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Home page > Research > Metabolic Genomics Group > Bioinformatics sequence analysis > Laboratory of bioinformatics sequence analysis (LABIS)

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Laboratory of bioinformatics sequence analysis (LABIS)





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Vitis vinifera
©M. ADRIAN /INRA
We are in the process of analyzing the sequence of the genome of the grapevine. A partial version of the assembly has revealed that this species has a proteome enriched in genes implicated in the synthesis of aromatic compounds. Furthermore, this sequence has not undergone numerous rearrangements since the origin of dicotlyledons, and in particular no recent whole genome duplication event of the type which has occurred in Arabidopsis thaliana and Populus trichocarpa. This characteristic has turned out to be an advantage, revealing that three different genomes have contributed to the structure of the karyotype of their last common ancestor. The genome of the grapevine is an excellent but unexpected model for the study of the evolution of flowering plants.

The eukaryotic genome analysis team studies the structure and evolution of eukaryotic genomes [using data] from sequencing projects, in partnership with laboratories from the Institut Genomique, or in collaboration with outside laboratories.

 
 

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Tetraodon nigroviridis

We have analyzed the DNA sequence of the fish, Tetraodon nigroviridis because of its very small size, 8 times smaller than the human sequence. The level of conservation of genes of these two species after 400 million years of evolution since their separation made it possible for us to estimate the number of genes in humans in 2000. In 2004, the reconstitution in silico of the chromosomes of Tetraodon provided evidence for a whole genome duplication event in this lineage. This duplication, which is called 3R by evolutionary biologists, had been previously suggested as one of the hypotheses which could explain the success of the teleost bony fish group, with their large number of species adapted to numerous different ecosystems.
 
 
  Analysis

For each species we perform a certain number of analyses relating to structural, functional and/or evolutionary characterization, in collaboration with other laboratories. We have developed savior-faire in the discovery of ancestral total genome duplication events (WGD) and other polypoloidizations. This type of evolutionary event is thought to be an essential agent in the acquisition of new functions and in the emergence of new species. Major evolutionary lineages such as those of teleost vertebrates or angiosperm plants almost certainly derive from polyploidizations. For these studies, the sequences of the genomes of the fish Tetraodon nigroviridis, the grapevine Vitis vinifera and the ciliate Paramecium tetraurelia are excellent models.
 
 

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Duplications of the Paramecium’s genome

The sequence of the genome of the macronucleus of Paramecium spectacularly conserves the trace of at least 3 whole genome duplications during evolution (the outer part of circle represents more recent events, inner parts of the circle, more ancient). Although very few duplicated genes remain following whole genome duplications (fish, plants, yeast), in this case 24 000 genes, representing 68% of the total, are maintained in 2 copies following the most recent duplication. Furthermore, very few chromosome rearrangements have occurred because the order of the genes has been preserved. These characteristics, essentially the large number of genes duplicated at three different evolutionary periods, show that the loss of genes is strongly constrained over the short term. In particular, the stochiometric effects on genes implicated in interactions is very strong.

Projects

 Tetraodon nigroviridis (link, GGB)
 Paramecium tetraurelia (link, GGB)
 Vitis vinifera (link, GGB)
 Oikopleura dioica (link, GGB)
 Tuber melanosporum (link, GGB)

Last update on 15 October 2013

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