Skip to main content
SpringerLink
Log in

Sequence evaluation of four specific cDNA libraries for developmental genomics of sunflower

  • Original Paper
  • Published:
Molecular Genetics and Genomics Aims and scope Submit manuscript

Abstract

Four different cDNA libraries were constructed from sunflower protoplasts growing under embryogenic and non-embryogenic conditions: one standard library from each condition and two subtractive libraries in opposite sense. A total of 22,876 cDNA clones were obtained and 4800 ESTs were sequenced, giving rise to 2479 high quality ESTs representing an unigene set of 1502 sequences. This set was compared with ESTs represented in public databases using the programs BLASTN and BLASTX, and its members were classified according to putative function using the catalog in the Kyoto Encyclopedia of Genes and Genomes (KEGG). Some 33% of sequences failed to align with existing plant ESTs and therefore represent putative novel genes. The libraries show a low level of redundancy and, on average, 50% of the present ESTs have not been previously reported for sunflower. Several potentially interesting genes were identified, based on their homology with genes involved in animal zygotic division or plant embryogenesis. We also identified two ESTs that show significantly different levels of expression under embryogenic and non-embryogenic conditions. The libraries described here represent an original and valuable resource for the discovery of yet unknown genes putatively involved in dicot embryogenesis and improving our knowledge of the mechanisms involved in polarity acquisition by plant embryos.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2a, b

Similar content being viewed by others

References

  • Alibert G, Aslane-Chanabe C, Burrus M (1994) Sunflower tissue and cell cultures and their use in biotechnology. Plant Physiol Biochem 32:31–44

    CAS  Google Scholar 

  • Belanger K, Quatrano R (2000) Polarity: the role of localized secretion. Curr Opin Plant Biol 3:67–72

    Article  CAS  PubMed  Google Scholar 

  • Boswell RE, Prout ME, Steichen JC (1991) Mutations in a newly identified Drosophila melanogaster gene, mago nashi , disrupt germ cell formation and result in the formation of mirror-image symmetrical double abdomen embryos. Development 113:373–384

    CAS  PubMed  Google Scholar 

  • Busch M, Mayer U, Jürgens G (1996) Molecular analysis of the Arabidopsis pattern formation gene GNOM: gene structure and intragenic complementation. Mol Gen Genet 250:681–691

    Article  CAS  PubMed  Google Scholar 

  • Caboche M, Boucly M (2000) The Genoplante programme, a mobilizing programme in plant genomics. Comptes Rend Acad Agric France 86:159–173

    Google Scholar 

  • Carmell MA, Xuan Z, Zhang MQ, Hannon GJ (2002) The Argonaute family: tentacles that reach into RNAi, developmental control, stem cell maintenance, and tumorigenesis. Genes Dev 16:2733–2742

    Article  CAS  PubMed  Google Scholar 

  • Chanabé C, Burrus M, Alibert G (1989) Factors affecting the improvement of colony formation from sunflower protoplasts. Plant Sci 64:125–132

    Article  Google Scholar 

  • Chanabé C, Burrus M, Bidney D, Alibert G (1991) Studies on plant regeneration from protoplasts in the genus Helianthus. Plant Cell Rep 9:635–638

    Google Scholar 

  • Chaudhury A, Koltunow A, Payne T, Luo M, Tucker M, Dennis E, Peacock W (2001) Control of early seed development. Annu Rev Cell Dev Biol 17:677–699

    Google Scholar 

  • Chen J, Ullah H, Young J, Sussman M, Jones A (2001) ABP1 is required for organized cell elongation and division in Arabidopsis embryogenesis. Genes Dev 15:902–911

    CAS  PubMed  Google Scholar 

  • Chomczynski P, Sacchi N (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162:156–159

    CAS  PubMed  Google Scholar 

  • Flores Berrios E, Gentzbittel L Kayyal H, Alibert G, Sarrafi A (2000) AFLP mapping of QTLs for in vitro organogenesis traits using recombinant inbred lines in sunflower ( Helianthus annuus L.). Theor Appl Genet 101:1299–1306

    Google Scholar 

  • Gentzbittel L, Abbott A, Galaud J, Georgi L, Fabre F, Liboz T, Alibert G (2002) A bacterial artificial chromosome (BAC) library for sunflower, and identification of clones containing genes for putative transmembrane receptors. Mol Genet Genomics 266:979–987

    Article  CAS  PubMed  Google Scholar 

  • Goldberg R, de Paiva G, Yadegari R (1994) Plant embryogenesis: zygote to seed. Science 266:605–614

    CAS  Google Scholar 

  • Hardtke C, Berleth T (1998) The Arabidopsis gene MONOPTEROS encodes a transcription factor mediating embryo axis formation and vascular development. EMBO J 17:1405–1411

    Article  CAS  PubMed  Google Scholar 

  • Jonak C, Hirt H (2002) Glycogen synthase 3/SHAGGY-like kinases in plant: an emerging family with novel functions. Trends Plant Sci 7:457–461

