Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome

Hoffman J (2011)
Molecular Ecology Resources 11(4): 703-710.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurde kein Volltext hochgeladen. Nur Publikationsnachweis!
Abstract / Bemerkung
Next-generation sequencing provides a powerful new approach for developing functional genomic tools for nonmodel species, helping to narrow the gap between studies of model organisms and those of natural populations. Consequently, massively parallel 454 sequencing was used to characterize a normalized cDNA library derived from skin biopsy samples of twelve Antarctic fur seal (Arctocephalus gazella) individuals. Over 412 Mb of sequence data were generated, comprising 1.4 million reads of average length 286 bp. De nova assembly using Newbler 2.3 yielded 156 contigs plus 22 869 isotigs, which in turn clustered into 18 576 isogroups. Almost half of the assembled transcript sequences showed significant similarity to the nr database, revealing a functionally diverse array of genes. Moreover, 97.9% of these mapped to the dog (Canis lupis familiaris) genome, with a strong positive relationship between the number of sequences locating to a given chromosome and the length of that chromosome in the dog indicating a broad genomic distribution. Average depth of coverage was also almost 20-fold, sufficient to detect several thousand putative microsatellite loci and single nucleotide polymor-phistns. This study constitutes an important step towards developing genomic resources with which to address consequential questions in pinniped ecology and evolution. It also supports an earlier but smaller study showing that skin tissue can be a rich source of expressed genes, with important implications for studying the genomics not only of marine mammals, but also more generally of species that cannot be destructively sampled.
Stichworte
single nucleotide polymorphism; 454 sequencing; expressed sequence tags; marine mammal; dog (Canis lupis familiaris); pinniped; microsatellite
Erscheinungsjahr
2011
Zeitschriftentitel
Molecular Ecology Resources
Band
11
Ausgabe
4
Seite(n)
703-710
ISSN
1755-098X
Page URI
https://pub.uni-bielefeld.de/record/2307149

Zitieren

Hoffman J. Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome. Molecular Ecology Resources. 2011;11(4):703-710.
Hoffman, J. (2011). Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome. Molecular Ecology Resources, 11(4), 703-710. doi:10.1111/j.1755-0998.2011.02999.x
Hoffman, J. (2011). Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome. Molecular Ecology Resources 11, 703-710.
Hoffman, J., 2011. Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome. Molecular Ecology Resources, 11(4), p 703-710.
J. Hoffman, “Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome”, Molecular Ecology Resources, vol. 11, 2011, pp. 703-710.
Hoffman, J.: Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome. Molecular Ecology Resources. 11, 703-710 (2011).
Hoffman, Joseph. “Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome”. Molecular Ecology Resources 11.4 (2011): 703-710.

15 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them
Humble E, A. Martinez‐Barrio, J. Forcada, P. N. Trathan, M. A. S. Thorne, M. Hoffmann, J. B. W. Wolf, J. I. Hoffman., Mol Ecol Resour 16(4), 2016
PMID: IND605237320
Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals.
Cammen KM, Andrews KR, Carroll EL, Foote AD, Humble E, Khudyakov JI, Louis M, McGowen MR, Olsen MT, Van Cise AM., J Hered 107(6), 2016
PMID: 27511190
De novo assembly of the dual transcriptomes of a polymorphic raptor species and its malarial parasite.
Pauli M, Chakarov N, Rupp O, Kalinowski J, Goesmann A, Sorenson MD, Krüger O, Hoffman JI., BMC Genomics 16(), 2015
PMID: 26645667
De novo assembly and characterization of spotted seal Phoca largha transcriptome using Illumina paired-end sequencing.
Gao X, Han J, Lu Z, Li Y, He C., Comp Biochem Physiol Part D Genomics Proteomics 8(2), 2013
PMID: 23396151
Molecular markers and their application in genetic diversity of penaeid shrimp
Vaseeharan B, Rajakamaran P, Jayaseelan D, Vincent AY., Aquac. Int. 21(2), 2013
PMID: IND500633541
Transcriptome and proteome data reveal candidate genes for pollinator attraction in sexually deceptive orchids.
Sedeek KE, Qi W, Schauer MA, Gupta AK, Poveda L, Xu S, Liu ZJ, Grossniklaus U, Schiestl FP, Schlüter PM., PLoS One 8(5), 2013
PMID: 23734209
De-novo transcriptome sequencing of a normalized cDNA pool from influenza infected ferrets.
Camp JV, Svensson TL, McBrayer A, Jonsson CB, Liljeström P, Bruder CE., PLoS One 7(5), 2012
PMID: 22606336
A novel approach for mining polymorphic microsatellite markers in silico.
Hoffman JI, Nichols HJ., PLoS One 6(8), 2011
PMID: 21853104

33 References

Daten bereitgestellt von Europe PubMed Central.

Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
Candidate genes versus genomewide associations: which are better for detecting genetic susceptibility to infectious disease?
Amos, Proceedings of the Royal Society of London Series B Biological Sciences (), 0
Pinniped phylogeny and a new hypothesis for their origin and dispersal.
Arnason U, Gullberg A, Janke A, Kullberg M, Lehman N, Petrov EA, Vainola R., Mol. Phylogenet. Evol. 41(2), 2006
PMID: 16815048

Boness, 1991
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
Density-dependent pup mortality in the Antarctic fur seal Arctocephalus gazella at South Georgia
Doidge, Journal of Zoology 202(), 1984
Projectile biopsy sampling of fur seals
Gemmell, Marine Mammal Science 13(), 1997
A proposal to obtain whole-genome sequence for 10 000 vertebrate species
Genome, Journal of Heredity 100(), 2009

AUTHOR UNKNOWN, 0
A panel of new microsatellite loci for genetic studies of Antarctic fur seals and other otariid species
Hoffman, Conservation Genetics 10(), 2007
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
Sampling the skin transcriptome of the North Atlantic right whale.
Ierardi JL, Mancia A, McMillan J, Lundqvist ML, Romano TA, Wise JP Sr, Warr GW, Chapman RW., Comp. Biochem. Physiol. Part D Genomics Proteomics 4(3), 2009
PMID: 20403765
A dolphin peripheral blood leukocyte cDNA microarray for studies of immune function and stress reactions.
Mancia A, Lundqvist ML, Romano TA, Peden-Adams MM, Fair PA, Kindy MS, Ellis BC, Gattoni-Celli S, McKillen DJ, Trent HF, Chen YA, Almeida JS, Gross PS, Chapman RW, Warr GW., Dev. Comp. Immunol. 31(5), 2006
PMID: 17084893
Genome sequencing in microfabricated high-density picolitre reactors.
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM., Nature 437(7057), 2005
PMID: 16056220
Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx.
Meyer E, Aglyamova GV, Wang S, Buchanan-Carter J, Abrego D, Colbourne JK, Willis BL, Matz MV., BMC Genomics 10(), 2009
PMID: 19435504
Territoriality and breeding behaviour of adult male Antarctic fur seal, Arctocephalus gazella
McCann, Journal of Zoology 192(), 1980
Tablet--next generation sequence assembly visualization.
Milne I, Bayer M, Cardle L, Shaw P, Stephen G, Wright F, Marshall D., Bioinformatics 26(3), 2009
PMID: 19965881
SNPs in ecology, evolution and conservation
Morin, Trends in Ecology and Evolution 19(), 2004
Harnessing genomics for evolutionary insights. Harnessing genomics for evolutionary insights
Rokas, Trends in Ecology and Evolution 24(), 2009
Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella.
Schwarz D, Robertson HM, Feder JL, Varala K, Hudson ME, Ragland GJ, Hahn DA, Berlocher SH., BMC Genomics 10(), 2009
PMID: 20035631
Gene mapping in the wild with SNPs: guidelines and future directions.
Slate J, Gratten J, Beraldi D, Stapley J, Hale M, Pemberton JM., Genetica 136(1), 2008
PMID: 18780148
Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing.
Vera JC, Wheat CW, Fescemyer HW, Frilander MJ, Crawford DL, Hanski I, Marden JH., Mol. Ecol. 17(7), 2008
PMID: 18266620
De novo characterization of a whitefly transcriptome and analysis of its gene expression during development.
Wang XW, Luan JB, Li JM, Bao YY, Zhang CX, Liu SS., BMC Genomics 11(), 2010
PMID: 20573269

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 21466659
PubMed | Europe PMC

Suchen in

Google Scholar