Table 2

Mean percentage amino acid identity of 454 reads matching database reference genes (NCBI-nr) shared between and unique to DNA and RNA samples

Percentage identity to reference genes present ina


Depth (m)

Data

DNA+RNAb

DNA onlyc

RNA only

Alld


OMZ

50

DNA

71.0

59.8

NA

60.8

RNA

73.8

NA

72.2

72.7

85

DNA

67.3

59.5

NA

59.8

RNA

68.4

NA

67.9

68.1

110

DNA

65.7

58.7

NA

59.7

RNA

68.5

NA

71.1

70.2

200

DNA

64.3

58.5

NA

59.1

RNA

67.0

NA

65.9

66.4

BATS 216

20

DNA

72.5

59.5

NA

62.7

RNA

75.6

NA

71.6

72.9

50

DNA

76.4

61.5

NA

64.4

RNA

78.3

NA

71.2

74.1

100

DNA

76.8

60.5

NA

63.9

RNA

78.6

NA

71.6

74.8

HOT 186

25

DNA

75.3

63.7

NA

65.7

RNA

76.4

NA

69.1

72.0

75

DNA

77.3

64.1

NA

65.6

RNA

77.5

NA

69.1

72.9

110

DNA

80.0

60.7

NA

62.4

RNA

81.3

NA

73.0

77.1

500

DNA

63.1

59.4

NA

59.6

RNA

64.0

NA

66.0

65.0

Soil

Surface

DNA

58.9

55.0

NA

56.1

RNA

59.8

NA

61.1

60.5


aMean percentage identity across all genes (unique accession numbers) identified via BLASTX against NCBI-nr (HSP alignment regions only; bit score cutoff = 50). bGenes present in both DNA and RNA datasets, that is, 'expressed' genes. cGenes present only in the DNA dataset, that is, 'non-expressed' genes. dGenes shared between datasets (in DNA + RNA) plus genes unique to a dataset. BATS, Bermuda Atlantic Time Series; BLAST, Basic Local Alignment Search Tool; HOT, Hawaii Ocean Time Series; HSP, high-scoring segment pair; NA, not applicable; NCBI-nr, National Center for Biotechnology Information non-redundant protein database; OMZ, oxygen minimum zone; rRNA, ribosomal RNA.

Stewart et al. Genome Biology 2011 12:R26   doi:10.1186/gb-2011-12-3-r26

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