    Article  CAS  PubMed  Google Scholar 

  • Jürgens G (1995) Axis formation in plant embryogenesis: cues and clues. Cell 81:467–470

    PubMed  Google Scholar 

  • Jürgens G (2001) Apical-basal pattern formation in Arabidopsis embryogenesis. EMBO J 20:3609–3616

    Article  PubMed  Google Scholar 

  • Jürgens G, Grebe M, Steinmann T (1997) Establishment of cell polarity during early plant development. Curr Opin Cell Biol 9:849–852

    Article  PubMed  Google Scholar 

  • Karsi A, Patterson A, Feng J, Liu Z (2002) Translational machinery of channel catfish: I. A transcriptomic approach to the analysis of 32 40S ribosomal protein genes and their expression. Gene 291:177–186

    Article  CAS  PubMed  Google Scholar 

  • Lynn K, Fernandez A, Aida M, Sedbrook J, Tasaka M, Masson P, Barton MK (1999) The PINHEAD/ZWILLE gene acts pleiotropically in Arabidopsis development and has overlapping functions with the ARGONAUTE1 gene. Development 126:469–481

    CAS  PubMed  Google Scholar 

  • Mayer U, Büttner G, Jürgens G (1993) Apical-basal pattern formation in the Arabidopsis embryo: studies on the role of the GNOM gene. Development 117:149–162

    Google Scholar 

  • Meinke DW (1985) Embryo-lethal mutants of Arabidopsis thaliana: analysis of mutants with a wide range of lethal phases. Theor Appl Genet 69:543–552

    Google Scholar 

  • Petitprez M, Briere C, Borin C, Kallerhoff J, Souvre A, Alibert G (1995) Characterisation of protoplasts from hypocotyls of Helianthus annuus in relation to their tissue origin. Plant Cell Tissue Org Cult 41:33–40

    Google Scholar 

  • Robertson N, Khetarpal U, Gutierrez-Espeleta G, Bieber F, Morton C (1994) Isolation of novel and known genes from a human fetal cochlear cDNA library using subtractive hybridization and differential screening. Genomics 23:42–50

    Google Scholar 

  • Souter M, Lindsey K (2000) Polarity and signalling in plant embryogenesis. J Exp Bot 51:971–983

    Article  CAS  PubMed  Google Scholar 

  • Stekel D, Git Y, Falciani F (2000) The comparison of gene expression from multiple cDNA libraries. Genome Res 10:2055–2061

    Article  CAS  PubMed  Google Scholar 

  • Tang S, Yu JK, Slabaugh B, Shintani K, Knapp J (2002) Simple sequence repeat map of the sunflower genome. Theor Appl Genet 105:1124–1136

    Google Scholar 

  • Torres-Ruiz R, Jürgens G (1994) Mutations in the FASS gene uncouple pattern formation and morphogenesis in Arabidopsis development. Development 120:2967–2978

    CAS  PubMed  Google Scholar 

  • West M, Harada JJ (1993) Embryogenesis in higher plants: an overview. Plant Cell 5:1361–1369

    PubMed  Google Scholar 

  • Williams RW, Rubin GM (2002) ARGONAUTE1 is required for efficient RNA interference in Drosophila embryos. Proc Natl Acad Sci USA 99:6889–6894

    Article  CAS  PubMed  Google Scholar 

  • Zimmerman JL (1993) Somatic embryogenesis: a model for early development in higher plants. Plant Cell 5:1411–1423

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

We thank Nathalie Ladouce for her technical support, Philippe Anson for protoplast production and Sébastien Moretti for assistance in EST annotation. This work was supported by grants from the Toulouse Genomics Center (French Network of Genomics Centers) and the Conseil Régional de Midi-Pyrénées (programme Génomique et PostGenomique). CT is supported by a doctoral fellowship of the French government

Author information

Authors and Affiliations

  1. Laboratoire de Biotechnologie et Amélioration des Plantes, Pôle de Biotechnologie Végétale, IFR40, Institut Nationale Polytechnique de Toulouse-Ecole Nationale Supérieure de Toulouse, 18 Chemin de Borde Rouge, Auzeville, 31326, Castanet Tolosan, France

    C. Tamborindeguy, C. Ben, T. Liboz & L. Gentzbittel

Authors
  1. C. Tamborindeguy
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. C. Ben
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. T. Liboz
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. L. Gentzbittel
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to L. Gentzbittel.

Additional information

Communicated by R. Hagemann

Rights and permissions

Reprints and permissions

About this article

Cite this article

Tamborindeguy, C., Ben, C., Liboz, T. et al. Sequence evaluation of four specific cDNA libraries for developmental genomics of sunflower. Mol Genet Genomics 271, 367–375 (2004). https://doi.org/10.1007/s00438-004-0989-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00438-004-0989-5

Keywords

Search

Navigation