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Table 4 Reduced representation sequencing (RRS) setups for seven individually optimized protocols

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

Class Target Species Restriction Enzyme (Combination) Size Window (bp) Assumed Genome Size (Mb) Coveragea Marker Densitya (bp per 1 SNP)
Ostracoda Macrocyprididae ApeKI 200–350 250 31.9× 1533
Malacostraca Charcotia obesa SbfI_MspI 200–320 27,000 32.5× 168,503
  Eusirus pontomedon EcoRI_SphI 200–260 7000 32.8× 44,045
Bivalvia Laternula elliptica and Aequiyoldia eightsii ApeKI 200–260 3000 30.2–39.0× 17,385 – 22,472
Asteroidea Bathybiaster loripes and Psilaster charcoti ApeKI 200–300 500 27.1–33.5× 2598 – 3212
Actinopterygii Trematomus bernacchii and T. loennbergii EcoRI_MspI 200–450 1500 27.5× 7352
Aves Pagodroma nivea nivea and P. nivea confusa PstI 200–300 1500 31.4× 9056
  1. These setups were optimized in order to be run on a HiSeq 2500 platform (Illumina). The choice of restriction enzyme(s) and size window was optimized to obtain approximately 30× coverage (or half that value in a worst-case scenario) with the assumed genome size (conservatively estimated based on available information, see Table 2). Marker density (the number of bp per sequenced SNP) was estimated as a comparable measure to the metastudy by Lowry et al. (2017) [34]
  2. a assuming 200 million reads of 125 bp length spread over 96 individuals and 0.01 SNP/bp