and C. elegans
essentially show a very predominant L1 isochore family and a minor L2 family, a compositional pattern mimicking that of zebrafish. The case of C. intestinalis
is of interest because a previous investigation by analytical ultracentrifugation in a CsCl density gradient had shown a remarkable homogeneity at an average molecular weight of 100 kb [12
]. The apparent discrepancy can, however, be explained by the fact that the CsCl investigation dealt with random fragments, whereas the present one with 100 kb unique segments. The latter show an average standard deviation of 1.3% GC (Cammarano R., Ph.D. Thesis) a value very slightly above the average standard deviation of 100 kb segments from human isochores from the L1 and L2 families. The dinucleotide patterns (observed/expected) present some significant differences (e.g. TA being much lower than AT in C. elegans
, but not in C. intestinalis
), which are also expectedly shown by trinucleotides.
Among insects, the Drosophilids exhibit similar isochore patterns that are intermediate between those of medaka and stickleback with a major H1 family and two minor L2 and H1 families. Another point of interest is the close similarity of GC levels of the isochore families as assessed on Drosophilids and Anopheles (see Table ). The compositional pattern of A. gambiae, although being mainly represented by H1 isochores, shows a substantial amount of H2 isochores. In fact, the GC-richer isochores of A. gambiae have probably been underestimated because of the presence of a large number of 100-kb GC-rich stretches that were pooled with the flanking regions because of the procedure used in assessing isochores (see below).
In the other cases, certainly a number of factors played a role and led to different compositional patterns. Indeed, we already noted that while the large evolutionary changes in isochore patterns occurring between mammals/birds and amphibians/fishes mainly depend upon body temperature, definitely other factors play a role as well in the case of fishes.
The average sizes exhibited by different isochore families of invertebrates showed a greater variability compared to those of the corresponding families from vertebrates [1
]. This may be due, however, to artefactual reasons, such as gaps, but also to the experimental approach used. Indeed, in the human genome [9
], isochores were taken to be at least 200 kb in size, a condition linked to the need of assessing standard deviations of the 100 Kb segments used in the analysis. Expectedly, this occasionally led to standard deviation higher than 3 % GC within a given isochore. Since however this only concerned ~7% of the human genome such "transition isochores" were accepted.
In the case of C. elegans
long stretches of DNA very low in GC and belonging to L1 isochores were present and interspersed short L2 isochores were neglected. If one accepts in this case isochores reaching a low size value of 100 Kb, the very long L1 structures are resolved into shorter stretches and the high size values are brought back to the 0.5-1 Mb range. For instance, in the case of C. elegans
the large size (3.37 Mb) estimated according to the criteria of Costantini et al. [9
], is reduced to 1.00 Mb, if 100 Kb segments belonging to the GC range of L2 isochores (and averaging 0.23 Mb in size) are considered separately. This considerations also applies to the large size of major families of insects as indicated by thin 100-kb lines appearing in the GC profiles.