Single nucleotide polymorphism discovery in cutthroat trout subspecies using genome reduction, barcoding, and 454 pyro-sequencing

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Houston, Derek D ^a   Elzinga, David B ^a   Maughan, Peter J ^a   Smith, Scott M ^a   Kauwe, John S K ^a   Evans, R Paul ^a   Stinger, Ryan B ^a   Shiozawa, Dennis K ^a  

^a BRIGHAM YOUNG UNIVERSITY   (United States)

Author keywords

Conservation genetics; Genetic admixture; Hybridization; KASPar; Oncorhynchus clarkii; Oncorhynchus mykiss; Population genomics; Rainbow trout; SNP

Indexed keywords

MITOCHONDRIAL DNA;

454 PYROSEQUENCING; ARTICLE; CONTROLLED STUDY; CUTTHROAT TROUT; DNA BARCODING; DNA EXTRACTION; GENE AMPLIFICATION; GENE LOCUS; GENETIC PROCEDURES; GENETIC VARIABILITY; GENOME REDUCTION; GENOTYPE; HYBRIDIZATION; NONHUMAN; PYROSEQUENCING; RAINBOW TROUT; SINGLE NUCLEOTIDE POLYMORPHISM; TROUT;

ANIMALS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; DNA BARCODING, TAXONOMIC; FISHERIES; GENOME; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HYBRIDIZATION, GENETIC; MOLECULAR SEQUENCE DATA; ONCORHYNCHUS; POLYMORPHISM, SINGLE NUCLEOTIDE;

AMADINA FASCIATA; ONCORHYNCHUS CLARKII; ONCORHYNCHUS MYKISS; PISCES; SALMONIDAE;

EID: 84872526330     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-724     Document Type: Article

References (55)

