Transcriptome of the dead: Characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Hoffman, Joseph I ^a   Thorne, Michael A S ^b   Trathan, Philip N ^b   Forcada, Jaume ^b  

^a BIELEFELD UNIVERSITY   (Germany)

^b BRITISH ANTARCTIC SURVEY   (United Kingdom)

Author keywords

Antarctic fur seal; Arctocephalus gazella; Genomics; Immune gene; Major Histocompatibility Complex (MHC); Marine mammal; Microsatellite; Non model organism; Pinniped; Post mortem; Single Nucleotide Polymorphism (SNP); Transcriptome

Indexed keywords

COMPLEMENTARY DNA; CONTIG; TRANSCRIPTOME;

ADULT ANIMAL; ANIMAL TISSUE; ARCTOCEPHALUS GAZELLA; ARTICLE; AUTOPSY; CARCASS; CELL DEATH; COMPUTER MODEL; CONTROLLED STUDY; DNA SEQUENCE; DOG; GENOMICS; HEART; INTESTINE; KIDNEY PARENCHYMA; LUNG PARENCHYMA; MAJOR HISTOCOMPATIBILITY COMPLEX; MALE; MARINE MAMMAL; MICROSATELLITE MARKER; NONHUMAN; SAMPLE; SEAL; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; SKIN; SOUTH GEORGIA AND THE SOUTH SANDWICH ISLANDS; SPECIES CONSERVATION; SPLEEN; TESTIS;

ANIMALS; AQUATIC ORGANISMS; AUTOPSY; COMPUTATIONAL BIOLOGY; DOGS; FUR SEALS; GENE EXPRESSION PROFILING; GENETIC MARKERS; MALE; ORGAN SPECIFICITY; RNA, MESSENGER;

ARCTOCEPHALUS GAZELLA; AVES; CANIS FAMILIARIS; MAMMALIA; PINNIPEDIA;

EID: 84872685602     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-52     Document Type: Article

References (47)

1. Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH. Rapid transcriptome characterization for a non-model organism using 454 pyrosequencing. Mol Ecol 2008, 17:1636-1647. 10.1111/j.1365-294X.2008.03666.x, 18266620.
2. Nagaraj SH, Gasser RB, Ranganathan S. A hitchhiker's guide to expressed sequence tag (EST) analysis. Briefings in Bioinformatics 2007, 8:6-21.
3. Bouck A, Vision T. The molecular ecologist's guide to expressed sequence tags. Mol Ecol 2007, 16:907-924.
4. Hudson ME. Sequencing breakthroughs for genomic ecology and evolutionary biology. Mol Ecol Resour 2008, 8:3-17. 10.1111/j.1471-8286.2007.02019.x, 21585713.
5. Wheat CW. Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing. Genetica 2010, 138:433-451. 10.1007/s10709-008-9326-y, 18931921.
6. Slate J, Santure AW, Feulner PGD, Brown EA, Ball AD, Johnston SE, Gratten J. Genome mapping in intensively studied wild vertebrate populations. Trends in Genetics 2010, 26:275-284. 10.1016/j.tig.2010.03.005, 20444518.
7. Ouborg NJ, Pertoldi C, Loeschcke V, Bilksma R, Hedrick PW. Conservation genetics in transition to conservation genomics. Trends in Genetics 2010, 26:177-187. 10.1016/j.tig.2010.01.001, 20227782.
8. Wang B, Ekblom R, Castoe TA, Jones EP, Kozma R, Bongcam-Rudloff E, Pollock DD, Hoglund J. Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development. Open Biology 2012, 2:120054. 10.1098/rsob.120054, 3376728, 22724064.
9. Vogel H, Altincicek B, Glockner G, Vilcinkas A. A comprehensive transcriptome and immune-gene repertoire of the lepidopteran model host Galleria mellonella. BMC Genomics 2011, 12:308. 10.1186/1471-2164-12-308, 3224240, 21663692.
10. Clark MS, Thorne MAS, Vieira FA, Cardoso JCR, Power DM, Peck LS. Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing. BMC Genomics 2010, 11:362. 10.1186/1471-2164-11-362, 2896379, 20529341.
11. 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.
12. Kang HJ, Kawasawa YI, Cheng F, Zhu Y, Xu X, Li M, Sousa AM, Pletikos M, Meyer KA, Sedmak G, et al. Spatio-temporal transcriptome of the human brain. Nature 2011, 478:483-489. 10.1038/nature10523, 22031440.
13. Cherel P, Herault F, Vincent A, Le Roy P, Damon M. Genetic variability of transcript abundance in pig skeletal muscle at slaughter: relationships with meat quality traits. J Anim Sci 2011, 90:699-708.
14. Hoffman JI, Grant SM, Forcada J, Phillips CD. Bayesian inference of a historical genetic bottleneck in a heavily exploited marine mammal. Mol Ecol 2011, 20:3989-4008. 10.1111/j.1365-294X.2011.05248.x, 21895820.
15. Read AJ. The looming crisis: interactions between marine mammals and fisheries. J Mammal 2008, 89:541-548.
16. Simmonds MP, Isaac SJ. The impacts of climate change on marine mammals: early signs of significant problems. Oryx 2007, 41:19-26.
17. Mancia A, Lundqvist ML, Romano TA, Peden-Adams M, Fair PA, Kindy MS, Ellis BC, Gattoni-Celli S, McKillen DJ, Trent HF, et al. A dolphin peripheral blood leukocyte cDNA microarray for studies of immune function and stress reactions. Dev Comp Immunol 2007, 31:520-529. 10.1016/j.dci.2006.07.011, 17084893.
18. Ierardi JL, Mancia A, McMillan J, Lundqvist ML, Romano TA, Wise JP, Warr GW, Chapman RW. Sampling the transcriptome of the North Atlantic right whale. Comp Biochem Physiol, Part D 2009, 4:154-158.
19. Osterhaus ADME, Groen J, Spijkers HEM, Broeders HWJ, UytdeHaag FGCM, de Vries P, Teppema JS, Visser IKG, van de Bildt MWG, Vedder EJ. Mass mortality in seals caused by a newly discovered virus-like morbillivirus. Vet Microbiol 1990, 23:343-350. 10.1016/0378-1135(90)90165-R, 2205971.
20. Mattlin RH. Pup mortality of the New Zealand fur seal (Arctocephalus forsteri lesson). N Z J Ecol 1978, 1:138-144.
21. Pyenson ND. The high fidelity of the cetacean stranding record: insights into measuring diversity by integrating taphonomy and macroecology. Proc R Soc London, Ser B online early.
22. McCann TS. Territoriality and breeding behaviour of adult male Antarctic fur seal, Arctocephalus gazella. J Zool (London) 1980, 192:295-310.
23. Doidge DW, Croxall JP, Ricketts C. Growth rates of Antarctic fur seal Arctocephalus gazella pups at South Georgia. J Zool (London) 1984, 203(MAY):87-93.
24. Hoffman JI, Boyd IL, Amos W. Male reproductive strategy and the importance of maternal status in the Antarctic fur seal Arctocephalus gazella. Evolution 2003, 57(8):1917-1930.
