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

Table 2 Genomic information useful for reduced representation sequencing (RRS) optimization in target species from six organism classes

Class	Target Species	Target Fragment Number	Genome Size Estimates (C)	Genome from Related Species, Genome Size (Mb), Accession Nr., and Reference	Simulated Genomes
Ostracoda	Macrocyprididae	50,000	0.17 ± 0.003^a	Cyprideis torosa, 286 Mb, GCA_905338395.1 [57]	100 Mb, 43.9% GC 500 Mb, 43.9% GC
Malacostraca	Charcotia obesa and Eusirus pontomedon	50,000	unknown (Amphipoda: 0.68–64.62^a)	Hyalella azteca, 551 Mb, GCA_000764305.2 [58] Parhyale hawaiensis, 4003 Mb, GCA_001587735.2 [59]	10,000 Mb, 38.5% GC 30,000 Mb, 40.8% GC
Bivalvia	Laternula elliptica and Aequiyoldia eightsii	50,000	unknown (0.65–5.40^a)	Crassostrea gigas, 558 Mb, GCA_000297895.2 [60] Pinctada imbricata, 991 Mb, GCA_002216045.1 [61] Bathymodiolus platifrons, 1658 Mb, GCA_002080005.1 [62]	1000 Mb, 35.3% GC 5000 Mb, 34.2% GC
Asteroidea	Bathybiaster loripes and Psilaster charcoti	20,000	unknown (Asteroidea: 0.54–0.96^a)	Acanthaster planci, 383 Mb, GCA_001949145.1 [63] Patiria miniata, 811 Mb, GCA_000285935.1 [64] Patiriella regularis, 949 Mb, GCA_900067625.1 [65]	1000 Mb, 41.3% GC 2000 Mb, 40.4% GC
Actinopterygii	Trematomus bernacchii and T. loennbergii	20,000	T. bernacchii: 1.12 ± 0.019^b; 1.19^c; 1.82^d; T. loennbergii: 1.34^b	Notothenia coriiceps, 637 Mb, GCA_000735185.1 [66]	1000 Mb, 40.8% GC 1800 Mb, 40.8% GC
Aves	Pagodroma nivea nivea and P. nivea confusa	50,000	unknown (0.91–2.16^a)	Fulmarus glacialis, 1141 Mb, GCA_000690835.1 [67]	1500 Mb, 41.2% GC 2000 Mb, 41.2% GC

For each class approximate targets for the number of fragments were defined and known genome size estimates from flow cytometry are listed. In species with unknown genome size, the range of published estimates from species from the same class is listed. Available genomes from related species and two simulated genomes per class were used for in silico digestions. The simulated genomes were simulated using the SimRAD R package based on two realistically large genome sizes with a GC content as known from related species
^a published estimates from various species of the same class (or where indicated order), as listed on genomesize.com on 9th January 2019; Ostracoda: Macrocyprididae: Jeffery et al., 2017 [68]
^b Auvinet et al., 2018 [69]
^c Hardie and Hebert, 2003 [70]
^d Morescalchi et al., 1996 [71]

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