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. 2009 Nov 30;76(2):609–617. doi: 10.1128/AEM.01258-09

TABLE 2.

BLASTx and clustering results for dmdA amplicons of the free-living size fraction from southeastern U.S. coastal seawatera

Primer name Clade Subclade % with correct clade(s) targeted % with correct subclade (of correct clade) targeted % with incorrect clade targeted % not dmdAb No. of sequences resampled Normalized no. of dmdA clustersc
dmdAU All All 94.0 N/A N/A 6.0 400 51
A/1-sp Clade A Subclade 1 99.2 99.8 0.5 0.3 2,500 30
A/2-sp Clade A Subclade 2 98.7 97.8 0.3 1.0 3,500 25
A/2-dg Clade A Subclade 2 99.1 99.4 0.1 0.8 3,500 24
A/2-ino Clade A Subclade 2 99.4 99.4 0.05 0.5 3,500 20*
B/3-sp Clade B Subclade 3 97.6 97.9 1.5 0.9 5,500 46
B/4-sp Clade B Subclade 4 33.6 99.3 65.4 0.9 1,500 20
C/2-sp Clade C Subclade 2 92.5 68.8 6.3 1.2 1,200 23
C/2-dg Clade C Subclade 2 64.2 81.8 33.8 2.0 1,200 35*
C/2-ino Clade C Subclade 2 71.7 98.8 26.2 2.2 1,200 20
D/1-sp Clade D Subclade 1 88.4 97.8 0.5 11.2 6,000 200
D/3-sp Clade D Subclade 3 99.6 91.5 0.10 0.3 4,300 30
D/3-dg Clade D Subclade 3 95.3 96.7 4.6 0.1 4,300 32
D/all-sp Clade D All 99.3d N/A 0.2 0.5 4,500 82
D/all-dg Clade D All 99.9d N/A 0.1 0 4,500 68*
D/all-ino Clade D All 99.8d N/A 0 0.2 4,500 74*
E/2-sp Clade E Subclade 2 96.65 99.99 1.58 1.77 3,000 43
E/2-dg Clade E Subclade 2 98.97 99.78 0.51 0.51 3,000 35*
a

For particle-associated data, see Table S3 in the supplemental material. N/A, not applicable.

b

Includes sequences with hits to gcvT and those with no hits.

c

Average of 1,000 resamplings (see Materials and Methods) using the population sizes indicated in the “No. of sequences resampled” column. Cluster numbers marked with an asterisk were significantly different (P < 0.05) from that obtained by the specific version of that primer pair.

d

For the D/all-sp primer pair, 16.2% of the hits were to subclade D/1 and 2.5% to subclade D/3; for the D/all-dg primer pair, 13.8% of the hits were to subclade D/1 and 6.7% to subclade D/3; and for the D/all-ino primer pair, 4.4% of the hits were to subclade D/1 and 6.3% to subclade D/3. The remaining correct hits were to clade D sequences not classified within a subclade.