1. Brumfeld RT, Beerli P, Nickerson DA, Edwards SV. The utility of single nucleotide polymorphisms in inferences of population history. Trends Ecol Evol 2003, 18:249-256.
2. Garvin MR, Saitoh K, Gharrett AJ. Application of single nucleotide polymorphisms to non-model species: a technical review. Mol Ecol Resour 2010, 10:915-934. 10.1111/j.1755-0998.2010.02891.x, 21565101.
3. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11:31-46. 10.1038/nrg2626, 19997069.
4. Helyar SJ, Hemmer-Hansen J, Bekkevold D, Taylor MI, Ogden R, Limborg MT, Cariani A, Maes GE, Diopere E, Carvalho GR, Nielsen EE. Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges. Mol Ecol Resour 2011, 11:123-136.
5. Hale MC, McCormick CR, Jackson JR, DeWoody JA. Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery. BMC Genomics 2009, 10:203. 10.1186/1471-2164-10-203, 2688523, 19402907.
6. Maughan PJ, Yourstone SM, Jellen EN, Udall JA. Snp Discovery Via Genomic Reduction, Barcoding, And 454-pyrosequencing In Amaranth. Plant Gen 2009, 2:260-270.
7. Wu X, Ren C, Joshi T, Vuong T, Xu D, Nguyen HT. SNP discovery by high-throughput sequencing in soybean. BMC Genomics 2010, 11:469. 10.1186/1471-2164-11-469, 3091665, 20701770.
8. Oliver RE, Lazo GR, Lutz JD, Rubenfield MJ, Tinker NA, Anderson JM, Morehead NHW, Adhikary D, Jellen EN, Maughan PJ, et al. Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology. BMC Genomics 2011, 12:77. 10.1186/1471-2164-12-77, 3041746, 21272354.
9. Williams LM, Ma X, Boyko AR, Bustamante CD, Oleksiak MF. SNP identification, verification, and utility for population genetics in a non-model genus. BMC Genet 2011, 11:32.
10. Aguilar A, Garza JC. Isolation of 15 single nucleotide polymorphisms from coastal steelhead, Oncorhynchus mykiss (Salmonidae). Mol Ecol Resour 2008, 8:659-662. 10.1111/j.1471-8286.2007.02038.x, 21585863.
11. Narum SR, Banks M, Beacham TD, Bellinger MR, Campbell MR, Dekoning J, Elz A, Guthrie CM, Kozfkay C, Miller KM, et al. Differentiating salmon populations at broad and fine geographical scales with microsatellites and single nucleotide polymorphisms. Mol Ecol 2008, 17:3464-3477.
12. Sušnik S, Sivka U, Snoj A. A set of nuclear DNA markers diagnostic for marble trout, Salmo marmoratus. Aquaculture 2008, 285:260-263.
13. Castaño-Sánchez C, Smith TP, Wiedmann RT, Vallejo RL, Salem M, Yao J, Rexroad CE. Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library. BMC Genomics C7 - 559 2009, 10:559.
14. Renaut S, Nolte AW, Rogers SM, Derome N, Bernatchez L. SNP signatures of selection on standing genetic variation and their association with adaptive phenotypes along gradients of ecological speciation in lake whitefish species pairs (Coregonus spp.). Mol Ecol 2011, 20:545-559. 10.1111/j.1365-294X.2010.04952.x, 21143332.
15. Campbell NR, Narum SR. Development of 54 novel single-nucleotide polymorphism (SNP) assays for sockeye and coho salmon and assessment of available SNPs to differentiate stocks within the Columbia River. Mol Ecol Resour 2011, 11:20-30.
16. Fridjonsson O, Olafsson K, Tompsett S, Bjornsdottir S, Consuegra S, Knox D, de Leaniz CG, Magnusdottir S, Olafsdottir G, Verspoor E, Hjorleifsdottir S. Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing. BMC Genomics 2011, 12:179. 10.1186/1471-2164-12-179, 3079667, 21473771.
17. Renaut S, Nolte AW, Bernatchez L. Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae). Mol Ecol 2010, 19:115-131.
18. Seeb JE, Pascal CE, Grau ED, Seeb LW, Templin WD, Harkins T, Roberts SB. Transcriptome sequencing and high-resolution melt analysis advance single nucleotide polymorphism discovery in duplicated salmonids. Mol Ecol Resour 2011, 11:335-348. 10.1111/j.1755-0998.2010.02936.x, 21429141.
19. Lamaze FC, Sauvage C, Marie A, Garant D, Bernatchez L. Dynamics of introgressive hybridization assessed by SNP population genomics of coding genes in stocked brook charr (Salvelinus fontinalis). Mol Ecol 2012, 21:2877-2895. 10.1111/j.1365-294X.2012.05579.x, 22548328.
20. Wilson WD, Turner TF. Phylogenetic analysis of the Pacific cutthroat trout (Oncorhynchus clarki ssp.: Salmonidae) based on partial mtDNA ND4 sequences: A closer look at the highly fragmented inland species. Mol Phylogenet Evol 2009, 52:406-415. 10.1016/j.ympev.2009.03.018, 19341807.
21. Loxterman J, Keeley E. Watershed boundaries and geographic isolation: patterns of diversification in cutthroat trout from western North America. BMC Evol Biol 2012, 12:38. 10.1186/1471-2148-12-38, 3320548, 22429757.
22. Trotter PC, Behnke RJ. The case for Humboldtensis: A subspecies name for the indigenous cutthroat trout (Oncorhynchus clarkii) of the Humboldt River, Upper Quinn River, and Coyote Basin drainages, Nevada and Oregon. Western North American Naturalist 2008, 68:58-65.
23. Montgomery MR. Many rivers to cross: of good running water, native trout, and the remains of wilderness 1995, New York: Touchstone.
24. Behnke RJ. Native trout of western North America. American Fisheries Society Monograph 1992, 6:1-275.
25. Behnke RJ. Trout and Salmon of North America 2002, New York, NY: The Free Press.
26. Johnson AE. Resolving phylogenetic relationships of selected cutthroat trout subspecies, Oncorhynchus clarki (Salmonidae) 2005, Department of Biology: Brigham Young University.
27. Busack CA, Gall GAE. Introgressive hybridization in populations of Paiute cutthroat trout (Salmo-clarki-seleniris). Can J Fish Aquat Sci 1981, 38:939-951.
