메뉴 건너뛰기




Volumn 14, Issue 1, 2013, Pages

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

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;

EID: 84872685602     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-52     Document Type: Article
Times cited : (25)

References (47)
  • 1
    • 41149167170 scopus 로고    scopus 로고
    • Rapid transcriptome characterization for a non-model organism using 454 pyrosequencing
    • 10.1111/j.1365-294X.2008.03666.x, 18266620
    • 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.
    • (2008) Mol Ecol , vol.17 , pp. 1636-1647
    • Vera, J.C.1    Wheat, C.W.2    Fescemyer, H.W.3    Frilander, M.J.4    Crawford, D.L.5    Hanski, I.6    Marden, J.H.7
  • 3
    • 33847051947 scopus 로고    scopus 로고
    • The molecular ecologist's guide to expressed sequence tags
    • Bouck A, Vision T. The molecular ecologist's guide to expressed sequence tags. Mol Ecol 2007, 16:907-924.
    • (2007) Mol Ecol , vol.16 , pp. 907-924
    • Bouck, A.1    Vision, T.2
  • 4
    • 36849073678 scopus 로고    scopus 로고
    • Sequencing breakthroughs for genomic ecology and evolutionary biology
    • 10.1111/j.1471-8286.2007.02019.x, 21585713
    • 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.
    • (2008) Mol Ecol Resour , vol.8 , pp. 3-17
    • Hudson, M.E.1
  • 5
    • 77949302709 scopus 로고    scopus 로고
    • Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing
    • 10.1007/s10709-008-9326-y, 18931921
    • 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.
    • (2010) Genetica , vol.138 , pp. 433-451
    • Wheat, C.W.1
  • 7
    • 77949915021 scopus 로고    scopus 로고
    • Conservation genetics in transition to conservation genomics
    • 10.1016/j.tig.2010.01.001, 20227782
    • 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.
    • (2010) Trends in Genetics , vol.26 , pp. 177-187
    • Ouborg, N.J.1    Pertoldi, C.2    Loeschcke, V.3    Bilksma, R.4    Hedrick, P.W.5
  • 8
    • 84864185743 scopus 로고    scopus 로고
    • Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development
    • 10.1098/rsob.120054, 3376728, 22724064
    • 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.
    • (2012) Open Biology , vol.2 , pp. 120054
    • Wang, B.1    Ekblom, R.2    Castoe, T.A.3    Jones, E.P.4    Kozma, R.5    Bongcam-Rudloff, E.6    Pollock, D.D.7    Hoglund, J.8
  • 9
    • 79958161502 scopus 로고    scopus 로고
    • A comprehensive transcriptome and immune-gene repertoire of the lepidopteran model host Galleria mellonella
    • 10.1186/1471-2164-12-308, 3224240, 21663692
    • 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.
    • (2011) BMC Genomics , vol.12 , pp. 308
    • Vogel, H.1    Altincicek, B.2    Glockner, G.3    Vilcinkas, A.4
  • 10
    • 77953125691 scopus 로고    scopus 로고
    • Insights into shell deposition in the Antarctic bivalve Laternula elliptica: gene discovery in the mantle transcriptome using 454 pyrosequencing
    • 10.1186/1471-2164-11-362, 2896379, 20529341
    • 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.
    • (2010) BMC Genomics , vol.11 , pp. 362
    • Clark, M.S.1    Thorne, M.A.S.2    Vieira, F.A.3    Cardoso, J.C.R.4    Power, D.M.5    Peck, L.S.6
  • 11
    • 77951936990 scopus 로고    scopus 로고
    • Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae)
    • 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.
    • (2010) Mol Ecol , vol.19 , pp. 115-131
    • Renaut, S.1    Nolte, A.W.2    Bernatchez, L.3
  • 13
    • 84857260551 scopus 로고    scopus 로고
    • Genetic variability of transcript abundance in pig skeletal muscle at slaughter: relationships with meat quality traits
    • 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.
    • (2011) J Anim Sci , vol.90 , pp. 699-708
    • Cherel, P.1    Herault, F.2    Vincent, A.3    Le Roy, P.4    Damon, M.5
  • 14
    • 80053285964 scopus 로고    scopus 로고
    • Bayesian inference of a historical genetic bottleneck in a heavily exploited marine mammal
    • 10.1111/j.1365-294X.2011.05248.x, 21895820
    • 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.
    • (2011) Mol Ecol , vol.20 , pp. 3989-4008
    • Hoffman, J.I.1    Grant, S.M.2    Forcada, J.3    Phillips, C.D.4
  • 15
    • 45249124290 scopus 로고    scopus 로고
    • The looming crisis: interactions between marine mammals and fisheries
    • Read AJ. The looming crisis: interactions between marine mammals and fisheries. J Mammal 2008, 89:541-548.
