Table 1 |
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Species included in the present phylome and their genomic coverage |
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| Group |
Code |
Species name |
Source |
Proteins included (%) |
Trees (%) |
|
|
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| Primates |
Hsa |
Homo sapiens |
Ensembl |
21,726 (99.1%) |
21,588 (100.0%) |
| Ptr |
Pan troglodytes |
Ensembl |
17,113 (79.3%) |
19,577 (90.7%) |
|
| Mmu |
Macaca mulatta |
Ensembl |
19,285 (89.2%) |
19,765 (91.6%) |
|
| Placental mammals |
Mms |
Mus musculus |
Ensembl |
19,934 (78.9%) |
18,825 (87.2%) |
| Rno |
Rattus norvegicus |
Ensembl |
18,675 (85.7%) |
18,585 (86.1%) |
|
| Cfa |
Canis familiaris |
Ensembl |
16,657 (91.8%) |
18,834 (87.2%) |
|
| Bta |
Bos taurus |
Ensembl |
18,457 (79.9%) |
18,736 (86.8%) |
|
| Mammals |
Mdo |
Monodelphis domestica |
Ensembl |
17,004 (80.7%) |
18,013 (83.4%) |
| Vertebrates |
Gga |
Gallus gallus |
Ensembl |
12,325 (66.5%) |
15,758 (73.0%) |
| Xtr |
Xenopus tropicalis |
Ensembl |
14,721 (60.6%) |
15,787 (73.1%) |
|
| Tni |
Tetraodon nigroviridis |
Ensembl |
14,896 (53.4%) |
14,585 (67.6%) |
|
| Fru |
Fugu rubripes |
Ensembl |
15,834 (72.3%) |
15,155 (70.2%) |
|
| Dre |
Danio rerio |
Ensembl |
16,042 (74.9%) |
14,808 (68.6%) |
|
| Chordates |
Cin |
Ciona intestinalis |
Ensembl |
5,588 (50.9%) |
9,421 (43.6%) |
| Metazoa |
Aga |
Anopheles gambiae |
Ensembl |
6,131 (43.0%) |
9,310 (43.1%) |
| Dme |
Drosophila melanogaster |
Ensembl |
6,812 (49.6%) |
9,771 (45.3%) |
|
| Ame |
Apis mellifera |
Ensembl |
4,484 (33.4%) |
8,616 (39.9%) |
|
| Cel |
Caenorhabditis elegans |
Ensembl |
5,826 (29.8%) |
8,190 (37.9%) |
|
| Cbr |
Caenorhabditis briggsae |
Integr8 |
5,171 (39.2%) |
7,899 (36.6%) |
|
| Opisthokonts |
Ago |
Ashbya gossypii |
Integr8 |
2,020 (42.8%) |
3,603 (16.7%) |
| Cal |
Candida albicans |
Other |
2,733 (33.8%) |
3,899 (18.1%) |
|
| Cgl |
Candida glabrata |
Integr8 |
2,129 (41.1%) |
3,627 (16.8%) |
|
| Cne |
Cryptococcus neoformans |
Integr8 |
2,532 (38.5%) |
4,102 (19.0%) |
|
| Dha |
Debaromyces hansenii |
Integr8 |
2,302 (36.5%) |
3,885 (18.0%) |
|
| Ecu |
Encephalitozoon cuniculi |
Integr8 |
626 (32.8%) |
1,203 (5.6%) |
|
| Gze |
Giberella zeae |
Integr8 |
3,076 (26.4%) |
4,412 (20.4%) |
|
| Kla |
Kluyveromyces lactis |
Integr8 |
2,077 (39.1%) |
3,715 (17.2%) |
|
| Ncr |
Neurospora crassa |
Other |
2,521 (23.7%) |
4,221 (19.6%) |
|
| Sce |
Saccharomyces cerevisiae |
Ensembl |
2,317 (35.1%) |
3,769 (17.5%) |
|
| Spb |
Schizosaccharomyces pombe |
Integr8 |
2,421 (48.8%) |
4,102 (19.0%) |
|
| Yli |
Yarrowia lipolytica |
Integr8 |
2,487 (38.1%) |
4,152 (19.2%) |
|
| Amoebozoa |
Ddi |
Dictyostelium discoideum |
Integr8 |
3,843 (29.4%) |
5,165 (23.9%) |
| Plants |
Ath |
Arabidopsis thaliana |
Integr8 |
9,450 (26.6%) |
5,390 (25.0%) |
| Cre |
Chlamydomonas reinhardtii |
Other |
2,303 (11.7%) |
3,504 (16.2%) |
|
| Diplomonad |
Gth |
Gillardia theta |
Integr8 |
161 (35.7%) |
458 (2.1%) |
| Apicomplexa |
Pfa |
Plasmodium falciparum |
Integr8 |
1,330 (25.3%) |
2,507 (11.6%) |
| Pyo |
Plasmodium yoelii |
Integr8 |
1,188 (15.3%) |
2,272 (10.5%) |
|
| Kinetoplastida |
Lma |
Leishmania major |
Integr8 |
2,082 (26.0%) |
3,130 (14.5%) |
| Pte |
Paramecium tetraurelia |
Integr8 |
140 (30.2%) |
345 (1.6%) |
|
|
|
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|
For each species: the 'Proteins included' column indicates the number of proteins present in trees of the human phylome and the percentage they represent; and the 'Trees' column indicates the number of trees in the phylome with proteins from that species (and the percentage from the phylome it represents). 'Source' indicates the database from which the protein data for that species were retrieved. |
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|
Huerta-Cepas et al. Genome Biology 2007 8:R109 doi:10.1186/gb-2007-8-6-r109 |
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