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Table 3 Restriction enzymes and combinations used for reduced representation sequencing (RRS) optimization

From: Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing

Restriction Enzyme (Combination) Recognition Site Approximate Fragment Numbera Special Features Reference
SbfI 5′--CCTGCA|GG--3′ 6000   e.g. [39, 74,75,76]
EcoRI 5′--G|AATTC--3’ 323,000 Methylation sensitive [13, 77]
SphI 5′--GCATG|C--3’ 143,000   
PstI 5′--CTGCA|G--3’ 145,000   [78, 79]
ApeKI 5′--G|CWGC--3’ 940,000 Methylation sensitive, degenerate site e.g. [80,81,82,83]
MspI 5′--C|CGG--3’ 1,590,000   
MseI 5′--T|TAA--3’ 8,100,000   [84]
SbfI_SphI   11,000   e.g. [33, 85,86,87]
SbfI_MspI   11,000   [88, 89]
PstI_MspI   265,000   e.g. [17, 90,91,92]
EcoRI_SphI   244,000   [93]
EcoRI_MspI   536,000   e.g. [94,95,96,97]
  1. Recognition site, the approximate expected fragment number in a 1000 Mb genome, any special enzyme characteristic and empirical studies that recently used this enzyme (combination) are listed.
  2. a For a 1000 Mb genome with 40% GC content and no size selection and rounded to the nearest thousand. Note that the double digest estimates are for ddRAD protocols where fragments with two different restriction sites but irrespective of orientation are retained. In the two enzyme GBS protocol this number would be halved as only fragments with the first restriction site first and the second restriction site second (and not vice versa) are retained during library construction. For more details see Peterson et al. (2012) [15] and Poland et al. (2012) [17]