    • (2008) J Mammal , vol.89 , pp. 541-548
    • Read, A.J.1
  • 16
    • 33847643237 scopus 로고    scopus 로고
    • The impacts of climate change on marine mammals: early signs of significant problems
    • Simmonds MP, Isaac SJ. The impacts of climate change on marine mammals: early signs of significant problems. Oryx 2007, 41:19-26.
    • (2007) Oryx , vol.41 , pp. 19-26
    • Simmonds, M.P.1    Isaac, S.J.2
  • 20
    • 0000722118 scopus 로고
    • Pup mortality of the New Zealand fur seal (Arctocephalus forsteri lesson)
    • Mattlin RH. Pup mortality of the New Zealand fur seal (Arctocephalus forsteri lesson). N Z J Ecol 1978, 1:138-144.
    • (1978) N Z J Ecol , vol.1 , pp. 138-144
    • Mattlin, R.H.1
  • 21
    • 84873453638 scopus 로고    scopus 로고
    • The high fidelity of the cetacean stranding record: insights into measuring diversity by integrating taphonomy and macroecology
    • online early
    • 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.
    • Proc R Soc London, Ser B
    • Pyenson, N.D.1
  • 22
    • 84985337571 scopus 로고
    • Territoriality and breeding behaviour of adult male Antarctic fur seal, Arctocephalus gazella
    • McCann TS. Territoriality and breeding behaviour of adult male Antarctic fur seal, Arctocephalus gazella. J Zool (London) 1980, 192:295-310.
    • (1980) J Zool (London) , vol.192 , pp. 295-310
    • McCann, T.S.1
  • 23
    • 84985407662 scopus 로고
    • Growth rates of Antarctic fur seal Arctocephalus gazella pups at South Georgia
    • 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.
    • (1984) J Zool (London) , vol.203 , Issue.MAY , pp. 87-93
    • Doidge, D.W.1    Croxall, J.P.2    Ricketts, C.3
  • 24
    • 0043286710 scopus 로고    scopus 로고
    • Male reproductive strategy and the importance of maternal status in the Antarctic fur seal Arctocephalus gazella
    • 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.
    • (2003) Evolution , vol.57 , Issue.8 , pp. 1917-1930
    • Hoffman, J.I.1    Boyd, I.L.2    Amos, W.3
  • 25
    • 5344273977 scopus 로고    scopus 로고
    • Exploring the relationship between parental relatedness and male reproductive success in the Antarctic fur seal Arctocephalus gazella
    • 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.
    • (2004) Evolution , vol.58 , Issue.9 , pp. 2087-2099
    • Hoffman, J.I.1    Boyd, I.L.2    Amos, W.3
  • 26
    • 77954990794 scopus 로고    scopus 로고
    • Getting long in the tooth: a strong positive correlation between canine size and heterozygosity in the Antarctic fur seal Arctocephalus gazella
    • 10.1093/jhered/esq045, 20457622
    • 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.
    • (2010) J Hered , vol.101 , pp. 527-538
    • Hoffman, J.I.1    Forcada, J.2    Amos, W.3
  • 27
    • 33847232920 scopus 로고    scopus 로고
    • Female fur seals show active choice for males that are heterozygous and unrelated
    • 10.1038/nature05558, 17287726
    • 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.
    • (2007) Nature , vol.445 , pp. 912-914
    • Hoffman, J.I.1    Forcada, J.2    Trathan, P.N.3    Amos, W.4
  • 28
    • 77954962527 scopus 로고    scopus 로고
    • Exploring the mechanisms underlying a heterozygosity-fitnesss correlation for canine size in the Antarctic fur seal Arctocephalus gazella
    • 10.1093/jhered/esq046, 20457623
    • 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.
    • (2010) J Hered , vol.101 , pp. 539-552
    • Hoffman, J.I.1    Forcada, J.2    Amos, W.3
  • 29
    • 79959215488 scopus 로고    scopus 로고
    • Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome
    • 10.1111/j.1755-0998.2011.02999.x, 21466659
    • 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.
    • (2011) Mol Ecol Resour , vol.11 , pp. 703-710
    • Hoffman, J.I.1
  • 30
    • 80051506034 scopus 로고    scopus 로고
    • A novel approach for mining polymorphic microsatellite markers in silico
    • 10.1371/journal.pone.0023283, 3154332, 21853104
    • 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.
    • (2011) PLoS One , vol.6
    • Hoffman, J.I.1    Nichols, H.J.2
  • 31
    • 84865285342 scopus 로고    scopus 로고
    • Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal
    • 10.1111/j.1755-0998.2012.03158.x, 22727236
    • 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.
    • (2012) Mol Ecol Resour , vol.12 , pp. 861-872
