Experimental validation of in silico predicted RAD locus frequencies using genomic resources and short read data from a model marine mammal

Vendrami D, Forcada J, Hoffman J (2019)
BMC Genomics 20(1): 72.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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DOI
Autor*in
Vendrami, DavidUniBi ; Forcada, Jaume; Hoffman, JosephUniBi
Einrichtung
Fakultät für Biologie > Verhaltensforschung
Erscheinungsjahr
2019
Zeitschriftentitel
BMC Genomics
Band
20
Ausgabe
1
Art.-Nr.
72
Urheberrecht / Lizenzen
Creative Commons Namensnennung 4.0 International Public License (CC-BY 4.0)
ISSN
1471-2164
eISSN
1471-2164
Page URI
https://pub.uni-bielefeld.de/record/2933567

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Vendrami D, Forcada J, Hoffman J. Experimental validation of in silico predicted RAD locus frequencies using genomic resources and short read data from a model marine mammal. BMC Genomics. 2019;20(1): 72.
Vendrami, D., Forcada, J., & Hoffman, J. (2019). Experimental validation of in silico predicted RAD locus frequencies using genomic resources and short read data from a model marine mammal. BMC Genomics, 20(1), 72. doi:10.1186/s12864-019-5440-8
Vendrami, David, Forcada, Jaume, and Hoffman, Joseph. 2019. “Experimental validation of in silico predicted RAD locus frequencies using genomic resources and short read data from a model marine mammal”. BMC Genomics 20 (1): 72.
Vendrami, D., Forcada, J., and Hoffman, J. (2019). Experimental validation of in silico predicted RAD locus frequencies using genomic resources and short read data from a model marine mammal. BMC Genomics 20:72.
Vendrami, D., Forcada, J., & Hoffman, J., 2019. Experimental validation of in silico predicted RAD locus frequencies using genomic resources and short read data from a model marine mammal. BMC Genomics, 20(1): 72.
D. Vendrami, J. Forcada, and J. Hoffman, “Experimental validation of in silico predicted RAD locus frequencies using genomic resources and short read data from a model marine mammal”, BMC Genomics, vol. 20, 2019, : 72.
Vendrami, D., Forcada, J., Hoffman, J.: Experimental validation of in silico predicted RAD locus frequencies using genomic resources and short read data from a model marine mammal. BMC Genomics. 20, : 72 (2019).
Vendrami, David, Forcada, Jaume, and Hoffman, Joseph. “Experimental validation of in silico predicted RAD locus frequencies using genomic resources and short read data from a model marine mammal”. BMC Genomics 20.1 (2019): 72.

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40 References

Daten bereitgestellt von Europe PubMed Central.


AUTHOR UNKNOWN, 0
Next-generation biology: Sequencing and data analysis approaches for non-model organisms.
da Fonseca RR, Albrechtsen A, Themudo GE, Ramos-Madrigal J, Sibbesen JA, Maretty L, Zepeda-Mendoza ML, Campos PF, Heller R, Pereira RJ., Mar Genomics 30(), 2016
PMID: 27184710
Developing genome-wide SNPs and constructing an ultrahigh-density linkage map in oil palm.
Bai B, Wang L, Zhang YJ, Lee M, Rahmadsyah R, Alfiko Y, Ye BQ, Purwantomo S, Suwanto A, Chua NH, Yue GH., Sci Rep 8(1), 2018
PMID: 29330432

