Table 2 Flowchart and main outcomes of each analysis performed in this study
Analysis | Outcome |
|---|---|
Identification of all vertebrate species that can be characterized as living fossil or radiated species, with available whole genome sequencing data and complete gene annotation | 20 living fossil species 24 radiated species |
Genes in common per group | Living fossil species: 2861 genes in common Radiated species: 3590 genes in common |
Genes in common per group, not found in the other group | Living fossil species: 1534 unique genes Radiated species: 2263 unique genes |
Pathway (biological processes) and reactome analyses, unique ones | Living fossil species: 0 pathways, 2 reactomes Radiated species: 7 pathways, 2 reactomes |
Significant process revealed by both algorithms | Living fossil species: None Radiated species: DNA repair and cellular response to DNA damage (FDR = 8.35 × 10−5; 7.15 × 10−6, respectively) |
Search for 151 known DNA repair genes in the 45 species’ genomes Mean comparison analysis | More DNA repair genes in radiated species than in living fossil species (p = 5.3 × 10−3) Most significant gene subcategory: Nucleotide excision repair (p = 5.00 × 10−4) |
Linear regression: DNA repair genes number vs genome size or protein number | Genome size/protein number is linearly related with the number of DNA repair genes (p < 1.0 × 10−4) |