Two Different High Throughput Sequencing Approaches Identify Thousands of De Novo Genomic Markers for the Genetically Depleted Bornean Elephant

PLoS ONE

Volumn 7, Issue 11, 2012, Pages

  Sharma, Reeta ^a   Goossens, Benoit ^b,c   Kun Rodrigues, Célia ^a   Teixeira, Tatiana ^a   Othman, Nurzhafarina ^b,c   Boone, Jason Q ^d   Jue, Nathaniel K ^e   Obergfell, Craig ^e   O'Neill, Rachel J ^e   Chikhi, Lounès ^a,f,g  

^a INSTITUTO GULBENKIAN DE CIÊNCIA   (Portugal)

^b CARDIFF UNIVERSITY   (United Kingdom)

^c Lower Kinabatangan Wildlife Sanctuary   (Malaysia)

^d Floragenex Inc   (United States)

^e UNIVERSITY OF CONNECTICUT   (United States)

^f CNRS   (France)

^g UNIVERSITÉ DE TOULOUSE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

ANALYTICAL EQUIPMENT; ARTICLE; BORNEAN ELEPHANT; CONTIG MAPPING; CONTROLLED STUDY; DNA FLANKING REGION; ELEPHANT; ENDANGERED SPECIES; FEASIBILITY STUDY; GENE LOCUS; GENETIC MARKER; GENETIC VARIABILITY; GENOME ANALYSIS; GENOME SIZE; GENOTYPE; HIGH THROUGHPUT SEQUENCING; MICROSATELLITE MARKER; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; RESTRICTION SITE; SAMPLE SIZE; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION PROCESS;

ANIMALS; CHROMOSOME MAPPING; CONTIG MAPPING; ELEPHANTS; GENETIC MARKERS; GENETIC VARIATION; GENETICS, POPULATION; GENOME; GENOMICS; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICROSATELLITE REPEATS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

ELEPHAS MAXIMUS; TETRA;

EID: 84869784350     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0049533     Document Type: Article

References (75)

