Table 4.
Comparison of the Numbers of Sea Urchin Genes to the Numbers of their Ciona and Human Orthologs Assigned in the Same CD/CDY Group of Protostome and Yeast Single-Copy Genes
| Compared organisms | Number of CD/CDY groups | Number of genes | Copy rate |
|---|---|---|---|
| Sea urchin:human | 1447 groups shared | 2489:5777 | 1.7:4.0 |
| 1:1 | 390 (26.95%) | ||
| 1:>1 | 586 (40.49%) | ||
| >1:1 | 72 (4.97%) | ||
| Sea urchin:Ciona | 1394 groups shared | 2432:3498 | 1.7:2.5 |
| 1:1 | 610 (43.75%) | ||
| 1:>1 | 320 (22.9%) | ||
| >1:1 | 128 (9.18%) | ||
| Ciona:human | 2740 groups shared | 5805:9289 | 2.1:3.4 |
| 1:1 | 837 (30.54%) | ||
| 1:>1 | 842 (30.72%) | ||
| >1:1 | 185 (6.75%) | ||
| Sea urchin:Ciona:human | 1337 groups shared | 2348:3363:5411 | 1.8:2.5:4 |
| 1:1>1 | 307 (22.96%) | ||
| 1:>1:>1 | 239 (17.87%) | ||
| 1:>1:1 | 65 (4.86%) | ||
| >1:1:1 | 44 (3.29%) | ||
| 1:>1:>Ciona | 145 (10.84%) | ||
| su = ci and hum > su = ci | 357 (26.70%) | ||
| 1:1:1 | 279 (20.86%) |
As an example, ∼11% of the single-copy sea urchin genes are duplicated in both Ciona and human, but have significantly more copies in human than Ciona. The 26.70% of all sea urchin genes that were assigned to the CD/CDY system have the same copy number in Ciona but have more duplicates in human, and 20.86% of the shared single-copy CD/CDY genes are found as single copy in all three organisms. Pairwise comparison of groups that are in common between two of the organisms shows elevated duplication frequencies in vertebrates more clearly, as 43.75% of the single-copy sea urchin genes are found also as single copy in Ciona, whereas only 26.95% are present as single copy in the human genome. Accordingly, we found 40.49% and 30.72% of the sea urchin and Ciona single-copy genes, respectively, duplicated in the human genome. The copy rates are calculated from the number of genes per orthologous (CD/CDY) group.