Fig. 5
From: Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes
Genomic characteristics of elusive genes and their non-elusive paralogs in the P. picta genome. (a) Fractions of the 259 elusive genes flanked by other elusive genes (100 kb on both ends). The expected values, which assumed a random distribution of elusive genes, are shown in a dotted line. The observed and expected values are significantly different (p = 8.27 × 10− 27, the exact test of goodness-of-fit). (b) Frequency distributions of the genes flanking the elusive and non-elusive genes related to the numbers of species retaining the orthologs. The genes that harbored one or more actinopterygians or coelacanth orthologs were used. The two distributions are significantly different from each other (p = 4.18 × 10− 19, Mann–Whitney U test). (c) Comparison of synonymous substitution rates (KS) between the genes flanking the elusive and the non-elusive genes. The distributions are significantly different between the two groups (p = 1.23 × 10− 17, Mann–Whitney U test). The KS values were computed for the individual ortholog pairs of the Madagascar ground gecko and Japanese gecko. (d) Gene densities of the flanking regions of the elusive genes and their non-elusive paralogs, which are significantly different from each other (p = 4.44 × 10− 16, Wilcoxon signed-rank test). Each dot denotes the gene densities of the flanking regions of an elusive gene and its non-elusive paralog. (e) Repeat densities of the genomic regions consisting of the elusive genes or non-elusive paralogs with their flanking regions, which are significantly different between the two groups (p = 1.58 × 10− 4, Wilcoxon signed-rank test). The repeats annotated with RepeatMasker excluding simple repeats and low-complexity regions were used. (f) GC content of the genomic regions consisting of the elusive genes or non-elusive paralogs with their flanking regions, which exhibit a significant difference between the two groups (p = 1.11 × 10− 10, Wilcoxon signed-rank test)