Genome-wide polymorphism and comparative analyses in the white-tailed deer (Odocoileus virginianus): A model for conservation genomics

PLoS ONE

Volumn 6, Issue 1, 2011, Pages

  Sabury, Christopher M ^a   Bhattarai, Eric K ^a   Taylor, Jeremy F ^b   Viswanathan, Ganesh G ^a   Cooper, Susan M ^c   Davis, Donald S ^a   Dowd, Scot E ^d   Lockwood, Mitch L ^e   Seabury, Paul M ^f  

^a TEXAS A AND M UNIVERSITY   (United States)

^b UNIVERSITY OF MISSOURI   (United States)

^c TEXAS A AND M UNIVERSITY   (United States)

^d Medical Biofilm Research Institute Lubbock   (United States)

^e TEXAS PARKS AND WILDLIFE DEPARTMENT   (United States)

^f ElanTech Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONSERVATION GENETICS; CONTROLLED STUDY; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC POLYMORPHISM; GENETIC VARIABILITY; HAPLOTYPE; MITOCHONDRIAL GENOME; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PYROSEQUENCING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION PROCESS; WHITE TAILED DEER; ANIMAL; CATTLE; COMPARATIVE STUDY; DEER; DNA SEQUENCE; ENDANGERED SPECIES; ENVIRONMENTAL PROTECTION; GENE LIBRARY; GENETIC ASSOCIATION; GENETICS; GENOMICS; METHODOLOGY; MOLECULAR GENETICS; NORTH AMERICA; PHYLOGENY;

BOS TAURUS; CERVIDAE; MAMMALIA; ODOCOILEUS VIRGINIANUS;

MITOCHONDRIAL DNA;

ANIMALS; CATTLE; CONSERVATION OF NATURAL RESOURCES; DEER; DNA, MITOCHONDRIAL; ENDANGERED SPECIES; GENE LIBRARY; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; NORTH AMERICA; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 79251646352     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0015811     Document Type: Article

References (55)

