Spreadsheet: 06a93dc0-d298-459b-a614-862c62841c30
Sheet: Table S6

 | Species | Study type | NGS platform used to identify SNPs | Number of  potential SNPs | Number of validated SNPs | Percentage validation | Methods used to  validate SNPs | References
 | Coral   ([NAME]) | Population  Genetics | NGS-454 | 33433 | 14 / 20 | 0.7 | Resequencing | Meyer et al. (2009)
 | [NAME]  ([NAME]) | Population  Genteics | NGS-Illumina | 2700000 | 0 | 0 | N/A | Li et al. (2010)
 | Turkey (Meleagris gallopavo) | undefined | NGS (RRL)-Illumina | 7952 | 340 / 384 | 0.885 | [NAME] | Kerstens et al.(2009)
 | [NAME] (Anas platyrhynchos) | Develop genomic resources | NGS (RRL)-Illumina | 150000 | 364 / 384 | 0.947 | [NAME] | Kraus et al.(2011)
 | [NAME]  (Parus major) | QTL mapping study | NGS (RRL)-Illumina | 20000 | 55 / 66 | 0.84 | Sanger sequencing | Van Bers et al.(2010)
 | European hake ([NAME]) | develop SNPs linked to functional loci | 454-Illumina | 454 (4,034),                 GAII (8,606) | 409 / 944,                                      296 / 684 | ~ 43% | [NAME] | Milano et al.(2011)
 | Eggplant (Solanum melongena L.) | Mapping | NGS (RAD)-Illumina | 10089 | 343 / 384 | 0.893 | [NAME] | Barchi et al.(2011)
 | [NAME] ([NAME] cardunculus L. var. [NAME]) | Mapping | NGS (RAD)-Illumina | 34000 | 19 / 24 | 0.79 | Cleaved Amplified Polymorphic Sequence (CAPS) assay | Scaligone et al.(2012)
 | Lake whitefish (Coregonus spp.) | Classification | NGS-454 | 6042 | 25 / 31 | 0.806 | Sequenom MassARRAY | Renaut et al.(2010)
 | Rainbow trout (Oncorhynchus  mykiss) | Mapping/Classification | NGS-454 | 13,140-24 ,627 | 183 / 384 | 0.476 | Golden Gate Assay | Sanchez et al. (2009)
 | Rose Gum  (Euclayptus grandis) | Classification | NGS-454 | 30108 | 279 /337 | 0.827 | Resequencing | Novaes et al.(2008)
 | Aphid (Aphis glycines) | Develop genomic resources | NGS-454,                    NGS (RRL)-Illumina | 635 | 11 /11 | 1 | [NAME] Extension (ASPE) assay | Bai et al.(2010)
 | Ascomycete(Ophiognomonia clavigignenti-juglandacearum) | Develop genomic resources | NGS-454 | 298 | 12 /32 | 0.375 | Sanger sequencing | Broders et al.(2011)
 | Teleost (Fundulus heteroclitus) | Population  Genetics | NGS-454 | 261 | 65 /81 | 0.8 | Sequenom MassARRAY | [NAME] et al.(2010)
 | Sockeye salmon (Oncorhynchus nerka) | Population Genomics | NGS-Solid | 1,928-5,657 | 51 /96 | 0.53 | PCR, HRMA, [NAME] sequencing, [NAME] | [NAME] (2011)
 | Threespine stickleback                           (Gasterosteus aculeatus) | Develop genomic resources | NGS (RAD)-Illumina | 40441 | 13 /13 | 1 | Sanger sequencing | Etter et al. (2011)
 | SNP:Single nucleotide polymorphism
 | RRL: Reduced representation library
 | NGS: Next generation sequencing
 | HRMA: High-resolution melt analysis
 | References
 | 1. Meyer E, Aglyamova GV, [NAME], [NAME] J, Abrego D, et [NAME]. (2009) Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx BMC Genomics 10.
 | 2. [NAME] R, [NAME], [NAME], [NAME], He L, et [NAME]. (2012) The sequence and de novo assembly of the giant panda genome. Nature 463: 311-317.
 | 3. [NAME], Crooijmans RP, [NAME], Dibbits BW, FC T, et [NAME]. (2009) Large scale  single  nucleotide  polymorphism  discovery  in  unsequenced genomes using second generation high throughput sequencing technology: applied to turkey. BMC Genomics 10: 479–489.
 | 4. [NAME], [NAME], [NAME], Crooijmans RP, [NAME], et [NAME]. (2011) Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos). BMC Genomics 12: 150.
 | 5. Van Bers NE, [NAME], Kerstens HH, Dibbits BW, Crooijmans RP, et [NAME]. (2010) Genome-wide SNP detection in the great tit Parus major using high throughput sequencing. Molecular Ecology 19: 89-99.
 | 6. Milano I, Babbucci M, Panitz F, Ogden R, Nielsen RO, et [NAME]. (2011) Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European Hake. [NAME] One  6.
 | 7. Barchi L, [NAME], Portis E, Acquadro A, Valè G, et [NAME]. (2011) Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genomics 12: 304.
 | 8. Scaglione D, Acquadro A, Portis E, Tirone M, Knapp SJ, et [NAME]. (2012) RAD tag sequencing as a source of SNP markers in Cynara cardunculus [NAME] 13: 3.
 | 9. Renaut S, [NAME], [NAME] (2010) Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whiteﬁsh species pairs (Coregonus spp. Salmonidae). Molecular Ecology  19 (Suppl. 1) 115–131.
 | 10. Sánchez CC, Smith TP, [NAME], [NAME], Salem M, et [NAME]. (2009) Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library. BMC Genomics 10.
 | 11. [NAME] E, Drost DR, [NAME], [NAME], Grattapaglia D, et [NAME]. (2008) High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 9
 | 12. Bai X, [NAME], Orantes L, Jun T-H, [NAME], et [NAME]. (2010) Combining Next-Generation Sequencing Strategies for Rapid Molecular Resource Development from an Invasive Aphid Species, Aphis glycines. [NAME] One 5.
 | 13. Broders KD, [NAME], [NAME], Westerman RP, Boland GJ (2011 ) Discovery of single-nucleotide polymorphisms (SNPs) in the uncharacterized genome of the ascomycete Ophiognomonia clavigignenti-juglandacearum from 454 sequence data. Molecular Ecology Resources 11: 693–702.
 | 14. [NAME] LM, [NAME], [NAME], [NAME] CD, Oleksiak MF (2010) SNP identification, verification, and utility for population genetics in a non-model genus. BMC Genetics 11.
 | 15. [NAME], [NAME], Seeb JE (2011) Short reads and nonmodel species: exploring the complexities of next-generation sequence assembly and SNP discovery in the absence of a reference genome. Molecular Ecology Resources 11: 93-108
 | 16. Etter PD, [NAME], [NAME], Cresko WA, [NAME] (2011) Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads. [NAME] One  6.