    • Hoffman, J.I.1    Tucker, R.2    Clark, M.S.3    Forcada, J.4    Slate, J.5
  • 33
    • 0032849859 scopus 로고    scopus 로고
    • CAP 3: a DNA sequence assembly program
    • 10.1101/gr.9.9.868, 310812, 10508846
    • 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.
    • (1999) Genome Res , vol.9 , pp. 868-877
    • Huang, X.1    Madan, A.2
  • 34
    • 77957926979 scopus 로고    scopus 로고
    • Comparing de novo assemblers for 454 transcriptome data
    • 10.1186/1471-2164-11-571, 3091720, 20950480
    • 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.
    • (2010) BMC Genomics , vol.11 , pp. 571
    • Kumar, S.1    Blaxter, M.L.2
  • 35
    • 77950535845 scopus 로고    scopus 로고
    • Digital gene expression analysis of the zebra finch genome
    • 10.1186/1471-2164-11-219, 2996964, 20359325
    • 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.
    • (2010) BMC Genomics , vol.11 , pp. 219
    • Ekblom, R.1    Balakrishnan, C.N.2    Burke, T.3    Slate, J.4
  • 36
    • 79957800445 scopus 로고    scopus 로고
    • Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing
    • 10.1186/1471-2164-12-283, 3125266, 21635727
    • 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.
    • (2011) BMC Genomics , vol.12 , pp. 283
    • Santure, A.W.1    Gratten, J.2    Mossman, J.A.3    Sheldon, B.C.4    Slate, J.5
  • 37
    • 0021400088 scopus 로고
    • Pathology of the Antarctic fur seal (Arctocephalus gazella) in South Georgia
    • 10.1016/0007-1935(84)90084-8, 6722508
    • 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.
    • (1984) Br Vet J , vol.140 , pp. 210-219
    • Baker, J.R.1    Doidge, D.W.2
  • 38
    • 33745988232 scopus 로고    scopus 로고
    • Is MHC enough for understanding wildlife immunogenetics?
    • 10.1016/j.tree.2006.05.010, 16764966
    • 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.
    • (2006) Trends Ecol Evol , vol.21 , Issue.8 , pp. 433-438
    • Acevedo-Whitehouse, K.1    Cunningham, A.A.2
  • 39
    • 38649115646 scopus 로고    scopus 로고
    • Phylogeny and divergence of the pinnipeds (Carnivora: Mammalia) assessed using a multigene dataset
    • 10.1186/1471-2148-7-216, 2245807, 17996107
    • 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.
    • (2007) BMC Evol Biol , vol.7 , pp. 216
    • Higdon, J.W.1    Bininda-Edmonds, O.R.P.2    Beck, R.M.D.3    Ferguson, S.H.4
  • 40
    • 79954544639 scopus 로고    scopus 로고
    • Development of a predicted physical map of microsatellite locus positions for pinnipeds, with wider applicability to the Carnivora
    • 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.
    • (2010) Mol Ecol Resour , vol.11 , pp. 503-513
    • Osborne, A.J.1    Brauning, R.2    Schultz, J.K.3    Kennedy, M.A.4    Slate, J.5    Gemmell, N.J.6
  • 41
    • 78651341450 scopus 로고    scopus 로고
    • The 2011 nucleic acids research database issue and the online molecular biology database collection
    • 10.1093/nar/gkq1243, 3013748, 21177655
    • 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.
    • (2011) Nucleic Acids Res , vol.39
    • Galperin, M.Y.1    Cochrane, G.R.2
  • 42
    • 0029916911 scopus 로고    scopus 로고
    • The SWISS-PROT protein sequence data bank and its new supplement TREMBL
    • 10.1093/nar/24.1.21, 145613, 8594581
    • 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.
    • (1996) Nucleic Acids Res , vol.24 , pp. 21-25
    • Bairoch, A.1    Apweiler, R.2
  • 44
    • 0347478283 scopus 로고    scopus 로고
    • Molecular organization of the canine major histocompatibility complex
    • 10.1093/jhered/esg002, 12692158
    • Wagner JL. Molecular organization of the canine major histocompatibility complex. J Hered 2003, 94(1):23-26. 10.1093/jhered/esg002, 12692158.
    • (2003) J Hered , vol.94 , Issue.1 , pp. 23-26
    • Wagner, J.L.1
  • 45
    • 10644230919 scopus 로고    scopus 로고
    • Genomic sequence of the class I region of the canine MHC: comparison with the MHC of other mammalian species
    • 10.1016/j.ygeno.2004.09.009, 15607421
    • 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.
    • (2005) Genomics , vol.85 , pp. 48-59
    • Debenham, S.L.1    Hart, E.A.2    Ashurst, J.L.3    Howe, K.L.4    Quail, M.A.5    Ollier, W.E.R.6    Binns, M.M.7
  • 46
    • 84873433378 scopus 로고    scopus 로고
    • Phobos 3.3.11 http://www.rub.de/spezzoo/cm/cm_phobos.htm.
    • Phobos 3.3.11


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.