1. Colbourne JK, Robison B, Bogart K, Lynch M, (2004) Five hundred and twenty-eight microsatellite markers for ecological genomic investigations using Daphnia. Molecular Ecology Notes 4: 485-490.
2. Sharma R, Stuckas H, Moll K, Khan I, Bhaskar R, et al. (2008) Fourteen new di- and tetranucleotide microsatellite loci for the critically endangered Indian tiger (Panthera tigris tigris). Molecular Ecology Resources 8: 1480-1482.
3. Salmona J, Dawson DA, Fouillot D, Ghestemme T, Thebaud C, et al. (2010) The utility of existing passerine microsatellite markers for genetic studies in endangered species: as demonstrated for a critically endangered forest bird endemic to Réunion Island, the Réunion cuckooshrike (Coracina newtoni). Conservation Genetics Resources.
4. Weber JN, Peters MB, Tsyusko OV, Linnen CR, et al. (2009) Five hundred microsatellite loci for Peromyscus. Conservation Genetics 11: 1243-1246.
5. Altshuler D, Pollara VJ, Cowles CR, Etten WJV, Baldwin J, et al. (2000) An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407: 513-516.
6. Brumfield RT, Beerli P, Nickerson DA, Edwards SV (2003) The utility of single nucleotide polymorphisms in inferences of population history Trends in Ecology and Evolution 18.
7. Slate J, Gratten J, Beraldi D, Stapley J, Hale M, et al. (2009) Gene mapping in the wild with SNPs: guidelines and future directions. Genetica 136: 97-107.
8. Williams LM, Ma X, Boyko AR, Bustamante CD, Oleksiak MF (2010) SNP identification, verification, and utility for population genetics in a non-model genus. BMC Genetics 11.
9. Van Bers NE, Oers Kv, Kerstens HH, Dibbits BW, Crooijmans RP, et al. (2010) Genome-wide SNP detection in the great tit Parus major using high throughput sequencing. Molecular Ecology 19: 89-99.
10. Renault S, Nolte AW, Bernatchez L (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.
11. Seddon JM, Parker HG, Ostrander EA, Ellegren H, (2005) SNPs in ecological and conservation studies: a test in the Scandinavian wolf population. Molecular Ecology 14: 503-511.
12. Morin PA, Mccarthy M, (2007) Highly accurate SNP genotyping from historical and low-quality samples. Molecular Ecology Notes 7: 937-946.
13. Bonin A, Bellemain E, Eidesen BP, Pompanon F, Brochmann C, et al. (2004) How to track and assess genotyping errors in population genetics studies. Molecular Ecology 13: 3261-3273.
14. Morin PA, Martien KK, Taylor BL, (2009) Assessing statistical power of SNPs for population structure and conservation studies. Molecular Ecology Resources 9: 66-73.
15. Wright S (1978) Variability Within and Among Natural Populations. University of Chicago Press, Chicago, IL. Evolution and the Genetics of Populations 4.
16. Nei M, (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals Genetics. 89: 583-590.
17. Weir BS, Cockerham CC, (1984) Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.
18. Aitken N, Smith S, Schwartz C, Morin PA, (2004) Single nucleotide polymorphism (SNP) discovery in mammals: a targeted-gene approach. Molecular Ecology 13: 1423-1431.
19. Smith S, Aitken N, Schwarz C, Morin PA, (2004) Characterization of 15 single nucleotide polymorphism markers for chimpanzees (Pan troglodytes). Molecular Ecology Notes 4: 348-351.
20. Morin PA, Aitken N, Rubio-Cisneros N, Dizon AE, Mesnick S, (2007) Characterization of 18 SNP markers for sperm whale (Physeter macrocephalus). Molecular Ecology Notes 7: 626-630.
21. Aguilar A, Garza JC, (2008) Isolation of 15 single nucleotide polymorphisms from coastal steelhead, Oncorhynchus mykiss (Salmonidae). Molecular Ecology Resources 8: 659-662.
22. Li S, Wan H, Ji H, Zhou K, Yang G (2009) SNP discovery based on CATS and genotyping in the finless porpoise (Neophocaena phocaenoides). Conserv Genet.
23. Nicod J-C, Largiadér CR (2003) SNPs by AFLP (SBA): a rapid SNP isolation strategy for non-model organisms. Nucleic Acids Research 31.
24. Roden SE, Dutton PH, Morin PA (2008) AFLP Fragment Isolation Technique as a method to produce random sequences for single nucleotide polymorphism discovery in the Green Turtle, Chelonia mydas. Journal of Heredity.
25. Moen T, Hayes B, Nilsen F, Delghandi M, Fjalestad KT, et al. (2008) Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection. BMC Genetics 9: 18.
26. Chikhi L, Bruford MW, Beaumont MA (2001) Estimation of Admixture Proportions: A Likelihood-Based Approach Using Markov Chain Monte Carlo. Genetics 158 1347-1362.
27. Vignal A, Milan D, SanCristobal M, Eggen A, (2002) A review on SNP and other types of molecular markers and their use in animal genetics. Genet Sel Evol 34: 275-305.
28. Garvin MR, Saitoh K, Gharrett AJ (2010) Application of single nucleotide polymorphisms to non-model species: a technical review. Molecular Ecology Resources.
29. Seeb JE, Carvalho G, Hauser L, Naish K, Roberts S, et al. (2011) Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms. Molecular Ecology Resources 11(Suppl. 1): 1-8.
30. Meyer M, Stenzel U, Myles S, Pruefer K, Hofreiter M (2007) Targeted high-throughput sequencing of tagged nucleic acid samples Nucleic Acids Research 35.
31. Novaes E, Drost DR, Farmerie WG, Jr GJP, Grattapaglia D, et al. (2008) High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome. BMC Genomics 9.
32. Davey JW, Hohenlohe PA, Etter PD, Boone JA, Catchen JM, et al. (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Review Genetics 12: 499.
33. VanTassell CP, Smith TPL, Matukumalli LK, Taylor JF, Schnabel RD, et al. (2008) SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nature Methods 5: 247-252.
34. Wiedmann RT, Smith TP, Nonneman DJ (2008) SNP discovery in swine by reduced representation and high throughput pyrosequencing. BMC Genetics 9.
35. Kerstens HH, Crooijmans RP, Veenendaal A, Dibbits BW, FC T, et al. (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.
