An analysis of the genome of Ciona intestinalis.

An analysis by CsCl density gradient centrifugation has shown that, at a fragment size of about 100 kb, the DNA of a urochordate, Ciona intestinalis, is remarkably homogeneous in base composition. Localization of 16 coding sequences from C. intestinalis, chosen so as to cover the distribution range of all available coding sequences for this organism, showed a nearly symmetrical distribution almost coinciding with the DNA distribution. Both distributions are remarkably different from those found in vertebrates, which are skewed towards high GC levels (to a greater extent in warm-blooded vertebrates). In order to account for this change in genome organization, we propose a working hypothesis that can be tested. Basically, we suggest that the genome duplication that occurred between urochordates and fishes was accompanied by a preferential integration of transposons in one compartment of the genome, which was made gene-poor (by lowering gene density) compared to the rest. Since the gene-poor compartment (the 'empty quarter') is characterized by a lower level of gene expression compared to the gene-rich compartment (the 'genome core') in the vertebrate genome, we further suggest, as a working hypothesis, that a compartmentalization according to gene expression already existed in urochordates.