Molecular Biology Reports

, Volume 37, Issue 2, pp 825–832 | Cite as

Composition and phylogenetic analysis of wheat cryptochrome gene family

  • Pei Xu
  • Hui Lan Zhu
  • Hai Bin Xu
  • Zheng Zhi Zhang
  • Cai Qin Zhang
  • Li Xia Zhang
  • Zheng Qiang Ma


Cryptochrome (CRY) gene family encodes photoreceptors mediating developmental responses to blue light throughout the life of plants. We report here the characterization of CRY gene family in hexaploid wheat. Degenerate PCR amplification of the regions encoding the conserved flavin-binding domain of CRY proteins yielded seven bands, resulting from amplification of CRY1a, CRY1b and CRY2 homologous genes. Assignment of individual amplicons to subgenomes was accomplished by comparing their sequence compositions with those from the ancestor species of wheat. ESTs coding for CRY-DASH like proteins were identified in wheat EST database in GenBank. Southern blot showed that TaCRY1a, TaCRY1b and TaCRY2 are single copy genes. We mapped TaCRY1a and TaCRY2 to chromosomes of homoeologous group 6, TaCRY1b to group 2, and TaCRY-DASH to group 7. Phylogenetic analysis showed that CRY subfamily diversification occurred before the divergence of monocots and dicots. The regulatory and functional changes of CRY members within subfamily are discussed.


Cryptochrome Gene family Phylogeny Wheat 





Expressed sequence tag


Polymerase chain reaction


Photolyase related



This study was partially supported by Outstanding Youth Funds of National Natural Science Foundation of China and Ministry of Education, and 2000s Trans-Century Talent Development Program of Ministry of Education, and Generation Challenging Program (SP2-1), and ‘111’ project (B08025).

Supplementary material

11033_2009_9628_MOESM1_ESM.xls (18 kb)
Supplementary material 1 (XLS 18 kb)


