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Table 1 Number and sources of genomes and sequences used in this study broken down into taxonomic categories

From: The conservation and evolutionary modularity of metabolism

Domain Taxonomic grouping Partial genomes Partial genome sequences Complete genomes Complete genome sequences nrsequences Total sequences
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
  1. 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].