The nuclear genome of unicellular eukaryotes

In this chapter, we will concentrate on the compositional patterns and gene distribution found in the very different genomes of unicellular eukaryotes. 

In conclusion, the compositional patterns of the Trypanosome genomes indicate that compartmentalization is a phylogenetically very widespread situation in eukaryotes, as already predicted (Bernardi et al., 1985b). 

A striking feature of P. falciparum, the unicellular parasite responsible for the most virulent and widespread form of human malaria, is that it hosts the GC-poorest (22% GC) nuclear genome known so far (Poliak et al., 1982, McCutchan et al., 1984). This genome, which only comprises 3 Mb of DNA (Weber, 1988) organized in 14 chromosomes (Kemp et al., 1987 Wellems et al., 1987), is, therefore, an excellent model for studying compositional constraints and their effects. 

The analysis of sequence data has provided useful information about the genes encoded in the nuclear genome of P. falciparum. The most relevant features are the following (i) the coding strand is purine-rich (ii) A is predominant in all codon positions (iii) the third codon positions are extremely GC-poor and, as a consequence, codon usage is strongly biased (Weber, 1988 Hyde and Sims, 1987). 

In an analysis of the nuclear coding sequences from P. falciparum, comprising 175 kb (Musto et al., 1995), we found that the trends described previously with more limited data sets are still valid. We then tried to understand whether the biases already noted are species-specific or determined by the composition of the genome, and whether they are different for sequences that display different expression levels and certainly are under different evolutionary pressures, like housekeeping and antigen genes (see also Part 11). 

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