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

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

Library Nr.	Class	Target Species	Protocol, Enzyme and Size Window (bp)	N + controls	Stacks parameter M and n	Expected Nr. of Fragments^a	Obtained Loci^b	Expected Coverage	Obtained Coverage^b
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)

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
^a only estimates from real (not from simulated) genomes listed
^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

ISSN: 1471-2164