Table 4

16S rDNA sequences close to full length identified in the four datasets.

Dataset

Sequence ID

Best matched 16S

Description of the next three matches4


ID1

Description

Bit score3

Identity (%)


D. magna GS 20

contig04123

S000437499

Daphnia endosymbiotic bacterium2

1970

99

uncultured Pasteuria sp., P. nishizawae, P. penetrans


contig03555

S000446092

aquatic bacterium R1-C1

1374

98

uncultured Cytophagales bacterium, aquatic bacterium R1-C5, uncultured bacterium


D. magna GS FLX

contig00041

S000893806

Shigella dysenteriae

2627

99

Escherichia coli W3110, E. coli K12, E. coli


contig06506

S000343002

uncultured Cytophagales bacterium

2468

96

uncultured bacterium, Flavobacterium sp. Nj-26, uncultured Flavobacteriales bacterium


contig06300

S000372741

uncultured bacterium

1947

93

Myxococcales str. NOSO-1, Chondromyces pediculatus, Polyangium thaxteri


contig06583

S000437499

Daphnia endosymbiotic bacterium2

1943

99

uncultured Pasteuria sp., P. nishizawae, P. penetrans


D. pulicaria

ANIT159445.g1

S000966592

Flavobacterium sp. MH45

1905

99

Arctic sea ice bacterium ARK10164, uncultured bacterium, Flavobacterium succinicans


ANIT198306.b1

S000799101

uncultured bacterium

1857

98

Comamonadaceae bacterium BP-1b,


ANIT159586.b1

S000639702

uncultured bacterium

1853

98

uncultured Burkholderiales bacterium, Comamonadaceae bacterium BP-1b, uncultured proteobacterium


ANIT82605.b1

S000634984

uncultured Burkholderiales bacterium

1846

99

uncultured bacterium, Comamonadaceae bacterium BP-1b, Comamonadaceae bacterium BP-1


ANIU5178.g2

S000429300

Flavobacterium sp. GOBB3-209

1653

98

uncultured bacterium, uncultured Cytophagales bacterium, uncultured Sphingobacteriales bacterium


ANIT142825.b1

S000634984

uncultured Burkholderiales bacterium

1570

98

uncultured beta proteobacterium, uncultured organism, Rhodoferax ferrireducens T118


ANIS174043.g1

S000446066

aquatic bacterium R1-B19

1485

99

uncultured beta proteobacterium, aquatic bacterium R1-B6, uncultured Burkholderiales bacterium


ANIT169338.b1

S000005772

Aeromonas eucrenophila

1465

99

Aeromonas sp. 'CDC 859-83', A. molluscorum, uncultured bacterium


ANIS242375.b1

S000658887

uncultured actinobacterium

1439

97

uncultured bacterium, Modestobacter multiseptatus, Sporichthya polymorpha


ANIS247631.y1

S000607919

Pseudomonas sp. R-25061

1419

99

Pseudomonas sp. R-25209, uncultured bacterium, P. pseudoalcaligenes


ANIU876.b3

S000948974

uncultured bacterium

1386

98

uncultured gamma proteobacterium, uncultured Pseudomonas sp., Pseudomonas sp. G2


ANIT143068.b1

S000550675

Pseudomonas sp. GD100

1318

96

Pseudomonas sp. Pb1(2006), P. poae, P. lurida


ANIT82605.g2

S000634984

uncultured Burkholderiales bacterium

1312

100

uncultured bacterium, Variovorax paradoxus, uncultured bacterium SJA-62


ANIT131207.y2

S000018838

uncultured Cytophagales bacterium

1304

91

uncultured bacterium, uncultured Bacteroidetes bacterium, rhizosphere soil bacterium RSC-II-81


ANIT102921.y2

S000895013

uncultured bacterium

1170

93

uncultured Cytophagales bacterium, uncultured Bacteroidetes bacterium, uncultured bacterium


ANIU1607.g2

S000799546

uncultured bacterium

1092

96

Hydrogenophaga sp. AH-24, Hydrogenophaga sp. CL3, Hydrogenophaga sp. YED1-18


D. pulex

scaffold_278

S000541019

Pseudomonas argentinensis

2785

98

P. argentinensis, P. fluorescens PfO-1,


scaffold_567

S000402041

uncultured bacterium

2680

97

uncultured soil bacterium, uncultured Comamonadaceae bacterium, uncultured beta proteobacterium


scaffold_1523

S000926010

Serratia proteamaculans 568

2615

96

Serratia proteamaculans 568, uncultured bacterium, uncultured proteobacterium


scaffold_6081

S000730527

Deefgea rivuli

1792

97

uncultured bacterium, Chitinibacter tainanensis, uncultured proteobacterium


scaffold_16248

S000736150

gamma proteobacterium GPTSA100-21

1711

98

gamma proteobacterium GPTSA100-22, uncultured bacterium, gamma proteobacterium GPTSA100-26


scaffold_10095

S000404820

Pseudomonas sp. Hsa.28

1378

99

uncultured bacterium, uncultured Pseudomonas sp., P. anguilliseptica


scaffold_1408

S000446066

aquatic bacterium R1-B19

1326

99

uncultured beta proteobacterium, aquatic bacterium R1-B6, aquatic bacterium R1-B7


scaffold_21984

S000656075

uncultured Pseudomonas sp.

1023

100

gamma proteobacterium LC-G-2, Pseudomonas sp. 7-1, P. fluorescens


1 Given as the ID in RDP.

2 Pasteuria ramosa, the parasite which was present in the D. magna datasets.

3 The BLAST bit scores obtained from a comparison of the contigs/scaffolds to annotated 16S rDNA sequences present in RDP are shown. A higher number indicates a more significant match.

4 The next top three unique matched species, if they were not the same as the best match

Qi et al. BMC Genomics 2009 10:172   doi:10.1186/1471-2164-10-172

Open Data