Fig. 2

Phylogenies, genome sizes and sequence distribution. Left side: Fungal (top) and algal (bottom) PhyML trees (LG + G + F + I) for C. grayi and A. glomerata involving, respectively, a random sample of 6000 and 4000 ungapped sites extracted from a concatenated alignment of 2137 and 683 orthologous protein families containing 794,828 and 159,356 ungapped sites. Bootstrap support values label internodes. Scales indicate nucleotide substitutions per site. Right side: Bars are proportional to genome size, and different shadings indicate the proportions of recent and older sequence replicas or of unique sequences. Duplicated sequences in genomes were revealed by BLAST alignment of the genomic sequence against itself at the nucleotide (BLASTN) or amino acid (TBLASTX) levels. The duplicated regions include regular genes as well as repeated elements (not yet fully characterized), but microsatellites and low complexity sequences were filtered out. Sequences that matched in both BLASTN and TBLASTX searches were only counted in the BLASTN category. Only alignments with e-values <1e^− 15 in both the BLASTN and TBLASTX analyses were considered