Table 2.
Gene duplication prevalence in different species of amphioxus and vertebrates. Genes in each species were filtered for proper correspondence between gene annotation and protein sequence (see numbers in Table S6). For example, from the 26,468 B. lanceolatum genes with strong evidence (see the “Methods” section), we used 25,946 genes for the orthology analysis. Percentages are calculated from the total number of genes or the total number of orthogroups in each species, respectively
| Genes | Amphioxus–vertebrate orthologous genes | Orthogroups | Mean # of genes in duplicated orthogroups | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Lineage | Species | Total | Duplicated | % | Total | Duplicated | % | Total | Duplicated | % | |
| Amphioxus | B. lanceolatum | 25946 | 11973 | 46.1 | 15269 | 8520 | 55.8 | 12691 | 2468 | 19.4 | 4.9 |
| B. floridae | 20541 | 10192 | 49.6 | 13074 | 7578 | 58.0 | 10568 | 1934 | 18.3 | 5.3 | |
| B. belcheri | 18413 | 8469 | 46.0 | 11944 | 6354 | 53.2 | 10533 | 1805 | 17.1 | 4.7 | |
| Vertebrates | D. rerio | 23912 | 13510 | 56.5 | 16664 | 11504 | 69.0 | 10587 | 3727 | 35.2 | 3.6 |
| G. gallus | 16558 | 7416 | 44.8 | 12250 | 6630 | 54.1 | 10455 | 2399 | 22.9 | 3.1 | |
| M. musculus | 21691 | 10660 | 49.1 | 14447 | 8518 | 59.0 | 12236 | 2847 | 23.3 | 3.8 | |
| H. sapiens | 19715 | 9799 | 49.7 | 13802 | 8015 | 58.1 | 12205 | 2997 | 24.6 | 3.3 | |