Table 1.
Descriptions of the RAD sequences and the studies from which they were obtained
| Species | Reference | Consensus sequence availability | Initial number of sequences | Sequence length (bp) | Post-processed number of sequences | Protocol and pipeline details | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| RAD-Seq library preparation protocol | Fragment size selection window (bp) | Sequencing platform | Sequence analysis pipeline | Minimum depth coverage per locus | ||||||
| Chinook salmon (Oncorhynchus tshawytscha) | Brieuc et al. [24]. G3, 4(3) | Online (SE)e | 62,249 | 75 | 62,249 | Baird et al. [25] | 200–500 | Illumina GAII/HiSeq | STACKS | Locus sequenced in 135 (85%) individuals |
| Sockeye salmon (Oncorhynchus nerka) | Everett et al. [26]. BMC Genomics, 13(521) | Provided by authors (SE) | 64,613 | 60 | 64,613 | Baird et al. [25] Etter et al. [27] |
400–800 | Illumina GAII/HiSeq | Custom-written Perl scripts, Bowtie, Novoalign | 10 reads per allele per locus per individual |
| Rainbow trout (Oncorhynchus mykiss) | Hecht et al. [28]. G3, 2(9) | Provided by authors (SE) | 12,073 | 67 | 32,027 | Miller et al. [29] Baird et al. [25] |
200–500 | Illumina GAII/HiSeq 2000 | Perl scripts from Miller et al. (2012), Novoalign | 5 reads per locus per individual |
| Hale et al. [30]. G3, 3(8) | Provided by authors (SE) | 277,469 | 89 | Miller et al. [31] | 300–600 | Illumina HiSeq | Perl scripts from Miller et al. (2012), Novocraft | 5 reads per locus per individual | ||
| Hohenlohe et al. [6]. Molecular Ecology, 22(11) | Online (PE)f | 77,141 | 147–552a | Etter et al. [27] | 330–400 | Illumina HiSeq | STACKS | Locus sequenced in 1/60 (2%) individuals after pooling across individuals | ||
| Miller et al. [31]. Molecular Ecology, 21(2) | Online (SE)g | 40,649 | 68 | Baird et al. [25] Hohenlohe et al. [6] |
200–500 | Illumina HiSeq | Custom-written Perl scripts, Novoalign | Locus sequenced in 3 individuals | ||
| Atlantic salmon (Salmo salar) | Gonen et al. [2]. BMC Genomics, 15(166) | Provided by authors (PE) | 366,219 | 95 | 65,758 | Etter et al. [27] with modifications from Houston et al. [1] | 250–500 | Illumina HiSeq 2000 | RADtools, STACKS | 500 reads per locus across 96 individuals |
| Houston et al. [1]. BMC Genomics, 13(244) | Provided by authors (PE) | 66,073b | 95 | Baird et al. [25] Etter et al. [27] |
250–500 | Illumina GAIIx/HiSeq 2000 | RADtools | 5 reads per allele per locus per individual | ||
| Lake whitefish (Coregonus clupeaformis) | Gagnaire et al. [8]. Evolution, 67(9) | Provided by authors (SE) | 193,258 | 69 | 193,258 | Baird et al. [25] | 200–500 | Illumina HiSeq 2000 | STACKS | Locus is present in at least one mapping parent |
| Three-spined stickleback (Gasterosterus aculeatus) | Roesti et al. [32]. Molecular Ecology, 21(12) | Provided by authors (SE) | 31,118c | 64 or 138d | 31,118 | Baird et al. [25] | 200–500 | Illumina HiSeq 2000 | Novoalign, SAMtools | 12 reads per locus across 284 individuals |
| Atlantic halibut (Hippoglossus hippoglossus) | Palaiokostas et al. [33]. BMC Genomics, 14(566) | Provided by authors (SE) | 83,678 | 96 | 83,678 | Baird et al. [25] Etter et al. [27] with modifications from Houston et al. [1] |
300–550 | Illumina HiSeq 2000 | STACKS | 30 reads per locus per individual |
| Baltic sea herring (Clupea harengus) | Corander et al. [7] Molecular Ecology, 22(11) | Online (SE)h | 63,742 | 95 | 63,742 | Baird et al. [25] Hohenlohe et al. [6] Emerson et al. [34] |
200–500 | Illumina HiSeq 2000 | FLORAGENEX unitag assembler v2.0, FLORAGENEX pipeline | 5 reads per locus per individual |
| Spotted gar (Lepisosteus oculatus) | Amores et al. [35] Genetics, 188(4) | Provided by authors (SE) | 64,483 | 75 | 64,483 | Miller et al. [28] Baird et al. [25] Hohenlohe et al. [6] |
200–500 | Illumina GAIIx | STACKS | Locus sequenced in 85 (90%) individuals |
| Gudgeon (Gnathopogon sp.) | Kakioka et al. [36]. BMC Genomics, 14(32) | Online (SE)i | 44,109 | 70 | 44,109 | Etter et al. [27] | 300–500 | Illumina GAIIx/HiSeq 2000 | STACKS | 3 reads per locus per individual |
SE single-end RAD-Seq, PE paired-end RAD-Seq.
aPaired-end RAD sequencing generated contigs of variable length.
b2 files from two families, sequence counts: 70,207 and 70,739. Subsequently combined into one file with 66,073 common sequences.
c46 files (one per individual). Sequence count range: 25,840 – 42,618. Subsequently combined into one file with 31,118 common sequences.
dTwo separate sequencing studies were implemented, resulting in two different read lengths.
e http://www.g3journal.org/lookup/ suppl/doi:10.1534/g3.113.009316/-/DC1.
f http://datadryad.org/resource/ doi:10.5061/dryad.32b88
g http://onlinelibrary.wiley.com/ doi:10.1111/j.1365-294X.2011.05305.x/
hdoi:10.5061/dryad.jr56h.