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
RAD sequencing resolves fine-scale population structure in a benthic invertebrate: implications for understanding phenotypic plasticity.
Vendrami DL, Telesca L, Weigand H, Weiss M, Fawcett K, Lehman K, Clark MS, Leese F, McMinn C, Moore H, Hoffman JI., R Soc Open Sci 4(2), 2017
PMID: 28386419
High-throughput sequencing reveals inbreeding depression in a natural population.
Hoffman JI, Simpson F, David P, Rijks JM, Kuiken T, Thorne MA, Lacy RC, Dasmahapatra KK., Proc. Natl. Acad. Sci. U.S.A. 111(10), 2014
PMID: 24586051
Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species.
Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE., PLoS ONE 7(5), 2012
PMID: 22675423
Measurement by flow cytometry of genomic AT/GC ratio and genome size.
Vinogradov AE., Cytometry 16(1), 1994
PMID: 7518377
Estimation of nuclear DNA content in plants using flow cytometry.
Dolezel J, Greilhuber J, Suda J., Nat Protoc 2(9), 2007
PMID: 17853881
Rapid SNP discovery and genetic mapping using sequenced RAD markers.
Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA., PLoS ONE 3(10), 2008
PMID: 18852878
RADSeq: next-generation population genetics.
Davey JW, Davey JL, Blaxter ML, Blaxter MW., Brief Funct Genomics 9(5-6), 2010
PMID: 21266344
Genome-wide genetic marker discovery and genotyping using next-generation sequencing.
Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML., Nat. Rev. Genet. 12(7), 2011
PMID: 21681211
De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species.
Carruthers M, Yurchenko AA, Augley JJ, Adams CE, Herzyk P, Elmer KR., BMC Genomics 19(1), 2018
PMID: 29310597
Characterization of the mantle transcriptome in bivalves: Pecten maximus, Mytilus edulis and Crassostrea gigas.
Yarra T, Gharbi K, Blaxter M, Peck LS, Clark MS., Mar Genomics 27(), 2016
PMID: 27160853
RNA-Seq analysis of Cocos nucifera: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches.
Fan H, Xiao Y, Yang Y, Xia W, Mason AS, Xia Z, Qiao F, Zhao S, Tang H., PLoS ONE 8(3), 2013
PMID: 23555859
Predicting RAD-seq Marker Numbers across the Eukaryotic Tree of Life.
Herrera S, Reyes-Herrera PH, Shank TM., Genome Biol Evol 7(12), 2015
PMID: 26537225

AUTHOR UNKNOWN, 0
Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq).
Graham CF, Glenn TC, McArthur AG, Boreham DR, Kieran T, Lance S, Manzon RG, Martino JA, Pierson T, Rogers SM, Wilson JY, Somers CM., Mol Ecol Resour 15(6), 2015
PMID: 25783180
Sequencing depth and coverage: key considerations in genomic analyses.
Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP., Nat. Rev. Genet. 15(2), 2014
PMID: 24434847
Density-dependent pup mortality in the Antarctic fur seal Arctocephalus gazella at South Georgia
Doidge DW, Croxall JP, Baker JR., 1984
Climate change selects for heterozygosity in a declining fur seal population.
Forcada J, Hoffman JI., Nature 511(7510), 2014
PMID: 25056064
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
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
Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success.
Humble E, Thorne MA, Forcada J, Hoffman JI., BMC Res Notes 9(1), 2016
PMID: 27562535
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, Gregorio I, Forcada J, Polikeit AC, Goldsworthy SD, Goebel ME, Kalinowski J, Wolf JBW, Hoffman JI., G3 (Bethesda) 8(8), 2018
PMID: 29954843

AUTHOR UNKNOWN, 0
Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome.
Hoffman JI., Mol Ecol Resour 11(4), 2011
PMID: 21466659
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
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

AUTHOR UNKNOWN, 0
Stacks: building and genotyping Loci de novo from short-read sequences.
Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH., G3 (Bethesda) 1(3), 2011
PMID: 22384329
Fast and accurate short read alignment with Burrows-Wheeler transform.
Li H, Durbin R., Bioinformatics 25(14), 2009
PMID: 19451168

AUTHOR UNKNOWN, 2017
Restriction site‐associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference
Mastretta‐Yanes A, Arrigo N, Alvarez N, Jorgensen TH, Pinero D, Emerson BC., Mol Ecol Resour 15(1), 2015
PMID: IND601379375
Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference
Shafer A, Peart CR, Tusso S, Maayan I, Brelsford A, Wheat CW, Wolf JB., 2017
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D., Genome Res. 15(8), 2005
PMID: 16024819
Human genome ultraconserved elements are ultraselected.
Katzman S, Kern AD, Bejerano G, Fewell G, Fulton L, Wilson RK, Salama SR, Haussler D., Science 317(5840), 2007
PMID: 17702936
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Teil dieser Dissertation
Application of cutting-edge genomic approaches to address key questions in ecology and evolution. Bringing molecular ecology to the genomic era
Vendrami D (2018)
Bielefeld: Universität Bielefeld.
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