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Table 4 16S rDNA sequences close to full length identified in the four datasets.

From: Comparative metagenomics of Daphnia symbionts

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. 1 Given as the ID in RDP.
  2. 2 Pasteuria ramosa, the parasite which was present in the D. magna datasets.
  3. 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. 4 The next top three unique matched species, if they were not the same as the best match
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BMC Genomics

ISSN: 1471-2164

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