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. 2015 Jul 8;8:299. doi: 10.1186/s13104-015-1261-2

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.

i http://www.biomedcentral.com/1471-2164/14/32/additional.