25. Hoffman JI, Boyd IL, Amos W. Exploring the relationship between parental relatedness and male reproductive success in the Antarctic fur seal Arctocephalus gazella. Evolution 2004, 58(9):2087-2099.
26. Hoffman JI, Forcada J, Amos W. Getting long in the tooth: a strong positive correlation between canine size and heterozygosity in the Antarctic fur seal Arctocephalus gazella. J Hered 2010, 101:527-538. 10.1093/jhered/esq045, 20457622.
27. Hoffman JI, Forcada J, Trathan PN, Amos W. Female fur seals show active choice for males that are heterozygous and unrelated. Nature 2007, 445:912-914. 10.1038/nature05558, 17287726.
28. Hoffman JI, Forcada J, Amos W. Exploring the mechanisms underlying a heterozygosity-fitnesss correlation for canine size in the Antarctic fur seal Arctocephalus gazella. J Hered 2010, 101:539-552. 10.1093/jhered/esq046, 20457623.
29. Hoffman JI. Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome. Mol Ecol Resour 2011, 11:703-710. 10.1111/j.1755-0998.2011.02999.x, 21466659.
30. Hoffman JI, Nichols HJ. A novel approach for mining polymorphic microsatellite markers in silico. PLoS One 2011, 6:e23283. 10.1371/journal.pone.0023283, 3154332, 21853104.
31. Hoffman JI, Tucker R, Clark MS, Forcada J, Slate J. Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal. Mol Ecol Resour 2012, 12:861-872. 10.1111/j.1755-0998.2012.03158.x, 22727236.
32. da Assunção Soares Franco M, Hoffman JI, Harwood J, Amos W. MHC genotype is a dominant predictor of mortality in the grey seal. Scientific Reports 2012, 2:659. 3447382, 22997548.
33. Huang X, Madan A. CAP 3: a DNA sequence assembly program. Genome Res 1999, 9:868-877. 10.1101/gr.9.9.868, 310812, 10508846.
34. Kumar S, Blaxter ML. Comparing de novo assemblers for 454 transcriptome data. BMC Genomics 2010, 11:571. 10.1186/1471-2164-11-571, 3091720, 20950480.
35. Ekblom R, Balakrishnan CN, Burke T, Slate J. Digital gene expression analysis of the zebra finch genome. BMC Genomics 2010, 11:219. 10.1186/1471-2164-11-219, 2996964, 20359325.
36. Santure AW, Gratten J, Mossman JA, Sheldon BC, Slate J. Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing. BMC Genomics 2011, 12:283. 10.1186/1471-2164-12-283, 3125266, 21635727.
37. Baker JR, Doidge DW. Pathology of the Antarctic fur seal (Arctocephalus gazella) in South Georgia. Br Vet J 1984, 140:210-219. 10.1016/0007-1935(84)90084-8, 6722508.
38. Acevedo-Whitehouse K, Cunningham AA. Is MHC enough for understanding wildlife immunogenetics?. Trends Ecol Evol 2006, 21(8):433-438. 10.1016/j.tree.2006.05.010, 16764966.
39. Higdon JW, Bininda-Edmonds ORP, Beck RMD, Ferguson SH. Phylogeny and divergence of the pinnipeds (Carnivora: Mammalia) assessed using a multigene dataset. BMC Evol Biol 2007, 7:216. 10.1186/1471-2148-7-216, 2245807, 17996107.
40. Osborne AJ, Brauning R, Schultz JK, Kennedy MA, Slate J, Gemmell NJ. Development of a predicted physical map of microsatellite locus positions for pinnipeds, with wider applicability to the Carnivora. Mol Ecol Resour 2010, 11:503-513.
41. Galperin MY, Cochrane GR. The 2011 nucleic acids research database issue and the online molecular biology database collection. Nucleic Acids Res 2011, 39:D1-D6. 10.1093/nar/gkq1243, 3013748, 21177655.
42. Bairoch A, Apweiler R. The SWISS-PROT protein sequence data bank and its new supplement TREMBL. Nucleic Acids Res 1996, 24:21-25. 10.1093/nar/24.1.21, 145613, 8594581.
43. Altschul SF, Gish W, Miller W, Myers EW, L DJ. Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
44. Wagner JL. Molecular organization of the canine major histocompatibility complex. J Hered 2003, 94(1):23-26. 10.1093/jhered/esg002, 12692158.
45. Debenham SL, Hart EA, Ashurst JL, Howe KL, Quail MA, Ollier WER, Binns MM. Genomic sequence of the class I region of the canine MHC: comparison with the MHC of other mammalian species. Genomics 2005, 85:48-59. 10.1016/j.ygeno.2004.09.009, 15607421.
46. Phobos 3.3.11 http://www.rub.de/spezzoo/cm/cm_phobos.htm.
47. Brockman W, Alvarez P, Young S, Garber M, Giannoukos G, Lee WL, Russ C, Lander ES, Nusbaum C, Jaffe DB. Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res 2008, 18:763-770. 10.1101/gr.070227.107, 2336812, 18212088.