Table 1 |
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|
Number and sources of genomes and sequences used in this study broken down into taxonomic categories |
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|
Domain |
Taxonomic grouping |
Partial genomes |
Partial genome sequences |
Complete genomes |
Complete genome sequences |
nr sequences |
Total sequences |
|
|
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|
Archaea |
Crenarchaeota |
- |
- |
4 |
11,120 |
12,339 |
23,459 |
|
Archaea |
Euryarchaeota |
- |
- |
14 |
30,396 |
38,863 |
69,259 |
|
Archaea |
Archaea - Other |
- |
- |
1 |
563 |
3,180 |
3,743 |
|
Archaea |
Total |
- |
- |
19 |
42,079 |
54,382 |
96,461 |
|
Bacteria |
Actinobacteridae |
- |
- |
14 |
49,608 |
68,041 |
117,649 |
|
Bacteria |
Alphaproteobacteria |
- |
- |
14 |
48,997 |
81,233 |
130,230 |
|
Bacteria |
Betaproteobacteria |
- |
- |
9 |
37,184 |
51,947 |
89,131 |
|
Bacteria |
Gammaproteobacteria |
- |
- |
27 |
94,933 |
188,458 |
283,391 |
|
Bacteria |
Deltaproteobacteria |
- |
- |
4 |
13,778 |
15,449 |
29,227 |
|
Bacteria |
Epsilonproteobacteria |
- |
- |
4 |
7,128 |
16,452 |
23,580 |
|
Bacteria |
Cyanobacteria |
- |
- |
6 |
20,983 |
32,380 |
53,363 |
|
Bacteria |
Firmicutes |
- |
- |
31 |
72,975 |
163,215 |
236,190 |
|
Bacteria |
Spirochaetes |
- |
- |
4 |
10,163 |
18,324 |
28,487 |
|
Bacteria |
Bacteria - Other |
- |
- |
14 |
36,760 |
61,550 |
98,310 |
|
Bacteria |
Total |
- |
- |
127 |
392,509 |
697,049 |
1,089,558 |
|
Eukarya |
Protist - Alveolata |
10 |
29,707 |
2 |
8,691 |
24,211 |
62,609 |
|
Eukarya |
Protist - Euglenozoa/Haptophyceae/Stramenophiles |
7 |
13,846 |
1* |
11,397* |
9,484 |
34,727 |
|
Eukarya |
Protist - Other |
- |
- |
- |
- |
12,862 |
12,862 |
|
Eukarya |
Protists - Total |
17 |
43,553 |
3 |
20,088 |
46,557 |
110,198 |
|
Eukarya |
Fungi - Ascomycota |
17 |
44,358 |
9 |
52,271 |
67,765 |
164,394 |
|
Eukarya |
Fungi - Basidiomycota |
7 |
14,785 |
1† |
431† |
10,264 |
25,049 |
|
Eukarya |
Fungi - Glomeromycota/Zygomycota |
3 |
3,398 |
- |
- |
734 |
4,132 |
|
Eukarya |
Fungi - Other |
- |
- |
1 |
1,996 |
2,558 |
4,554 |
|
Eukarya |
Fungi - Total |
27 |
62,541 |
10 |
52,271 |
78,763 |
193,575 |
|
Eukarya |
Metazoa - Lophotrochozoa |
4 |
14,631 |
- |
- |
12,416 |
27,047 |
|
Eukarya |
Metazoa - Arthropods/Tardigrades |
17 |
22,528 |
2 |
33,585 |
95,953 |
152,066 |
|
Eukarya |
Metazoa - Deuterostomes |
21 |
90,244 |
2 |
57,406 |
276,682 |
424,332 |
|
Eukarya |
Metazoa - Nematoda |
34 |
95,345 |
2 |
39,464 |
38,657 |
173,466 |
|
Eukarya |
Metazoa - Other |
- |
- |
- |
- |
3,424 |
3,424 |
|
Eukarya |
Metazoa - Total |
76 |
222,748 |
6 |
130,455 |
427,132 |
780,335 |
|
Eukarya |
Plantae |
76 |
221,896 |
2 |
30,533 |
190,711 |
443,140 |
|
Eukarya |
Total |
196 |
550,738 |
21 |
233,347 |
743,163 |
1,527,248 |
|
Total |
196 |
550,738 |
167 |
667,935 |
1,494,594 |
2,713,267 |
|
|
|
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|
All partial genome sequences were obtained from PartiGeneDB [26]. Complete genome sequences refer to protein coding sequences obtained from the COGENT database [56] with the exception of those marked with an asterix, which represents the genome of Thalassiosira pseudonana, obtained from the Joint Genome Institute [58], and those marked with a dagger, which represent the genome contigs of Coprinopsis cinerea, obtained from the Broad Institute [59]. |
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|
Peregrín-Alvarez et al. Genome Biology 2009 10:R63 doi:10.1186/gb-2009-10-6-r63 |
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