  1. 1.
    Todo T (1999) Functional diversity of the DNA photolyase/blue light receptor family. Mutat Res 434:89–97PubMedGoogle Scholar
  2. 2.
    Lin C, Robertson DE, Ahmad M, Raibekas AA, Jorns MS, Dutton PL, Cashmore AR (1995) Association of flavin adenine dinucleotide with the Arabidopsis blue light receptor CRY1. Science 269:968–970CrossRefPubMedGoogle Scholar
  3. 3.
    Cashmore AR, Jarillo JA, Wu YJ, Liu D (1999) Cryptochrome: blue light receptors for plant and animals. Science 284:760–765CrossRefPubMedGoogle Scholar
  4. 4.
    Ahmad M, Cashmore AR (1993) HY4 gene of A. thaliana encodes a protein with characteristics of a blue-light photoreceptor. Nature 366:162–166CrossRefPubMedGoogle Scholar
  5. 5.
    Lin C, Ahmad M, Cashmore AR (1996) Arabidopsis Cryptochrome 1 is a soluble protein mediating blue light-dependent regulation of plant growth and development. Plant J 10:893–902CrossRefPubMedGoogle Scholar
  6. 6.
    Somers DE, Devlin PF, Kay SA (1998) Phytochromes and cryptochromes in the entrainment of the Arabidopsis circadian clock. Science 282:1488–1490CrossRefPubMedGoogle Scholar
  7. 7.
    Guo H, Yang H, Mockler TC, Lin C (1998) Regulation of flowering time by Arabidopsis photoreceptors. Science 279:1360–1363CrossRefPubMedGoogle Scholar
  8. 8.
    Brudler R, Hitomi K, Daiyasu H, Toh H, Kucho K, Ishiura M, Kanehisa M et al (2003) Identification of a new cryptochrome class: structure, function, and evolution. Mol Cell 11:59–67CrossRefPubMedGoogle Scholar
  9. 9.
    Kleine T, Lockhart P, Batschauer A (2003) An Arabidopsis protein closely related to Synechocystis Cryptochrome is targeted to organelles. Plant J 35:93–103CrossRefPubMedGoogle Scholar
  10. 10.
    Selby CP, Sancar A (2006) A cryptochrome/photolyase class of enzymes with single-stranded DNA-specific photolyase activity. Proc Natl Acad Sci USA 103:17696–17700CrossRefPubMedGoogle Scholar
  11. 11.
    Pokorny R, Klar T, Hennecke U, Carell T, Batschauer A, Essen LO (2008) Recognition and repair of UV lesions in loop structures of duplex DNA by DASH-type cryptochrome. Proc Natl Acad Sci USA 105:21023–21027CrossRefPubMedGoogle Scholar
  12. 12.
    Imaizumi T, Kadota A, Hasebe M, Wada M (2002) Cryptochrome light signals control development to suppress auxin sensitivity in the moss Physcomitrella patens. Plant Cell 14:373–386CrossRefPubMedGoogle Scholar
  13. 13.
    Imaizumi T, Kanegae T, Wada M (2000) Cryptochrome nucleocytoplasmic distribution and gene expression are regulated by light quality in the fern Adiantum capillus-veneris. Plant Cell 12:81–95CrossRefPubMedGoogle Scholar
  14. 14.
    Lin C, Ahmad M, Chan J, Cashmore AR (1996) CRY2, a second member of the Arabidopsis cryptochrome gene family. Plant Physiol 110:1047CrossRefGoogle Scholar
  15. 15.
    Perrotta G, Ninu L, Flamma F, Weller JL, Kendrick RE, Nebuloso E, Giuliano G (2000) Tomato contains homologues of Arabidopsis Cryptochrome 1 and 2. Plant Mol Biol 42:765–773CrossRefPubMedGoogle Scholar
  16. 16.
    Perrotta G, Yahoubyan G, Nebuloso E, Renzi L, Giuliano G (2001) Tomato and barley contain duplicated copies of Cryptochrome 1. Plant Cell Environ 24:991–997CrossRefGoogle Scholar
  17. 17.
    Platten JD, Foo E, Foucher F, Hecht V, Reid JB, Well JL (2005) The cryptochrome gene family in pea includes two differentially expressed CRY2 genes. Plant Mol Biol 59:683–696CrossRefPubMedGoogle Scholar
  18. 18.
    Hirose F, Shinomura T, Tanabata T, Shimada H, Takano M (2006) Involvement of rice cryptochromes in de-etiolation responses and flowering. Plant Cell Physiol 47:915–925CrossRefPubMedGoogle Scholar
  19. 19.
    Zhang YC, Gong SF, Li QH, Sang Y, Yang HQ (2006) Functional and signalling mechanism analysis of rice CRYPTOCHROME 1. Plant J 46:971–983CrossRefPubMedGoogle Scholar
  20. 20.
    Szücs P, Karsai I, von Zitzewitz J, Mészáros K, Cooper LL, Gu YQ, Chen TH, Hayes PM, Skinner JS (2006) Positional relationships between photoperiod response QTL and photoreceptor and vernalization genes in barley. Theor Appl Genet 112:1277–1285CrossRefPubMedGoogle Scholar
  21. 21.
