Table 2.
Composition of the clades of OrthoDB v10 used by BRAKER2
| # of species in the OrthoDB clade | ||||||||
|---|---|---|---|---|---|---|---|---|
| Species | Genus | Family | Order | Class | Phylum | Kingdom | Name of the largest OrthoDB segment | # of proteins in the OrthoDB segment |
| A. thaliana | 2 | 8 | 10 | 100 | 117 | Plantae | 3 510 742 | |
| C. elegans | 3 | 3 | 5 | 6 | 7 | 448 | Metazoa | 8 266 016 |
| D. melanogaster | 20 | 20 | 56 | 148 | 170 | Arthropoda | 2 601 995 | |
| P. trichocarpa* | 1 | 5 | 5 | 100 | 117 | Plantae | 3 510 742 | |
| M. truncatula | 1 | 10 | 10 | 100 | 117 | Plantae | 3 510 742 | |
| S. lycopersicum | 2 | 10 | 11 | 100 | 117 | Plantae | 3 510 742 | |
| B. terrestris* | 1 | 7 | 40 | 148 | 170 | Arthropoda | 2 601 995 | |
| R. prolixus | 1 | 1 | 16 | 148 | 170 | Arthropoda | 2 601 995 | |
| P. tepidariorum | 1 | 1 | 2 | 10 | 170 | Arthropoda | 2 601 995 | |
| T. nigroviridis* | 0 | 1 | 1 | 50 | 246 | Chordata | 5 003 104 | |
| D. rerio | 1 | 5 | 5 | 50 | 246 | Chordata | 5 003 104 | |
| X. tropicalis | 2 | 2 | 3 | 3 | 246 | Chordata | 5 003 104 | |
Numbers in black bold show the largest numbers of species used to support gene predictions for a given species (left column). The numbers of species removed from the largest OrthoDB segment in the tests described below are shown in blue. Species whose proteins are not present in OrthoDB v10 are marked with asterisks.