cyanea, on the one hand, and S. viridis, S. azurea and S. marina, on the other hand, was generated with the Genome-to-Genome Distance Calculator (GGDC) [56-58]. This system calculates the distances by comparing the genomes to obtain HSPs (high-scoring segment pairs) and interfering distances necessary via a set of formulas (1, HSP length / total length; 2, identities / HSP length; 3, identities / total length). For convenience the GGDC also reports model-based DDH estimates along with their confidence intervals [58]. Table 5 shows the results of the pairwise comparison. Table 5 Pairwise comparison of S. cyanea with S. viridis, S. azurea and S. marina using the GGDC (Genome-to-Genome Distance Calculator). The comparison of S. cyanea with S. azurea reached the highest scores using the GGDC, 71% of the average of genome length are covered with HSPs.
The identity within the HSPs was 85%, whereas the identity over the whole genome was 61%. The lowest similarity scores were observed in the comparison of S. cyanea with S. marina with only 28% of the average of both genome lengths covered with HSPs. The identity within these HSPs was 79%, whereas the identity over the whole genome was only 22%. With regard to S. cyanea and S. azurea the corresponding DDH estimates were below the 70% threshold under formulas 1-3 throughout: 52.6% (��3), 28.6% (��3) and 45.4% (��3). The DDH estimates confidence intervals are given in parentheses as provided by [58]. The remaining pairings resulted in even smaller DDH estimates (data not shown).
As expected, those distances relating HSP coverage (formula 1) and number of identical base pairs within HSPs to total genome length (formula 3) are higher between S. cyanea and S. azurea than between S. cyanea and S. viridis or S. marina, respectively. That the distances relating the number of identical base pairs to total HSP length (formula 2) behave differently indicates that the genomic similarities between all four type strain genomes are strongly restricted to more conserved sequences, a kind of saturation phenomenon [56]. In order to further compare the genomes of S. cyanea, S. viridis, S. azurea and S. marina, correlation values (Pearson coefficient) according to the similarity on the level of COG category, pfam and TIGRfam were calculated (see Table 6). The highest correlation value (0.97) was reached for S. cyanea and S.
azurea on the level of pfam data; the correlation values on the basis of COG and TIGRfam data were only slightly smaller with 0.96 and 0.93, respectively. As a correlation value of 1 indicates the highest correlation, we can find a very high correlation between the genomes of S. cyanea and S. azurea considering the above data [55]. Table 6 Carfilzomib Pearson’s correlation coefficients according to the similarity on the level of Pfam, COG category and TIGRfam (in this order and separated by slashes). The synteny dot plots in Figure 4 shows nucleotide-based comparisons of the genomes of S.