Table 1

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

Domain

Taxonomic grouping

Partial genomes

Partial genome sequences

Complete genomes

Complete genome sequences

nr sequences

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


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].

Peregrín-Alvarez et al. Genome Biology 2009 10:R63   doi:10.1186/gb-2009-10-6-r63

Open Data