1. Baker RH (1984) White-tailed Deer: Ecology and Management Halls LK, ed. Harrisburg: Stackpole Books. pp 1-18.
2. Nowak RM (1999) Walker's Mammals of the World Volume II, sixth ed. Baltimore and London: The Johns Hopkins University Press. pp 1114-1118.
3. Wilson DE, Reeder DM (2005) Mammal Species of the World: A Taxonomic and Geographic Reference, third ed. Baltimore: The Johns Hopkins University Press. pp 657-685.
4. Gallagher DS, Jr., Derr JN, Womack JE (1994) Chromosome conservation among the advanced pecorans and determination of the primitive bovid karyotype. J Hered 85: 204-210.
5. st century. Wildlife Society Bulletin 25: 213-214.
6. Bubenik GA, Brown RD, Schams D, Bartos L (1999) The effect of ACTH on the GnRH-induced release of LH and testosterone in male white-tailed deer. Comp Biochem Physiol C Pharmacol Toxicol Endocrinol 122: 173-179.
7. DeYoung RW, Demarais S, Honeycutt RL, Rooney AP, Gonzales RA, et al. (2003) Genetic consequences of white-tailed deer (Odocoileus virginianus) restoration in Mississippi. Mol Ecol 12: 3237-3252.
8. Locke SL, Cook MW, Harveson LA, Davis DS, Lopez RL, et al. (2007) Effectiveness of Spayvac® for reducing white-tailed deer fertility. J Wildl Dis 43: 726-730.
9. Anderson JD, Honeycutt RL, Gonzales RA, Gee KL, Skow LC, et al. (2002) Development of microsatellite DNA markers for the automated genetic characterization of white-tailed deer populations. J Wildl Manage 66: 67-74.
10. DeYoung RW, Demarais S, Honeycutt RL, Gonzales RA, Gee KL, et al. (2003) Evaluation of a deer microsatellite panel useful for genetic exclusion studies in white-tailed deer. Wildlife Society Bulletin 31: 220-232.
11. Griffin JF, Mackintosh CG (2000) Tuberculosis in deer: perceptions, problems, and progress. Vet J 160: 202-219.
12. Waters WR, Palmer MV, Thacker TC, Orloski K, Nol P, et al. (2008) Blood culture and stimulation conditions for the diagnosis of tuberculosis in cervids by the Cervigam assay. Vet Rec 162: 203-208.
13. Haley NJ, Seelig DM, Zabel MD, Telling GC, Hoover EA (2009)Detection of CWD prions in urine and saliva of deer by transgenic mouse bioassay. PLoS One 4: e4848.
14. Joly DO, Samuel MD, Langenberg JA, Rolley RE, Keane DP (2009) Surveillance to detect chronic wasting disease in white-tailed deer in Wisconsin. J Wildl Dis 45: 989-997.
15. Keane D, Barr D, Osborn R, Langenberg J, O'Rourke K, et al. (2009) Validation of use of rectoanal mucosa-associated lymphoid tissue for immunohistochemical diagnosis of chronic wasting disease in white-tailed deer (Odocoileus virginianus). J Clin Microbiol 47: 1412-1417.
16. O'Brien DJ, Schmitt SM, Lyashchenko KP, Waters WR, Berry DE, et al. (2009) Evaluation of blood assays for detection of Mycobacterium bovis in white-tailed deer (Odocoileus virginianus) in Michigan. J Wildl Dis 45: 153-164.
17. Wobeser G (2009) Bovine tuberculosis in Canadian wildlife: An Updated history. Can Vet J 50: 1169-1176.
18. Allison AB, Goekjian VH, Potgieter AC, Wilson WC, Johnson DJ, et al. (2010) Detection of a novel reassortant epizootic hemorrhagic disease virus (EHDV) in the USA containing RNA segments derived from both exotic (EHDV-6) and endemic (EHDV-2) serotypes. J Gen Virol 91: 430-439.
19. DeYoung RW, Demarais S, Gonzales RA, Honeycutt RL, Gee KL (2002) Multiple paternity in white-tailed deer (Odocoileus virginianus) revealed by DNA microsatellites. J Mammal 83: 884-892.
20. Ernest HB, Hoar BR, Well JA, O'Rourke KI (2010) Molecular genealogy tools for white-tailed deer with chronic wasting disease. Can J Vet Res 74: 153-156.
21. Williams ES, Miller MW (2002) Chronic wasting disease in deer and elk in North America. Rev Sci Tech 21: 305-316.
22. O'Rourke KI, Spraker TR, Hamburg LK, Besser TE, Brayton KE, et al. (2004) Polymorphisms in the prion precursor functional gene but not the pseudogene are associated with susceptibility to chronic wasting disease in white-tailed deer. J Gen Virol 85: 1339-1346.
23. Blanchong JA, Heisey DM, Scribner KT, Libants SV, Johnson C, et al. (2009) Genetic susceptibility to chronic wasting disease in free-ranging white-tailed deer: complement component C1q and PRNP polymorphisms. Infect Genet Evol 9: 1329-1335.
24. Wilson GA, Nakada SM, Bollinger TK, Pybus MJ, Merrill EH, et al. (2009) Polymorphisms at the PRNP gene influence susceptibility to chronic wasting disease in two species of deer (Odocoileus Spp) in western Canada. J Toxicol Environ Health A 72: 1025-1029.
