Max Planck Institute for Molecular Genetics
Max Planck Institute for Molecular Genetics - Ihnestraße 73 - 14195 Berlin - Germany - Phone: (+49 30) 8413 0 - Fax: (+49 30) 8413 1388
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 Evolution and Development Group

Evolution and Development

Sea Urchin

Amphioxus
RESEARCH INTERESTS
  Genome Evolution
  Gene duplication and evolution of gene function
  Gene orthology
GENERATED RESOURCES
  An Amphioxus gene catalogue
PUBLICATION RELATED MATERIAL
  An Amphioxus gene catalogue and the 2R hypothesis Panopoulou et al., 2003
PUBLICATIONS
  Publications
PEOPLE IN AMPHIOXUS RELATED PROJECTS IN THE GROUP
  List of People


GENERATED RESOURCES

An Amphioxus gene catalogue

We have generated a non-redundant catalogue comprised of 14,000 ESTs of amphioxus (Branchiostoma floridae) genes expressed at gastrula (5-6hrs) and neurula stages (26hrs). The cDNA clones to be EST sequenced were selected as representing different transcripts according to the prior to sequencing oligonucleotide fingerprinting normalisation step that was applied to the cDNA libraries.

Oligonucleotide Fingerprinting is based on the sequential hybridisation of short oligonucleotides (8mers) on high density arrays of clones creating a sequence based hybridisation pattern (fingerprint) of positive or negative signals for each clone (Meier-Ewert, S.et al.,(1993). An automated approach to generating expressed sequence catalogues. Nature 351:375-6, Clark, M. D.et al.(1999) Construction and analysis of arrayed cDNA libraries. Methods in Enzymology 303:205-33). Clones sharing similar fingerprints and therefore highly overlapping sequence are grouped together in Clusters of clones, while unique clones remain unclustered (singletons).

Oligonucleotide fingerprinting has several advantages over biochemical normalisation methods:

  • conventional oligodT cDNA libraries without additional manipulations which might result in the destortion of the representation of transcripts, can be used.
  • the information on the relative expression levels of each transcript is retained. The size of each Cluster is an indication of how abundant is the gene encoded by each of the clones that belong to this cluster.
  • the fingerprint information for each clone is retained and can be used for recognising the same transcript in the subsequently fingerprinted libraries
  • clustering of the fingerprints of transcripts from different tissue libraries of the same organisms can indicate the transcripts that are differentially expressed.

The fingerprinting results on the two amphioxus cDNA libraries used for the EST sequencing are explained in Panopoulou et. al. submitted.

These results will appear in the future through this page.
At present all single ESTs generated are available for blast searches at dbEST while single clones can be ordered at RZPD (Resource center-Primary Database).

Through this page the consensus of these single ESTs are available for similarity searches.

Blast against the consensus sequences of amphioxus (Branchiostoma floridae species) single 5' ESTs !!!

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