-213.

 

Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S., 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol.  Biol. Evol. 30, 2725-2729.

Tan, B. C., Joseph, L.M., Deng, W.T., Liu, l., Li, Q.B., Cline, K., McCarty, D.R. 2003. Molecular characterization of the Arabidopsis 9-cis epoxycarotenoid dioxygenase gene family. Plant J. 35, 44–56.

Tandon, J.S., Katti, S.B., and Rüedi, P., 1979. Crocetin‐dialdehyde from Coleusforskohlii BRIQ., Labiatae. Helv. Chim. Acta. 62(8), 2706-2707.

Tramontano, A., Leplae, R., and Morea, V., 2001. Analysis and assessment of comparative modeling predictions in CASP4. Proteins. 45(S5), 22-38.

Vogel, J.T., Tan, B.C., McCarty, D.R., and Klee, H.J., 2008. The carotenoid cleavage dioxygenase I enzyme has broad substrate specificity, cleaving multiple carotenoids at two different bond positions. J. Biol. Chem. 283(17), 11364-11373.

 Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F.T., de Beer, T.A.P., Rempfer, C., Bordoli, L., Lepore, R., and Schwede, T., 2018. SWISS-MODEL: Homology modelling of protein structures and complexes. Nucleic Acids Res. 46(W1), W296-W303.

 Yousefi Javan, I., and Gharari, F., 2017. The structure of the protein and gene expression of PIC2 affecting blooming flowers (Crocus sativus L.). Saffron Agron. & Technol. 5(1), 73-90. [in Persian with English Summary].