25. 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.
26. Wiedmann RT, Smith TPL, Nonneman DJ (2008) SNP Discovery in swine by reduced representation and high-throughput pyrosequencing. BMC Genet 9: 81.
27. Everts-van der Wind A, Larkin DM, Green CA, Eliott JS, Olmstead CA, et al. (2005) A high-resolution whole-genome cattle-human comparative map reveals details of mammalian chromosome evolution. Proc Natl Acad Sci USA 102: 18526-18531.
28. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology, The Gene Ontology Consortium. Nat Genet 25: 25-29.
29. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, et al. (1999) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 27: 29-34.
30. Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, et al. (2005) The universal protein resource (UniProt). Nucleic Acids Res 33: D154-D159.
31. Dowd SE, Zaragoza J, Rodriguez JR, Oliver MJ, Payton PR (2005) Windows. NET network distributed basic local alignment search toolkit (W.ND-BLAST). BMC Bioinformatics 6: 93.
32. Dennis G, Jr., Sherman BT, Hosack DA, Yang J, Gao W, et al. (2003) DAVID: Database for annotation, visualization, and integrated discovery.Genome Biol 4: P3.
33. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964.
34. Seabury CM, Seabury PM, Decker JE, Schnabel RD, Taylor JF, et al. (2010) Diversity and evolution of 11 innate immune genes in Bos taurus taurus and Bos taurus indicus cattle. Proc Natl Acad Sci USA 107: 151-156.
35. Ronquist F, Huelsenbeck JP (2003) MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
36. Douzery E, Randi E (1997) The mitochondrial control region of Cervidae: Evolutionary patterns and phylogenetic content. Mol Biol Evol 14: 1154-1166.
37. Wada K, Nishibori M, Yokohama M (2007) The complete nucleotide sequence of mitochondrial genome in the Japanese Sika deer (Cervus Nippon), and a phylogenetic analysis between Cervidae and Bovidae. Small Ruminant Res 69: 46-54.
38. Pang H, Liu W, Chen Y, Fang L, Zhang X, et al. (2008) Identification of complete mitochondrial genome of the tufted deer. Mitochondrial DNA 19: 411-417.
39. Gilbert C, Ropiquet A, Hassanin A (2006) Mitochondrial and nuclear phylogenies of Cervidae (Mammalia, Ruminantia): Systematics, morphology, and biogeography. Mol Phylogenet Evol 40: 101-117.
40. Decker JE, Pires JC, Conant GC, McKay SD, Heaton MP, et al. (2009) Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics. Proc Natl Acad Sci USA 106: 18644-18649.
41. Baker SV, Fritsch JA (1997) New territory for deer management: human conflicts on the suburban frontier. Wildlife Society Bulletin 25: 404-407.
42. Peterson NM, Lopez RR, Silvy NJ, Owen CB, Frank PA (2003) Evaluation of deer-exclusion grates in urban areas. Wildlife Society Bulletin 31: 1198-1204.
43. Lopez RR, Viera ME, Silvy NJ, Frank PA, Whisenant SW (2003) Survival, mortality, and life expectancy of Florida Key deer. J Wildl Manage 67: 34-45.
44. Rhyan JC, Spraker TR (2010) Emergence of diseases from wildlife reservoirs. Vet Pathol 47: 34-39.
45. Taylor LH, Latham SM, Woolhouse MEJ (2001) Risk factors for human disease emergence. Phil Trans R Soc Lond B Biol Sci 356: 983-989.
46. Jones KE, Patel NG, Levy MA, Storeygard A, Balk D, et al. (2008) Global trends in emerging infectious diseases. Nature 451: 990-993.
47. Cutler SJ, Fooks AR, van der Poel WHM (2010) Public health threat of new reemerging, and neglected zoonoses in the industrialized world. Emerg Infect Dis 16: 1-7.
48. Liu Y, Qin X, Song X-Z, Jian H, Shen Y, et al. (2009) Bos taurus genome assembly. BMC Genomics 10: 180.
49. Eid J, Fehr A, Gray J, Luong K, Lyle J, et al. (2009) Real-time DNA sequencing from single polymerase molecules. Science 323: 133-138.
50. Lewin HA, Larkin DM, Pontius J, O'Brien SJ (2009) Every genome sequence needs a good map. Genome Res 19: 1925-1928.
51. Van Tassell 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. Nat Methods 5: 247-252.
52. Sanchez CC, Smith TPL, Wiedman RT, Vallejo RL, Salem M, et al. (2009) Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library. BMC Genomics 10: 559.
53. Guha S, Goyal SP, Kashyap VK (2007) Molecular phylogeny of the musk deer: A genomic view with mitochondrial 16S rRNA and cytochrome b gene. Mol Phylogenet Evol 42: 585-597.
54. Brockman W, Alvarez P, Young S, Garber M, Giannoukos G, et al. (2008) Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res 18: 763-770.
55. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599.