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

Hoffman J, Thorne MA, Trathan PN, Forcada J (2013)
BMC Genomics 14(1).

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BACKGROUND: Transcriptomes are powerful resources, providing a window on the expressed portion of the genome that can be generated rapidly and at low cost for virtually any organism. However, because many genes have tissue-specific expression patterns, developing a complete transcriptome usually requires a 'discovery pool' of individuals to be sacrificed in order to harvest mRNA from as many different types of tissue as possible. This hinders transcriptome development in large, charismatic and endangered species, many of which stand the most to gain from such approaches. To circumvent this problem in a model pinniped species, we 454 sequenced cDNA from testis, heart, spleen, intestine, kidney and lung tissues obtained from nine adult male Antarctic fur seals (Arctocephalus gazella) that died of natural causes at Bird Island, South Georgia. RESULTS: After applying stringent quality control criteria based on length and annotation, we obtained 12,397 contigs which, in combination with 454 data previously obtained from skin, gave a total of 23,096 unique contigs. Homology was found to 77.0% of dog (Canis lupus familiaris) transcripts, suggesting that the combined assembly represents a substantial proportion of this species' transcriptome. Moreover, only 0.5% of transcripts revealed sequence similarity to bacteria, implying minimal contamination, and the percentage of transcripts involved in cell death was low at 2.6%. Transcripts with immune-related annotations were almost five-fold enriched relative to skin and represented 13.2% of all spleen-specific contigs. By reference to the dog, we also identified transcripts revealing homology to five class I, ten class II and three class III genes of the Major Histocompatibility Complex and derived the putative genomic distribution of 17,121 contigs, 2,119 in silico mined microsatellites and 9,382 single nucleotide polymorphisms. CONCLUSIONS: Our findings suggest that transcriptome development based on samples collected post mortem may greatly facilitate genomic studies, not only of marine mammals but also more generally of species that are of conservation concern.
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Article Processing Charge funded by the Deutsche Forschungsgemeinschaft and the Open Access Publication Fund of Bielefeld University.
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Hoffman J, Thorne MA, Trathan PN, Forcada J. Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal. BMC Genomics. 2013;14(1).
Hoffman, J., Thorne, M. A., Trathan, P. N., & Forcada, J. (2013). Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal. BMC Genomics, 14(1).
Hoffman, J., Thorne, M. A., Trathan, P. N., and Forcada, J. (2013). Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal. BMC Genomics 14.
Hoffman, J., et al., 2013. Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal. BMC Genomics, 14(1).
J. Hoffman, et al., “Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal”, BMC Genomics, vol. 14, 2013.
Hoffman, J., Thorne, M.A., Trathan, P.N., Forcada, J.: Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal. BMC Genomics. 14, (2013).
Hoffman, Joseph, Thorne, Michael As, Trathan, Philip N, and Forcada, Jaume. “Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal”. BMC Genomics 14.1 (2013).
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PMID: 25424897
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47 References

Data provided by Europe PubMed Central.

Female fur seals show active choice for males that are heterozygous and unrelated.
Hoffman JI, Forcada J, Trathan PN, Amos W., Nature 445(7130), 2007
PMID: 17287726
A novel approach for mining polymorphic microsatellite markers in silico.
Hoffman JI, Nichols HJ., PLoS ONE 6(8), 2011
PMID: 21853104
MHC genotype and near-deterministic mortality in grey seals.
de Assuncao-Franco M, Hoffman JI, Harwood J, Amos W., Sci Rep 2(), 2012
PMID: 22997548
CAP3: A DNA sequence assembly program.
Huang X, Madan A., Genome Res. 9(9), 1999
PMID: 10508846
Comparing de novo assemblers for 454 transcriptome data.
Kumar S, Blaxter ML., BMC Genomics 11(), 2010
PMID: 20950480
Digital gene expression analysis of the zebra finch genome.
Ekblom R, Balakrishnan CN, Burke T, Slate J., BMC Genomics 11(), 2010
PMID: 20359325
Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing.
Santure AW, Gratten J, Mossman JA, Sheldon BC, Slate J., BMC Genomics 12(), 2011
PMID: 21635727
Pathology of the antarctic fur seal (Arctocephalus gazella) in south Georgia.
Baker JR, Doidge DW., Br. Vet. J. 140(2), 1984
PMID: 6722508
Is MHC enough for understanding wildlife immunogenetics?
Acevedo-Whitehouse K, Cunningham AA., Trends Ecol. Evol. (Amst.) 21(8), 2006
PMID: 16764966
Phylogeny and divergence of the pinnipeds (Carnivora: Mammalia) assessed using a multigene dataset.
Higdon JW, Bininda-Emonds OR, Beck RM, Ferguson SH., BMC Evol. Biol. 7(), 2007
PMID: 17996107
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., Mol Ecol Resour 11(3), 2011
PMID: 21481208
The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection.
Galperin MY, Cochrane GR., Nucleic Acids Res. 39(Database issue), 2011
PMID: 21177655
The SWISS-PROT protein sequence data bank and its new supplement TREMBL.
Bairoch A, Apweiler R., Nucleic Acids Res. 24(1), 1996
PMID: 8594581
Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
Genomic sequence of the class II region of the canine MHC: comparison with the MHC of other mammalian species.
Debenham SL, Hart EA, Ashurst JL, Howe KL, Quail MA, Ollier WE, Binns MM., Genomics 85(1), 2005
PMID: 15607421

AUTHOR UNKNOWN, 0
Quality scores and SNP detection in sequencing-by-synthesis systems.
Brockman W, Alvarez P, Young S, Garber M, Giannoukos G, Lee WL, Russ C, Lander ES, Nusbaum C, Jaffe DB., Genome Res. 18(5), 2008
PMID: 18212088

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