Gene organization features in A/T-rich organisms.
Several species have genomes in which the four nucleotides are not equally represented (Glöckner 2000). Interestingly, shifts to very high A/T or G/C levels can occur in several distinct branches of the tree of life. The underlying reasons for these shifts therefore may be of different origin. Now entire chromosome sequences from two different A/T-rich genomes, Dictyostelium discoideum and Plasmodium falciparum, are available (Bowman et al. 1999; Gardner et al. 2002; Glöckner et al. 2002). This gives us the opportunity to investigate how a high A/T content may influence the signals that are the landmarks for gene specification. We found that, in contrast with most known metazoan and plant genomes, splice signals contain, little information other than the canonical GT-AG dinucleotides. Intron lengths in A/T rich organisms, on the other hand, are comparable to those of other lower eukaryotes. Intergenic regions show, dependent on the orientation of adjacent genes, a size pattern with a ratio of 1 (3'-3') to 2 (3'-5') to 3 (5'-5'). Overall, gene organization patterns seem not to be influenced by the A/T bias. Surprisingly, the slightly higher A/T content of the P. falciparum genome compared to that of D. discoideum (80.1 versus 77.4%) is not achieved by increased A/T richness in intergenic regions. Instead both the shift of the nucleotide usage in coding regions to A/T-rich codons and the longer intergenic regions make an equal contribution to the higher A/T content in this organism.
Szafranski
Karol
K
Department of Genome Analysis, Institute for Molecular Biotechnology Jena, Beutenbergstr. 11, D-07745 Jena, Germany.
Lehmann
Rüdiger
R
Parra
Genis
G
Guigo
Roderic
R
Glöckner
Gernot
G
D020856:AT Rich Sequence / Q000235:genetics*; D017398:Alternative Splicing / Q000235:genetics; D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D001482:Base Composition / Q000235:genetics; D001483:Base Sequence; D021901:DNA, Intergenic / Q000235:genetics; D004023:Dictyostelium / Q000235:genetics*; D005091:Exons; D005800:Genes, Fungal / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D017125:Genes, Protozoan / Q000235:genetics*; D007438:Introns; D010963:Plasmodium falciparum / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D013045:Species Specificity
D021901:DNA, Intergenic