Table of Contents Author Guidelines Submit a Manuscript
International Journal of Genomics
Volume 2016 (2016), Article ID 2374610, 12 pages
http://dx.doi.org/10.1155/2016/2374610
Review Article

Integrating Genomic Data Sets for Knowledge Discovery: An Informed Approach to Management of Captive Endangered Species

1College of Veterinary Medicine, Western University of Health Sciences, 309 East Second Street, Pomona, CA 91766, USA
2The Applied Genomics Center, Graduate College of Biomedical Sciences, Western University of Health Sciences, 309 East Second Street, Pomona, CA 91766, USA
3Danforth Center, 975 N. Warson Road, St. Louis, MO 63132, USA

Received 24 December 2015; Revised 19 March 2016; Accepted 21 March 2016

Academic Editor: Ettore Randi

Copyright © 2016 Kristopher J. L. Irizarry et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. R. Ekblom and J. B. W. Wolf, “A field guide to whole-genome sequencing, assembly and annotation,” Evolutionary Applications, vol. 7, no. 9, pp. 1026–1042, 2014. View at Publisher · View at Google Scholar · View at Scopus
  2. N. J. Ouborg, C. Pertoldi, V. Loeschcke, R. K. Bijlsma, and P. W. Hedrick, “Conservation genetics in transition to conservation genomics,” Trends in Genetics, vol. 26, no. 4, pp. 177–187, 2010. View at Publisher · View at Google Scholar · View at Scopus
  3. C. C. Steiner, A. S. Putnam, P. E. A. Hoeck, and O. A. Ryder, “Conservation genomics of threatened animal species,” Annual Review of Animal Biosciences, vol. 1, pp. 261–281, 2013. View at Publisher · View at Google Scholar · View at Scopus
  4. Z. Jiang, H. Wang, J. J. Michal et al., “Genome wide sampling sequencing for SNP genotyping: methods, challenges and future development,” International Journal of Biological Sciences, vol. 12, no. 1, pp. 100–108, 2016. View at Publisher · View at Google Scholar
  5. A. B. Shafer, J. B. Wolf, P. C. Alves et al., “Genomics and the challenging translation into conservation practice,” Trends in Ecology & Evolution, vol. 30, no. 2, pp. 78–87, 2015. View at Google Scholar
  6. F. Tekaia, “Inferring orthologs: open questions and perspectives,” Genomics Insights, vol. 9, pp. 17–28, 2016. View at Publisher · View at Google Scholar
  7. B. J. Mcmahon, E. C. Teeling, and J. Höglund, “How and why should we implement genomics into conservation?” Evolutionary Applications, vol. 7, no. 9, pp. 999–1007, 2014. View at Publisher · View at Google Scholar · View at Scopus
  8. M. H. Kohn, W. J. Murphy, E. A. Ostrander, and R. K. Wayne, “Genomics and conservation genetics,” Trends in Ecology and Evolution, vol. 21, no. 11, pp. 629–637, 2006. View at Publisher · View at Google Scholar · View at Scopus
  9. M. N. Romanov, M. Koriabine, M. Nefedov, P. J. de Jong, and O. A. Ryder, “Construction of a California condor BAC library and first-generation chicken-condor comparative physical map as an endangered species conservation genomics resource,” Genomics, vol. 88, no. 6, pp. 711–718, 2006. View at Publisher · View at Google Scholar · View at Scopus
  10. M. N. Romanov, E. M. Tuttle, M. L. Houck et al., “The value of avian genomics to the conservation of wildlife,” BMC Genomics, vol. 10, supplement 2, article S10, 2009. View at Publisher · View at Google Scholar · View at Scopus
  11. R. G. Felton, C. C. Steiner, B. S. Durrant, D. H. Keisler, M. R. Milnes, and C. W. Tubbs, “Identification of California condor estrogen receptors 1 and 2 and their activation by endocrine disrupting chemicals,” Endocrinology, vol. 156, no. 12, pp. 4448–4457, 2015. View at Publisher · View at Google Scholar
  12. B. Ujvari and K. Belov, “Major Histocompatibility Complex (MHC) markers in conservation biology,” International Journal of Molecular Sciences, vol. 12, no. 8, pp. 5168–5186, 2011. View at Publisher · View at Google Scholar · View at Scopus
