Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs

Hoffman J, Thorne MAS, McEwing R, Forcada J, Ogden R (2013)
PLoS ONE 8(7): e68365.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
OA
DOI
URN
urn:nbn:de:0070-pub-26152930
Autor*in
Hoffman, JosephUniBi ; Thorne, Michael A. S.; McEwing, Rob; Forcada, Jaume; Ogden, Rob
Einrichtung
Fakultät für Biologie > Verhaltensforschung
Abstract / Bemerkung
High-density SNP arrays developed for humans and their companion species provide a rapid and convenient tool for generating SNP data in closely-related non-model organisms, but have not yet been widely applied to phylogenetically divergent taxa. Consequently, we used the CanineHD BeadChip to genotype 24 Antarctic fur seal (Arctocephalus gazella) individuals. Despite seals and dogs having diverged around 44 million years ago, 33,324 out of 173,662 loci (19.2%) could be genotyped, of which 173 were polymorphic and clearly interpretable. Two SNPs were validated using KASP genotyping assays, with the resulting genotypes being 100% concordant with those obtained from the high-density array. Two loci were also confirmed through in silico visualisation after mapping them to the fur seal transcriptome. Polymorphic SNPs were distributed broadly throughout the dog genome and did not differ significantly in proximity to genes from either monomorphic SNPs or those that failed to cross-amplify in seals. However, the nearest genes to polymorphic SNPs were significantly enriched for functional annotations relating to energy metabolism, suggesting a possible bias towards conserved regions of the genome.
Erscheinungsjahr
2013
Zeitschriftentitel
PLoS ONE
Band
8
Ausgabe
7
Art.-Nr.
e68365
ISSN
1932-6203
eISSN
1932-6203
Page URI
https://pub.uni-bielefeld.de/record/2615293

Zitieren

Hoffman J, Thorne MAS, McEwing R, Forcada J, Ogden R. Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs. PLoS ONE. 2013;8(7): e68365.
Hoffman, J., Thorne, M. A. S., McEwing, R., Forcada, J., & Ogden, R. (2013). Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs. PLoS ONE, 8(7), e68365. doi:10.1371/journal.pone.0068365
Hoffman, Joseph, Thorne, Michael A. S., McEwing, Rob, Forcada, Jaume, and Ogden, Rob. 2013. “Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs”. PLoS ONE 8 (7): e68365.
Hoffman, J., Thorne, M. A. S., McEwing, R., Forcada, J., and Ogden, R. (2013). Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs. PLoS ONE 8:e68365.
Hoffman, J., et al., 2013. Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs. PLoS ONE, 8(7): e68365.
J. Hoffman, et al., “Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs”, PLoS ONE, vol. 8, 2013, : e68365.
Hoffman, J., Thorne, M.A.S., McEwing, R., Forcada, J., Ogden, R.: Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs. PLoS ONE. 8, : e68365 (2013).
Hoffman, Joseph, Thorne, Michael A. S., McEwing, Rob, Forcada, Jaume, and Ogden, Rob. “Cross-Amplification and Validation of SNPs Conserved over 44 Million Years between Seals and Dogs”. PLoS ONE 8.7 (2013): e68365.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
Dieses Objekt ist durch das Urheberrecht und/oder verwandte Schutzrechte geschützt. [...]
Volltext(e)
Name
Access Level
OA Open Access
Zuletzt Hochgeladen
2019-09-06T09:18:18Z
MD5 Prüfsumme
6213d1c2d83d6df839d87213afb1ba61


