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Table 5 Setup and results of five test libraries for reduced representation sequencing (RRS) from eight species/groups

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

Library Nr. Class Target Species Protocol, Enzyme and Size Window (bp) N + controls Stacks parameter M and n Expected Nr. of Fragmentsa Obtained Locib Expected Coverage Obtained Coverageb
1 Ostracoda Macrocyprididae GBS, ApeKI, 200–350 8 + 2 6 65,244 69,817 (±63,114) 31.9× 28.2× (±5.4)
2 Bivalvia Laternula elliptica
Aequiyoldia eightsii
GBS, ApeKI, 200–260 8 + 2
10 + 2
4 53,399 – 69,027 125,305 (±22,828)
143,551 (±28,676)
30.2–39.0× 21.6× (±5.1)
20.0× (±2.6)
3 Asteroidea Bathybiaster loripes
Psilaster charcoti
GBS, ApeKI, 200–300 10 + 2
14 + 2
5 62,272 – 76,988 82,945 (±43,521)
115,608 (±30,589)
27.1–33.5× 21.0× (±6.8)
27.6× (±4.6)
4 Actinopterygii Trematomus bernacchii
T. loennbergii
ddRAD, EcoRI_MspI, 200–450 10 + 2
10 + 2
3 81,605 21,121 (±3539)
23,609 (±2362)
27.5× 42.3× (±13.5)
49.6× (±6.2)
5 Aves Pagodroma nivea nivea GBS, PstI, 200–300 6 + 2 3 66,258 140,972 (±26,444) 31.4× 10.0× (±0.4)
  1. Restriction enzyme(s) and size window was optimized for number of fragments and coverage as in Table 4, these estimates are listed here again as expected values and compared to empirical results regarding average (and standard deviation of) number of loci and average (and standard deviation of) coverage per sample based on data processing using Stacks v2.4 with optimized parameters
  2. a only estimates from real (not from simulated) genomes listed
  3. b as reported in the output file gstacks.log.distribs after using denovo_map.pl with m = 3 and M = n as listed in column six