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

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

Class	Target Species	Restriction Enzyme (Combination)	Size Window (bp)	Assumed Genome Size (Mb)	Coverage^a	Marker Density^a (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

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]
^a assuming 200 million reads of 125 bp length spread over 96 individuals and 0.01 SNP/bp

ISSN: 1471-2164