    Chatterjee M, Sharma P, Khurana JP (2006) Cryptochrome 1 from Brassica napus is up-regulated by blue light and controls hypocotyl/stem growth and anthocyanin accumulation. Plant Physiol 141:61–74CrossRefPubMedGoogle Scholar
  22. 22.
    Xie XZ, Chen ZP, Wang XJ (2005) Cloning and expression analysis of CRY2 gene in Sorghum bicolor. J Plant Physiol Mol Biol 31:261–268Google Scholar
  23. 23.
    Giliberto L, Perrotta G, Pallara P, Weller JL, Fraser PD, Bramley PM, Fiore A et al (2005) Manipulation of the blue light photoreceptor cryptochrome 2 in tomato affects vegetative development, flowering time, and fruit antioxidant content. Plant Physiol 137:199–208CrossRefPubMedGoogle Scholar
  24. 24.
    Okazawa A, Trakulnaleamsai C, Hiramatsu H, Fukusaki E, Koichi Yoneyama K, Takeuchi Y, Kobayashi A (2005) Cloning of a cryptochrome homologue from the holoparasitic plant Orobanche minor Sm. Plant Physiol Biochem 43:499–502CrossRefPubMedGoogle Scholar
  25. 25.
    Zhang Q, Li H, Li R, Hu R, Fan C, Chen F, Wang Z, Liu X, Fu Y, Lin C (2009) Association of the circadian rhythmic expression of GmCRY1a with a latitudinal cline in photoperiodic flowering of soybean. Proc Natl Acad Sci USA 105:21028–21033CrossRefGoogle Scholar
  26. 26.
    Petersen G, Seberg O, Yde M, Berthelsen K (2006) Phylogenetic relationships of Triticum and Aegilops and evidence for the origin of the A, B, and D genomes of common wheat (Triticum aestivum). Mol Phylogenet Evol 39:70–82CrossRefPubMedGoogle Scholar
  27. 27.
    Ma ZQ, Sorrells ME (1995) Genetic analysis of fertility restoration in wheat using restriction fragment length polymorphisms. Crop Sci 35:1137–1143CrossRefGoogle Scholar
  28. 28.
    Xu P, Xiang Y, Zhu HL, Xu HB, Zhang ZZ, Zhang CQ, Zhang LX, Ma ZQ (2009) Wheat cryptochromes: subcellular localization and involvement in photomorphogenesis and osmotic stress responses. Plant Physiol 149:760–774CrossRefPubMedGoogle Scholar
  29. 29.
    Huang SX, Sirikhachornkit A, Su XJ, Faris J, Gill B, Haselkorn R, Gornicki P (2002) Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum-Aegilops complex and the evolutionary history of polyploid wheat. PNAS 99:8133–8138CrossRefPubMedGoogle Scholar
  30. 30.
    Salse J, Chagué V, Bolot S, Magdelenat G, Huneau C, Pont C, Belcram H, Couloux A, Gardais S, Evrard A et al (2008) New insights into the origin of the B genome of hexaploid wheat: evolutionary relationships at the SPA genomic region with the S genome of the diploid relative Aegilops speltoides. BMC Genomics 9:555CrossRefPubMedGoogle Scholar
  31. 31.
    Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92CrossRefPubMedGoogle Scholar
  32. 32.
    Sorrells ME, Rota ML, Catherine E, Bermudez-Kandianis CE et al (2003) Comparative DNA sequence analysis of wheat and rice genomes. Genome Res 13:1818–1827PubMedGoogle Scholar
  33. 33.
    Sang Y, Li QH, Rubio V, Zhang YC, Mao J, Deng XW, Yang HQ (2005) Arabidopsis cryptochrome 1 N-terminal domain-mediated homodimerization is required for its photoreceptor activity. Plant Cell 17:1569–1584CrossRefPubMedGoogle Scholar
  34. 34.
    Sheehan MJ, Farmer PR, Brutnell TP (2004) Structure and expression of maize phytochrome family homeologs. Genetics 167:1395–1405CrossRefPubMedGoogle Scholar
  35. 35.
    Gaut BS (2002) Evolutionary dynamics of grass genomes. New Phytol 154:15–28CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Pei Xu
    • 1
    • 2
    • 4
  • Hui Lan Zhu
    • 1
    • 2
  • Hai Bin Xu
    • 1
    • 2
  • Zheng Zhi Zhang
    • 1
    • 2
  • Cai Qin Zhang
    • 1
    • 2
  • Li Xia Zhang
    • 1
    • 2
  • Zheng Qiang Ma
    • 1
    • 2
    • 3
  1. 1.The Applied Plant Genomics Lab, Crop Genomics and Bioinformatics CenterNanjing Agricultural UniversityJiangsuPeople’s Republic of China
  2. 2.National Key Lab of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityJiangsuPeople’s Republic of China
  3. 3.College of Agricultural SciencesNanjing Agricultural UniversityNanjingPeople’s Republic of China
  4. 4.Institute of VegetablesZhejiang Academy of Agricultural SciencesHangzhouPeople’s Republic of China

Personalised recommendations