  13. J. B. Hans, A. Haubner, M. Arandjelovic et al., “Characterization of MHC class II B polymorphism in multiple populations of wild gorillas using non-invasive samples and next-generation sequencing,” American Journal of Primatology, vol. 77, no. 11, pp. 1193–1206, 2015. View at Publisher · View at Google Scholar · View at Scopus
  14. S. A. Ellis and J. A. Hammond, “The functional significance of cattle major histocompatibility complex class I genetic diversity,” Annual Review of Animal Biosciences, vol. 2, pp. 285–306, 2014. View at Publisher · View at Google Scholar · View at Scopus
  15. J. H. Robinson and A. A. Delvig, “Diversity in MHC class II antigen presentation,” Immunology, vol. 105, no. 3, pp. 252–262, 2002. View at Publisher · View at Google Scholar · View at Scopus
  16. J. E. Deakin and K. Belov, “A comparative genomics approach to understanding transmissible cancer in Tasmanian devils,” Annual Review of Genomics and Human Genetics, vol. 13, pp. 207–222, 2012. View at Publisher · View at Google Scholar · View at Scopus
  17. T. Callicrate, R. Dikow, J. W. Thomas, J. C. Mullikin, E. D. Jarvis, and R. C. Fleischer, “Genomic resources for the endangered Hawaiian honeycreepers,” BMC Genomics, vol. 15, no. 1, article 1098, 2014. View at Publisher · View at Google Scholar · View at Scopus
  18. C. Der Sarkissian, L. Ermini, M. Schubert et al., “Evolutionary genomics and conservation of the endangered Przewalski's horse,” Current Biology, vol. 25, no. 19, pp. 2577–2583, 2015. View at Publisher · View at Google Scholar
  19. R. A. Griffiths and L. Pavajeau, “Captive breeding, reintroduction, and the conservation of amphibians,” Conservation Biology, vol. 22, no. 4, pp. 852–861, 2008. View at Publisher · View at Google Scholar · View at Scopus
  20. G. Harding, R. A. Griffiths, and L. Pavajeau, “Developments in amphibian captive breeding and reintroduction programs,” Conservation Biology, vol. 30, no. 2, pp. 340–349, 2016. View at Publisher · View at Google Scholar
  21. W. Miller, S. J. Wright, Y. Zhang, S. C. Schuster, and V. M. Hayes, “Optimization methods for selecting founder individuals for captive breeding or reintroduction of endangered species,” in Proceedings of the 15th Pacific Symposium on Biocomputing (PSB '10), pp. 43–53, January 2010. View at Scopus
  22. Z. Wang, M. Gerstein, and M. Snyder, “RNA-Seq: a revolutionary tool for transcriptomics,” Nature Reviews Genetics, vol. 10, no. 1, pp. 57–63, 2009. View at Publisher · View at Google Scholar · View at Scopus
  23. S. Bhatia, “Genetic variation as a modifier of association between therapeutic exposure and subsequent malignant neoplasms in cancer survivors,” Cancer, vol. 121, no. 5, pp. 648–663, 2015. View at Publisher · View at Google Scholar · View at Scopus
  24. S. J. O'Brien, “A role for molecular genetics in biological conservation,” Proceedings of the National Academy of Sciences of the United States of America, vol. 91, no. 13, pp. 5748–5755, 1994. View at Publisher · View at Google Scholar
  25. J. M. Heather and B. Chain, “The sequence of sequencers: the history of sequencing DNA,” Genomics, vol. 107, no. 1, pp. 1–8, 2016. View at Publisher · View at Google Scholar
  26. R. J. Elshire, J. C. Glaubitz, Q. Sun et al., “A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species,” PLoS ONE, vol. 6, no. 5, Article ID e19379, 2011. View at Publisher · View at Google Scholar · View at Scopus
  27. W. B. Barbazuk, S. J. Emrich, H. D. Chen, L. Li, and P. S. Schnable, “SNP discovery via 454 transcriptome sequencing,” Plant Journal, vol. 51, no. 5, pp. 910–918, 2007. View at Publisher · View at Google Scholar · View at Scopus
  28. G. K. Wong, B. Liu, J. Wang et al., “A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms,” Nature, vol. 432, no. 7018, pp. 717–722, 2004. View at Google Scholar
  29. “The Human Genome Project Completion: Frequently Asked Questions,” March 2016, http://www.genome.gov/11006943.