28. Finger AJ, Stephens MR, Clipperton NW, May B. Six diagnostic single nucleotide polymorphism markers for detecting introgression between cutthroat and rainbow trouts. Mol Ecol Resour 2009, 9:759-763. 10.1111/j.1755-0998.2009.02532.x, 21564737.
29. Behnke RJ. Systematic and zoogeographical interpretation of Great Basin trouts. Fishes In North American Deserts 1981, 95-124. New York: John Wiley & Sons, Soltz N.
30. Loudenslager EJ, Gall GAE. Geographic Patterns of Protein Variation and Subspeciation in Cutthroat Trout, Salmo clarki. Syst Zool 1980, 29:27-42.
31. Martin MA, Shiozawa DK, Loudenslager EJ, Jensen JN. Electrophoretic study of cutthroat trout populations in Utah. Great Basin Naturalist 1985, 45:677-687.
32. Smith GR, Dowling T, Gobalet K, Lugaski T, Shiozawa DK, Evans RP. Biogeography and timing of evolutionary events among Great Basin fishes. Great Basin Aquatic Systems History 2002, 175-234. Washington, D. C: Smithsonian Institution Press, 33, Smithsonian Contributions to the Earth Sciences.
33. Malde HE. The catastrophic late Pleistocene Bonneville Flood in the Snake River Plain, Idaho 1968, Washington, D. C: United States Government Printing Office.
34. Bouchard DP, Kaufman DS, Hochberg A, Quade J. Quaternary history of the Thatcher Basin, Idaho, reconstructed from the Sr-87/Sr-86 and amino acid composition of lacustrine fossils: implications for the diversion of the Bear River into the Bonneville Basin. Palaeogeogr Palaeoclimatol Palaeoecol 1998, 141:95-114.
35. Johnson JB. Evolution after the flood: phylogeography of the desert fish Utah Chub (Gila atraria). Evolution 2002, 56:948-960.
36. Metcalf JL, Love Stowell S, Kennedy CM, Rogers KB, McDonald D, Epp J, Keepers K, Cooper A, Austin JJ, Martin AP. Historical stocking data and 19th century DNA reveal human-induced changes to native diversity and distribution of cutthroat trout. Mol Ecol 2012, 21:5194-5207. 10.1111/mec.12028, 22998121.
37. Allendorf FW, Leary RF. Conservation and distribution of genetic variation in a polytypic species the cutthroat trout. Conserv Biol 1988, 2:170-184.
38. Trotter PC. Cutthroat native trout of the west 2008, Berkeley, CA: University of California Press, 2.
39. Hohenlohe PA, Amish SJ, Catchen JM, Allendorf FW, Luikart G. Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Mol Ecol Resour 2011, 11:117-122.
40. McGlauflin MT, Smith MJ, Wang JT, Young SF, Chen N, Lee YC, Pascal C, Seeb LW, Stevens J, Seeb JE. High-Resolution Melting Analysis for the Discovery of Novel Single-Nucleotide Polymorphisms in Rainbow and Cutthroat Trout for Species Identification. Trans Am Fish Soc 2011, 139:676-684.
41. Pritchard VL, Abadía-Cardoso A, Garza JC. Discovery and characterization of a large number of diagnostic markers to discriminate Oncorhynchus mykiss and O. clarkii. Mol Ecol Resour 2012, 12:918-931. 10.1111/j.1755-0998.2012.03149.x, 22591214.
42. Amish SJ, Hohenlohe PA, Painter S, Leary RF, Muhlfeld C, Allendorf FW, Luikart G. RAD sequencing yields a high success rate for westslope cutthroat and rainbow trout species-diagnostic SNP assays. Mol Ecol Resour 2012, 12:653-660. 10.1111/j.1755-0998.2012.03157.x, 22672623.
43. Kalinowski ST, Novak BJ, Drinan DP, Jennings R, Vu NV. Diagnostic single nucleotide polymorphisms for identifying westslope cutthroat trout (Oncorhynchus clarki lewisi), Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri) and rainbow trout (Oncorhynchus mykiss). Mol Ecol Resour 2011, 11:389-393. 10.1111/j.1755-0998.2010.02932.x, 21429151.
44. Harwood AS, Phillips RB. A suite of twelve single nucleotide polymorphism markers for detecting introgression between cutthroat and rainbow trout. Mol Ecol Resour 2011, 11:382-385. 10.1111/j.1755-0998.2010.02930.x, 21429149.
45. Campbell NR, Amish SJ, Pritchard VL, McKelvey KS, Young MK, Schwartz MK, Garza JC, Luikart G, Narum SR. Development and evaluation of 200 novel SNP assays for population genetic studies of westslope cutthroat trout and genetic identification of related taxa. Mol Ecol Resour 2012, 12:942-949. 10.1111/j.1755-0998.2012.03161.x, 22697369.
46. Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0 1996-2010 2010, http://www.repeatmasker.org.
47. KBiosciences PrimerPicker Lite for KASPar v.0.26 2009, Hoddesdon, UK: KBiosciences Ltd, KBiosciences.
48. Wang J, Lin M, Crenshaw A, Hutchinson A, Hicks B, Yeager M, Berndt S, Huang W-Y, Hayes RB, Chanock SJ, et al. High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays. BMC Genomics 2009, 10.
49. Maughan PJ, Smith SM, Fairbanks DJ, Jellen EN. Development, Characterization, and Linkage Mapping of Single Nucleotide Polymorphisms in the Grain Amaranths (Amaranthus sp.). Plant Gen 2011, 4:92-101.
50. Fluidigm Fluidigm SNP Genotyping Analysis v.3.0.2 2011, South San Francisco, CA: Fluidigm Corporation, Fluidigm.
51. Huson DH, Bryant D. Application of Phylogenetic Networks in Evolutionary Studies. Mol Biol Evol 2006, 23:254-267.
52. Goslee SC, Urban DL. The ecodist package for dissimilarity-based analysis of ecological data. J Stat Softw 2007, 22:1-19.
53. R Development Core Team. R A language and environment for statistical computing 2012, Vienna, Austria: R Foundation for Statistical Computing, http://www.R-project.org, R Development Core Team. R.
54. Pritchard JK, Stephens M, Donnelly P. Inference of Population Structure Using Multilocus Genotype Data. Genetics 2000, 155:945-959. 1461096, 10835412.
55. Earl DA, VonHoldt BM. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 2012, 4:359-361.