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

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

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 ± 0.003a 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: 0.68–64.62a) 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 (0.65–5.40a) 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: 0.54–0.96a) 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 ± 0.019b; 1.19c; 1.82d; T. loennbergii: 1.34b 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 (0.91–2.16a) Fulmarus glacialis, 1141 Mb, GCA_000690835.1 [67] 1500 Mb, 41.2% GC
2000 Mb, 41.2% GC
  1. 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
  2. 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]
  3. b Auvinet et al., 2018 [69]
  4. c Hardie and Hebert, 2003 [70]
  5. d Morescalchi et al., 1996 [71]