  30. R. VanBuren, D. Bryant, P. P. Edger et al., “Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum,” Nature, vol. 527, no. 7579, pp. 508–511, 2015. View at Publisher · View at Google Scholar
  31. M. Baker, “Functional genomics: the changes that count,” Nature, vol. 482, no. 7384, pp. 257–262, 2012. View at Publisher · View at Google Scholar · View at Scopus
  32. J.-W. Choi, X. Liao, S. Park et al., “Massively parallel sequencing of Chikso (Korean brindle cattle) to discover genome-wide SNPs and InDels,” Molecules and Cells, vol. 36, no. 3, pp. 203–211, 2013. View at Publisher · View at Google Scholar · View at Scopus
  33. A. Dousse, T. Junier, and E. M. Zdobnov, “CEGA-a catalog of conserved elements from genomic alignments,” Nucleic Acids Research, vol. 44, no. 1, pp. D96–D100, 2016. View at Publisher · View at Google Scholar
  34. B. Grumbt, S. H. Eck, T. Hinrichsen, and K. Hirv, “Diagnostic applications of next generation sequencing in immunogenetics and molecular oncology,” Transfusion Medicine and Hemotherapy, vol. 40, no. 3, pp. 196–206, 2013. View at Publisher · View at Google Scholar · View at Scopus
  35. K. E. Grogan, G. J. McGinnis, M. L. Sauther, F. P. Cuozzo, and C. M. Drea, “Next-generation genotyping of hypervariable loci in many individuals of a non-model species: technical and theoretical implications,” BMC Genomics, vol. 17, no. 1, p. 204, 2016. View at Google Scholar
  36. S. Mishra, S. K. Singh, A. K. Munjal, J. Aspi, and S. P. Goyal, “Panel of polymorphic heterologous microsatellite loci to genotype critically endangered Bengal tiger: a pilot study,” SpringerPlus, vol. 3, article 4, 2014. View at Publisher · View at Google Scholar · View at Scopus
  37. W. Wang, Y. Qiao, Y. Zheng, and M. Yao, “Isolation of microsatellite loci and reliable genotyping using noninvasive samples of a critically endangered primate, Trachypithecus leucocephalus,” Integrative Zoology, 2016. View at Publisher · View at Google Scholar
  38. M. A. Nobrega and L. A. Pennacchio, “Comparative genomic analysis as a tool for biological discovery,” Journal of Physiology, vol. 554, no. 1, pp. 31–39, 2004. View at Publisher · View at Google Scholar · View at Scopus
  39. M. H. de Angelis, G. Nicholson, M. Selloum et al. et al., “Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics,” Nature Genetics, vol. 47, no. 9, pp. 969–978, 2015. View at Publisher · View at Google Scholar
  40. N. Ring, T. F. Meehan, A. Blake et al., “A mouse informatics platform for phenotypic and translational discovery,” Mammalian Genome, vol. 26, no. 9-10, pp. 413–421, 2015. View at Publisher · View at Google Scholar · View at Scopus
  41. C. J. Bult, J. T. Eppig, J. A. Blake, J. A. Kadin, and J. E. Richardson, “Mouse genome database 2016,” Nucleic Acids Research, vol. 44, no. 1, pp. D840–D847, 2016. View at Publisher · View at Google Scholar
  42. S. J. O'Brien and N. Yuhki, “Comparative genome organization of the major histocompatibility complex: lessons from the Felidae,” Immunological Reviews, vol. 167, pp. 133–144, 1999. View at Publisher · View at Google Scholar · View at Scopus
  43. M. A. Menotti-Raymond and S. O'Brien, “Evolutionary conservation of ten microsatellite loci in four species of felidae,” Journal of Heredity, vol. 86, no. 4, pp. 319–322, 1995. View at Google Scholar · View at Scopus
  44. D. C. Salim, A. A. Akimoto, C. B. Carvalho et al., “Genetic variability in maned wolf based on heterologous short-tandem repeat markers from domestic dog,” Genetics and Molecular Research, vol. 6, no. 2, pp. 348–357, 2007. View at Google Scholar · View at Scopus
  45. C. R. Miller, J. R. Adams, and L. P. Waits, “Pedigree-based assignment tests for reversing coyote (Canis latrans) introgression into the wild red wolf (Canis rufus) population,” Molecular Ecology, vol. 12, no. 12, pp. 3287–3301, 2003. View at Publisher · View at Google Scholar · View at Scopus
