TABLE 1.

Summary of the numbers of OTUs and density indices associated with restriction endonuclease digests from 4,603 SSU rDNA sequences

Restriction endonucleaseRecognition siteTotal no. of OTUsNo. of OTUs in the range from 50 to 500 bpNo. of T-RFs in the range from 50 to 500 bpD1a,bD2a,c
Hpy188IIITC^NNGA571 (1)d320 (2)3,129 (11)38.5 (1)6.29 (1)
HhaIeGCG^C563 (2)271 (5)2,817 (15)32.8 (5)5.36 (5)
DpnIIe^GATC542 (3)255 (9)3,430 (9)29.8 (10)4.87 (10)
ScrFICC^NGG532 (4)263 (7)2,697 (16)31.6 (6)5.17 (6)
BfaIeC^TAG524 (5)244 (12)2,876 (14)29.3 (11)4.79 (11)
RsaIGT^AC513 (6)253 (10)3,011 (12)31.0 (7)5.06 (7)
Tsp509I^AATT512 (7)295 (3)2,682 (17)36.7 (2b)5.99 (2b)
MseIT^TAA502 (8)235 (14)2,247 (18)30.3 (9)4.96 (9)
HpyCH4IVeA^CGT456 (9)230 (15)3,973 (6)24.1 (18)3.94 (18)
HinfIG^ANTC422 (10)248 (11)4,103 (3)28.4 (12)4.64 (12)
MspIeC^CGG406 (11)322 (1)4,027 (5)36.7 (2a)5.99 (2a)
HaeIIIGG^CC346 (12)241 (13)3,956 (7)27.6 (14)4.51 (14)
Hpy1881TCN^GA345 (13)283 (4)3,258 (10)33.9 (4)5.55 (4)
BslICCN5^NNGG315 (14)265 (6)3,708 (8)30.8 (8)5.04 (8)
AluIAG^CT294 (15)210 (18)2,993 (13)25.5 (15)4.18 (15)
BstUIeCG^CG292 (16)262 (8)4,353 (1)27.9 (13)4.56 (13)
DdeIC^TNAG280 (17)228 (16)4,130 (2)24.6 (17)4.03 (17)
Sau96IG^GNCC273 (18)221 (17)4,088 (4)25.4 (16)4.16 (16)
  • a Calculated for T-RFs for the range from 50 to 500 bp. Data were randomly removed to obtain 2,247 T-RFs per restriction endonuclease in order to remove the effects of sample size.

  • b For a community of 2,247 individuals the range of possible values was 0 to 291.

  • c For a community of 2,247 individuals the range of possible values was 0 to 47.

  • d The numbers in parentheses are ranks.

  • e The restriction endonuclease has one or more known isoschizomers.