12 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Evaluation of a Chicken 600K SNP genotyping array in non-model species of grouse.
Minias P, Dunn PO, Whittingham LA, Johnson JA, Oyler-McCance SJ., Sci Rep 9(1), 2019
PMID: 31015535
Evaluation of SNP Genotyping in Alpacas Using the Bovine HD Genotyping Beadchip.
More M, Gutiérrez G, Rothschild M, Bertolini F, Ponce de León FA., Front Genet 10(), 2019
PMID: 31105741
Nuclear Genetic Analysis of the Red Fox Across its Trans-Pacific Range.
Sacks BN, Lounsberry ZT, Statham MJ., J Hered 109(5), 2018
PMID: 29889225
RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding.
Humble E, Dasmahapatra KK, Martinez-Barrio A, Gregório I, Forcada J, Polikeit AC, Goldsworthy SD, Goebel ME, Kalinowski J, Wolf JBW, Hoffman JI., G3 (Bethesda) 8(8), 2018
PMID: 29954843
Cross-Species Application of SNP Chips is Not Suitable for Identifying Runs of Homozygosity.
Shafer AB, Miller JM, Kardos M., J Hered 107(2), 2016
PMID: 26774056
Response to "Cross-Species Application of SNP Chips is Not Suitable for Identifying Runs of Homozygosity" by Shafer, Miller, and Kardos.
Kharzinova V, Sermyagin AA, Gladyr EA, Brem G, Zinovieva NA., J Hered 107(2), 2016
PMID: 26809969
Applying SNP-Derived Molecular Coancestry Estimates to Captive Breeding Programs.
Ivy JA, Putnam AS, Navarro AY, Gurr J, Ryder OA., J Hered 107(5), 2016
PMID: 27208150
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
A single-nucleotide polymorphism-based approach for rapid and cost-effective genetic wolf monitoring in Europe based on noninvasively collected samples.
Kraus RH, vonHoldt B, Cocchiararo B, Harms V, Bayerl H, Kühn R, Förster DW, Fickel J, Roos C, Nowak C., Mol Ecol Resour 15(2), 2015
PMID: 25042673
A flexible multi-species genome-wide 60K SNP chip developed from pooled resequencing of 240 Eucalyptus tree genomes across 12 species.
Silva-Junior OB, Faria DA, Grattapaglia D., New Phytol 206(4), 2015
PMID: 25684350
A single‐nucleotide polymorphism‐based approach for rapid and cost‐effective genetic wolf monitoring in Europe based on noninvasively collected samples
Kraus RHS, vonHoldt B, Cocchiararo B, Harms V, Bayerl H, Kühn R, Förster DW, Fickel J, Roos C, Nowak C., Mol Ecol Resour 15(2), 2015
PMID: IND601379377
A Study of Applicability of SNP Chips Developed for Bovine and Ovine Species to Whole-Genome Analysis of Reindeer Rangifer tarandus.
Kharzinova VR, Sermyagin AA, Gladyr EA, Okhlopkov IM, Brem G, Zinovieva NA., J Hered 106(6), 2015
PMID: 26447215

53 References

Daten bereitgestellt von Europe PubMed Central.

Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms
AUTHOR UNKNOWN, 2011
Development and application of high-density SNP arrays in genomic studies of domestic animals
AUTHOR UNKNOWN, 2010
Genome variability in European and American bison detected using the BovineSNP50 BeadChip
Pertoldi C, Wojcik JM, Tokarska M, Kawalko A, Kristensen TN, Loeschcke V, Gregersen VR, Coltman D, Wilson GA, Randi E, Henryon M, Bendixen C., Conserv. Genet. 11(2), 2010
PMID: IND44340059
A genome-wide set of SNPs detects population substructure and long range linkage disequilibrium in wild sheep
AUTHOR UNKNOWN, 2011
Identification of novel single nucleotide polymorphisms (SNPs) in deer (Odocoileus spp.) using the BovineSNP50 BeadChip.
Haynes GD, Latch EK., PLoS ONE 7(5), 2012
PMID: 22590559
A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids
AUTHOR UNKNOWN, 2012
Consistent divergence times and allele sharing measured from cross-species application of SNP chips developed for three domestic species
AUTHOR UNKNOWN, 2012
The use of cross-species genome-wide arrays to discover SNP markers for conservation genetics: a case study from Arabian and scimitar-horned oryx
AUTHOR UNKNOWN, 2012
The effect of SNP discovery method and sample size on estimation of population genetic data for Chinese and Indian rhesus macaques (Macaca mulatta).
Trask JA, Malhi RS, Kanthaswamy S, Johnson J, Garnica WT, Malladi VS, Smith DG., Primates 52(2), 2011
PMID: 21207104
Ancestral polymorphisms in Drosophila pseudoobscura and Drosophila miranda
AUTHOR UNKNOWN, 2011
Characterization of 42 single nucleotide polymorphism (SNP) markers for the bowhead whale (Balaena mysticetus) for use in discriminating populations
AUTHOR UNKNOWN, 2010
Sperm whale population structure in the eastern and central North Pacific inferred by the use of single-nucleotide polymorphisms, microsatellites and mitochondrial DNA
AUTHOR UNKNOWN, 2011
Highly accurate SNP genotyping from historical and low-quality samples
MORIN PA, MCCARTHY M., Mol. Ecol. Notes 7(6), 2007
PMID: IND43974548
A simple route to single-nucleotide-polymorphisms in a nonmodel species: identification and characterization of SNPs in the Arctic ringed seal (Pusa hispida hispida)
AUTHOR UNKNOWN, 2011
Characterization of 18 SNP markers for sperm whale (Physeter macrocephalus)
MORIN PA, AITKEN NC, RUBIO‐CISNEROS N, DIZON AE, MESNICK S., Mol. Ecol. Notes 7(4), 2007
PMID: IND43929568
Male reproductive strategy and the importance of maternal status in the Antarctic fur seal Arctocephalus gazella.
Hoffman JI, Boyd IL, Amos W., Evolution 57(8), 2003
PMID: 14503632
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
Exploring the relationship between parental relatedness and male reproductive success in the Antarctic fur seal Arctocephalus gazella.
Hoffman JI, Boyd IL, Amos W., Evolution 58(9), 2004
PMID: 15521464
No relationship between microsatellite variation and neonatal fitness in Antarctic fur seals, Arctocephalus gazella.
Hoffman JI, Forcada J, Amos W., Mol. Ecol. 15(7), 2006
PMID: 16689914
Getting long in the tooth: a strong positive correlation between canine size and heterozygosity in Antarctic fur seals Arctocephalus gazella.
Hoffman JI, Hanson N, Forcada J, Trathan PN, Amos W., J. Hered. 101(5), 2010
PMID: 20457622
Does kin selection influence fostering behaviour in Antarctic fur seals (Arctocephalus gazella)?
AUTHOR UNKNOWN, 2005
Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome
AUTHOR UNKNOWN, 2011
Hoffman JI, Tucker R, Clark MS, Forcada J, Slate J (2012 ) Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal
AUTHOR UNKNOWN, 0
Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal.
Hoffman JI, Thorne MA, Trathan PN, Forcada J., BMC Genomics 14(), 2013
PMID: 23347513
Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material.
Walsh PS, Metzger DA, Higuchi R., BioTechniques 10(4), 1991
PMID: 1867860