  46. J. J. Johnston and L. G. Biesecker, “Databases of genomic variation and phenotypes: existing resources and future needs,” Human Molecular Genetics, vol. 22, no. 1, Article ID ddt384, pp. R27–R31, 2013. View at Publisher · View at Google Scholar · View at Scopus
  47. M. A. Care, J. R. Bradford, C. J. Needham, A. J. Bulpitt, and D. R. Westhead, “Combining the interactome and deleterious SNP predictions to improve disease gene identification,” Human Mutation, vol. 30, no. 3, pp. 485–492, 2009. View at Publisher · View at Google Scholar · View at Scopus
  48. P. J. Seddon, C. J. Griffiths, P. S. Soorae, and D. P. Armstrong, “Reversing defaunation: restoring species in a changing world,” Science, vol. 345, no. 6195, pp. 406–412, 2014. View at Publisher · View at Google Scholar · View at Scopus
  49. P. H. Silverman, “Commerce and genetic diagnostics,” Hastings Center Report, vol. 25, supplement 3, pp. S15–S18, 1995. View at Google Scholar · View at Scopus
  50. P. Kelly, D. Stack, and J. Harley, “A review of the proposed reintroduction program for the far eastern leopard (Panthera pardus orientalis) and the role of conservation organizations, veterinarians, and zoos,” Topics in Companion Animal Medicine, vol. 28, no. 4, pp. 163–166, 2013. View at Publisher · View at Google Scholar · View at Scopus
  51. H. B. Shaffer, M. Gidiş, E. McCartney-Melstad et al., “Conservation genetics and genomics of amphibians and reptiles,” Annual Review of Animal Biosciences, vol. 3, pp. 113–138, 2015. View at Publisher · View at Google Scholar · View at Scopus
  52. R. R. Swaisgood, F. Wei, W. J. Mcshea, D. E. Wildt, A. J. Kouba, and Z. Zhang, “Can science save the giant panda (Ailuropoda melanoleuca)? Unifying science and policy in an adaptive management paradigm,” Integrative Zoology, vol. 6, no. 3, pp. 290–296, 2011. View at Publisher · View at Google Scholar · View at Scopus
  53. A. L. Holder, J. A. Price, J. P. Adams, H. A. Volk, and B. Catchpole, “A retrospective study of the prevalence of the canine degenerative myelopathy associated superoxide dismutase 1 mutation (SOD1:c.118G > A) in a referral population of German Shepherd dogs from the UK,” Canine Genetics and Epidemiology, vol. 1, no. 1, p. 10, 2014. View at Publisher · View at Google Scholar
  54. M. Menotti-Raymond, V. A. David, S. Pflueger et al., “Widespread retinal degenerative disease mutation (rdAc) discovered among a large number of popular cat breeds,” Veterinary Journal, vol. 186, no. 1, pp. 32–38, 2010. View at Publisher · View at Google Scholar · View at Scopus
  55. M. E. McCue, S. M. Anderson, S. J. Valberg et al., “Estimated prevalence of the Type 1 Polysaccharide Storage Myopathy mutation in selected North American and European breeds,” Animal Genetics, vol. 41, no. 2, pp. 145–149, 2010. View at Publisher · View at Google Scholar · View at Scopus
  56. A. Vinson and M. J. Raboin, “A practical approach for designing breeding groups to maximize genetic diversity in a large colony of captive rhesus macaques (Macaca mulatta),” Journal of the American Association for Laboratory Animal Science, vol. 54, no. 6, pp. 700–707, 2015. View at Google Scholar
  57. J. Rubes, P. Musilova, and G. F. Mastromonaco, “Cytogenetics of wild and captive bred non-domestic animals,” Cytogenetic and Genome Research, vol. 120, no. 1-2, pp. 61–68, 2008. View at Publisher · View at Google Scholar · View at Scopus
  58. R. Hopley and A. Zimmer, “MouseBank: a database application for managing transgenic mouse breeding programs,” Biotechniques, vol. 30, no. 1, pp. 130–132, 2001. View at Google Scholar
  59. D. Boichard and M. Brochard, “New phenotypes for new breeding goals in dairy cattle,” Animal, vol. 6, no. 4, pp. 544–550, 2012. View at Publisher · View at Google Scholar · View at Scopus