36. Kraus RH, Kerstens HH, Hooft PV, Crooijmans RP, Poel JJVD, et al. (2011) Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos). BMC Genomics 12: 150.
37. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, et al. (2008) Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers. PLoS One 3: 110-115.
38. Hohenlohe PA, Bassham S, Etter PD, Stiffler N, Johnson EA, et al. (2010) Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags. PLoS Genetics 6: e1000862.
39. Emerson KJ, Merz CR, Catchen JM, Hohenlohe PA, Cresko WA, et al. (2010) Resolving postglacial phylogeography using high-throughput sequencing. PNAS 107: 16196-16200.
40. Rowe HC, Renaut S, Guggisberg A, (2011) RAD in the realm of next-generation sequencing technologies. Molecular Ecology 20: 3499-3502.
41. Etter PD, Preston JL, Bassham S, Cresko WA, Johnson EA (2011) Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads. PLoS One 6.
42. Fernando P, Vidya TNC, Payne J, Stuewe M, Davison G, et al. (2003) DNA analysis indicates that Asian elephants are native to Borneo and are therefore a high priority for conservation. PLoS Biology 1: 110-115.
43. Cranbrook E, Payne J, Leh CMU (2008) Origin of the elephants Elephas maximus L. of Borneo Sarawak Museum Journal.
44. Silva SGD, (1968) Elephants of Sabah. Sabah Society Journal III (4): 169-181.
45. Shim PS, (2003) Another look at the Borneo elephant. Sabah Society Journal 20: 7-14.
46. Alfred R, Ahmad AH, Payne J, William C, Ambu L, (2010) Density and Population Estimation of the Bornean Elephants (Elephas maximus borneensis) in Sabah Online Journal of Biological Sciences 10. (2): 92-102.
47. Barchi L, Lanteri S, Portis E, Acquadro A, Valè G, et al. (2011) Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genomics 12: 304.
48. James MR, Roth RB, Michael MS, Kammerer S, Nelson MR, et al. (2005) BRAF Polymorphisms and Risk of Melanocytic Neoplasia. The Jornal of Investigative Dermatology: 1252-1258.
49. Ouborg NJ, Pertoldi C, Loeschcke V, Bijlsma RK, Hedrick PW (2010) Conservation genetics in transition to conservation genomics. Trends in Genetics 26 No (4): 177-187.
50. Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA, (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res 17: 240-248.
51. Lewis ZA, Shiver AL, Stiffler N, Miller MR, Johnson EA, et al. (2007) High-Density Detection of Restriction-Site-Associated DNA Markers for Rapid Mapping of Mutated Loci in Neurospora. Genetics 177: 1163-1171.
52. Chutimanitsakun Y, Nipper RW, Cuesta-Marcos A, Cistué L, Corey A, et al. (2011) Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley. BMC Genomics 12: 4.
53. O'Rourke SM, Yochem J, Connolly AA, Price MH, Carter L, et al. (2011) Rapid Mapping and Identification of Mutations in Caenorhabditis elegans by Restriction Site-Associated DNA Mapping and Genomic Interval Pull-Down Sequencing. Genetics 189: 767-778.
54. Scaglione D, Acquadro A, Portis E, Tirone M, Knapp SJ, et al. (2012) RAD tag sequencing as a source of SNP markers in Cynara cardunculus L. BMC Genomics. 13: 3.
55. Davey JW, Blaxter ML, (2011) RADSeq: next-generation population genetics. Briefings in Functional Genomics 9 5: 416-423.
56. Li R, Fan W, Tian G, Zhu H, He L, et al. (2010) The sequence and de novo assembly of the giant panda genome. Nature 463: 311-317.
57. Ogden R, (2011) Unlocking the potential of genomic technologies for wildlife forensics. Molecular Ecology Resources 11: 109-116.
58. Abdelkrim J, Robertson BC, Stanton J-AL, Gemmell NJ, (2009) Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing. BioTechniques 46: 185-192.
59. Castoe TA, Poole AW, Gu W, Koning APJD, Daza JM, et al. (2010) Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence. Molecular Ecology Resources 10: 341-347.
60. Perry JC, Rowe L, (2011) Rapid Microsatellite Development for Water Striders by Next-Generation Sequencing. Journal of Heredity 102: 125-129.
61. Gardner MG, Fitch AJ, Bertozzi T, Lowe AJ, (2011) Rise of the machines-recommendations for ecologists when using next generation sequencing for microsatellite development. Molecular Ecology Resources 11: 1093-1101.
62. Glenn TC, (2011) Field guide to next-generation DNAsequencers. Molecular Ecology Resources 11: 759-769.
63. Broders KD, Woeste KE, Sanmiguel PJ, 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.
64. Hohenlohe PA, Amish SJ, Catchen JM, Aleendorf FW, Luinkart G, (2011) Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout. Molecular Ecology Resources 11(Suppl. 1): 117-122.
65. Zerbino D, Birney E, (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18: 821-829.
66. Li H, Ruan J, Durbin R, (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research 18: 1851-1858.
67. Gabriel S, Ziaugra L, Tabbaa D (2009) SNP Genotyping Using the Sequenom MassARRAY iPLEX Platform. Current Protocols in Human Genetics 2.12.11-12.12.18.
68. Taberlet P, Griffin S, Goossens B, Questiau S, Manceau V, et al. (1996) Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Research 24: 3189-3194.
69. Schlötterer C, Tautz D, (1992) Slippage synthesis of simple sequence DNA. Nucleic Acids Research 20: 211-215.
70. Valière N, (2002) GIMLET: a computer program for analysing genetic individual identification data. Molecular Ecology Notes 2: 377-379.
71. Xu S, Gupta S, Jin L, (2010) PEAS V1.0: a package for elementary analysis of SNP data. Molecular Ecology Resources 10: 1085-1088.
72. Rohland N, Reich D, Mallick S, Meyer M, Green RE, et al. (2010) Genomic DNA Sequences from Mastodon and Woolly Mammoth Reveal Deep Speciation of Forest and Savanna Elephants. PLoS Biology.
73. Li H, Durbin R, (2009) Fast and accurate short read alignment with burrows-wheeler transform Bioinformatics. 25: 1754-1760.
74. Faircloth BC, (2008) MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design. Molecular Ecology Resources 8: 92-94.
75. Rychlik W, Rhoads RE, (1989) A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA. Nucleic Acids Res 17: 8543-8551.