AUTHOR UNKNOWN, 0
Genome sequence, comparative analysis and haplotype structure of the domestic dog.
Lindblad-Toh K, Wade CM, Mikkelsen TS, Karlsson EK, Jaffe DB, Kamal M, Clamp M, Chang JL, Kulbokas EJ 3rd, Zody MC, Mauceli E, Xie X, Breen M, Wayne RK, Ostrander EA, Ponting CP, Galibert F, Smith DR, DeJong PJ, Kirkness E, Alvarez P, Biagi T, Brockman W, Butler J, Chin CW, Cook A, Cuff J, Daly MJ, DeCaprio D, Gnerre S, Grabherr M, Kellis M, Kleber M, Bardeleben C, Goodstadt L, Heger A, Hitte C, Kim L, Koepfli KP, Parker HG, Pollinger JP, Searle SM, Sutter NB, Thomas R, Webber C, Baldwin J, Abebe A, Abouelleil A, Aftuck L, Ait-Zahra M, Aldredge T, Allen N, An P, Anderson S, Antoine C, Arachchi H, Aslam A, Ayotte L, Bachantsang P, Barry A, Bayul T, Benamara M, Berlin A, Bessette D, Blitshteyn B, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Brown A, Cahill P, Calixte N, Camarata J, Cheshatsang Y, Chu J, Citroen M, Collymore A, Cooke P, Dawoe T, Daza R, Decktor K, DeGray S, Dhargay N, Dooley K, Dooley K, Dorje P, Dorjee K, Dorris L, Duffey N, Dupes A, Egbiremolen O, Elong R, Falk J, Farina A, Faro S, Ferguson D, Ferreira P, Fisher S, FitzGerald M, Foley K, Foley C, Franke A, Friedrich D, Gage D, Garber M, Gearin G, Giannoukos G, Goode T, Goyette A, Graham J, Grandbois E, Gyaltsen K, Hafez N, Hagopian D, Hagos B, Hall J, Healy C, Hegarty R, Honan T, Horn A, Houde N, Hughes L, Hunnicutt L, Husby M, Jester B, Jones C, Kamat A, Kanga B, Kells C, Khazanovich D, Kieu AC, Kisner P, Kumar M, Lance K, Landers T, Lara M, Lee W, Leger JP, Lennon N, Leuper L, LeVine S, Liu J, Liu X, Lokyitsang Y, Lokyitsang T, Lui A, Macdonald J, Major J, Marabella R, Maru K, Matthews C, McDonough S, Mehta T, Meldrim J, Melnikov A, Meneus L, Mihalev A, Mihova T, Miller K, Mittelman R, Mlenga V, Mulrain L, Munson G, Navidi A, Naylor J, Nguyen T, Nguyen N, Nguyen C, Nguyen T, Nicol R, Norbu N, Norbu C, Novod N, Nyima T, Olandt P, O'Neill B, O'Neill K, Osman S, Oyono L, Patti C, Perrin D, Phunkhang P, Pierre F, Priest M, Rachupka A, Raghuraman S, Rameau R, Ray V, Raymond C, Rege F, Rise C, Rogers J, Rogov P, Sahalie J, Settipalli S, Sharpe T, Shea T, Sheehan M, Sherpa N, Shi J, Shih D, Sloan J, Smith C, Sparrow T, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Stone S, Sykes S, Tchuinga P, Tenzing P, Tesfaye S, Thoulutsang D, Thoulutsang Y, Topham K, Topping I, Tsamla T, Vassiliev H, Venkataraman V, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Yang S, Yang X, Young G, Yu Q, Zainoun J, Zembek L, Zimmer A, Lander ES., Nature 438(7069), 2005
PMID: 16341006

AUTHOR UNKNOWN, 0
Highly parallel SNP genotyping.
Fan JB, Oliphant A, Shen R, Kermani BG, Garcia F, Gunderson KL, Hansen M, Steemers F, Butler SL, Deloukas P, Galver L, Hunt S, McBride C, Bibikova M, Rubano T, Chen J, Wickham E, Doucet D, Chang W, Campbell D, Zhang B, Kruglyak S, Bentley D, Haas J, Rigault P, Zhou L, Stuelpnagel J, Chee MS., Cold Spring Harb. Symp. Quant. Biol. 68(), 2003
PMID: 15338605
Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce.
Namroud MC, Beaulieu J, Juge N, Laroche J, Bousquet J., Mol. Ecol. 17(16), 2008
PMID: 18662225
The transcriptional programme of Salmonella enterica serovar Typhimurium reveals a key role for tryptophan metabolism in biofilms.
Hamilton S, Bongaerts RJ, Mulholland F, Cochrane B, Porter J, Lucchini S, Lappin-Scott HM, Hinton JC., BMC Genomics 10(), 2009
PMID: 20003355
In vitro vs in silico detected SNPs for the development of a genotyping array: what can we learn from a non-model species?
Lepoittevin C, Frigerio JM, Garnier-Gere P, Salin F, Cervera MT, Vornam B, Harvengt L, Plomion C., PLoS ONE 5(6), 2010
PMID: 20543950
Genepop (Version 1.2) - population genetics software for exact tests of ecumenicism
AUTHOR UNKNOWN, 1995
Controlling the false discovery rate: a practical and powerful approach to multiple testing
AUTHOR UNKNOWN, 1995
Statistical significance for genomewide studies.
Storey JD, Tibshirani R., Proc. Natl. Acad. Sci. U.S.A. 100(16), 2003
PMID: 12883005
Basic local alignment search tool.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ., J. Mol. Biol. 215(3), 1990
PMID: 2231712
The SWISS-PROT protein sequence data bank.
Bairoch A, Boeckmann B., Nucleic Acids Res. 19 Suppl(), 1991
PMID: 2041811
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G., Nat. Genet. 25(1), 2000
PMID: 10802651
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
The conservation and evolutionary modularity of metabolism.
Peregrin-Alvarez JM, Sanford C, Parkinson J., Genome Biol. 10(6), 2009
PMID: 19523219
Balancing selection and its effects on sequences in nearby genome regions.
Charlesworth D., PLoS Genet. 2(4), 2006
PMID: 16683038
A limited role for balancing selection.
Asthana S, Schmidt S, Sunyaev S., Trends Genet. 21(1), 2005
PMID: 15680511
Scan of human genome reveals no new Loci under ancient balancing selection.
Bubb KL, Bovee D, Buckley D, Haugen E, Kibukawa M, Paddock M, Palmieri A, Subramanian S, Zhou Y, Kaul R, Green P, Olson MV., Genetics 173(4), 2006
PMID: 16751668
Targets of balancing selection in the human genome.
Andres AM, Hubisz MJ, Indap A, Torgerson DG, Degenhardt JD, Boyko AR, Gutenkunst RN, White TJ, Green ED, Bustamante CD, Clark AG, Nielsen R., Mol. Biol. Evol. 26(12), 2009
PMID: 19713326
High MHC diversity maintained by balancing selection in an otherwise genetically monomorphic mammal.
Aguilar A, Roemer G, Debenham S, Binns M, Garcelon D, Wayne RK., Proc. Natl. Acad. Sci. U.S.A. 101(10), 2004
PMID: 14990802
Signature of balancing selection at the MC1R gene in Kunming dog populations.
Wang GD, Cheng LG, Fan RX, Irwin DM, Tang SS, Peng JG, Zhang YP., PLoS ONE 8(2), 2013
PMID: 23424634
Molecular signatures of natural selection.
Nielsen R., Annu. Rev. Genet. 39(), 2005
PMID: 16285858
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
Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems.
Minoche AE, Dohm JC, Himmelbauer H., Genome Biol. 12(11), 2011
PMID: 22067484
Sequencing breakthroughs for genomic ecology and evolutionary biology
AUTHOR UNKNOWN, 2008
Rapidly developing functional genomics in ecological model systems via 454 transcriptome sequencing.
Wheat CW., Genetica 138(4), 2008
PMID: 18931921
RADSeq: next-generation population genetics
AUTHOR UNKNOWN, 2011
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
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 23874599
PubMed | Europe PMC

Suchen in

Google Scholar