Detection and removal of PCR duplicates in population genomic ddRAD studies by addition of a degenerate base region (DBR) in sequencing adapters

Biological Bulletin

Volumn 227, Issue 2, 2014, Pages 146-160

  Schweyen, Hannah ^a   Rozenberg, Andrey ^a   Leese, Florian ^a  

^a RUHR UNIVERSITY BOCHUM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; AQUATIC ENVIRONMENT; DETECTION METHOD; ENZYME ACTIVITY; GENETIC MARKER; GENOMICS; INVERTEBRATE; POLLUTANT REMOVAL; POLYMERASE CHAIN REACTION; POLYMORPHISM;

RESTRICTION ENDONUCLEASE;

ANIMAL; DNA SEQUENCE; GENETIC POLYMORPHISM; GENETICS; INVERTEBRATE; METABOLISM; METAGENOMICS; POLYMERASE CHAIN REACTION; PROCEDURES; STANDARDS;

ANIMALS; DNA RESTRICTION ENZYMES; INVERTEBRATES; METAGENOMICS; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 84911376420     PISSN: 00063185     EISSN: None     Source Type: Journal    
DOI: 10.1086/BBLv227n2p146     Document Type: Article

References (27)

1. Aird, D., M. Ross, W. Chen, M. Danielsson, T. Fennell, C. Russ, D. Jaffe, C. Nusbaum, and A. Gnirke. 2011. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol. 12: R18.
2. Andrews, K., and G. Luikart. 2014. Recent novel approaches for population genomics data analysis. Mol. Ecol. 23: 1661-1667.
3. Arnold, B., R. Corbett-Detig, D. Hartl, and K. Bomblies. 2013. RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling. Mol. Ecol. 22: 3179-3190.
4. Baird, N., P. Etter, T. Atwood, M. Currey, A. Shiver, Z. Lewis, E. Selker, W. Cresko, and E. Johnson. 2008. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3: e3376.
5. Bolger, A., M. Lohse, and B. Usadel. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics btu170.
6. Casbon, J., R. Osborne, S. Brenner, and C. Lichtenstein. 2011. A method for counting PCR template molecules with application to next-generation sequencing. Nucleic Acids Res. 39: e81.
7. Catchen, J., P. Hohenlohe, S. Bassham, A. Amores, and W. Cresko. 2013. Stacks: an analysis tool set for population genomics. Mol. Ecol. 22: 3124-3140.
8. Davey, J., T. Cezard, P. Fuentes-Utrilla, C. Eland, K. Gharbi, and M. Blaxter. 2013. Special features of RAD sequencing data: implications for genotyping. Mol. Ecol. 22: 3151-3164.
9. Emerson, K., C. Merz, J. Catchen, P. Hohenlohe, W. Cresko, W. Bradshaw, and C. Holzapfel. 2010. Resolving postglacial phylogeography using high-throughput sequencing. Proc. Natl. Acad. Sci. USA 107: 16196-16200.
10. Evoeco radtools Github repository. 2014. [Online]. Available https://github. com/evoeco/radtools [2014, 17 Oct].
11. Gautier, M., K. Gharbi, T. Cezard, J. Foucaud, C. Kerdelhué, P. Pudlo, J. Cornuet, and A. Estoup. 2013. The effect of RAD allele dropout on the estimation of genetic variation within and between populations. Mol. Ecol. 22: 3165-3178.
12. Hess, J., N. Campbell, D. Close, M. Docker, and S. Narum. 2013. Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species. Mol. Ecol. 22: 2898-2916.
13. Hohenlohe, P. A., S. Bassham, M. Currey, and W. A. Cresko. 2012. Extensive linkage disequilibrium and parallel adaptive divergence across three spine stickleback genomes. Philos. Trans. R. Soc. B 367: 395-408.
14. Hohenlohe, P. A., M. D. Day, S. J. Amish, M. R. Miller, N. Kamps-Hughes, M. C. Boyer, C. C. Muhlfeld, F. W. Allendorf, E. A. Johnson, and G. Luikart. 2013. Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing. Mol. Ecol. 22: 3002-3013.
15. Kozarewa, I., Z. Ning, M. Quail, M. Sanders, M. Berriman, and D. Turner. 2009. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G_C)-biased genomes. Nat. Methods 6: 291-295.
16. Mamanova, L., R. Andrews, K. James, E. Sheridan, P. Ellis, C. Langford, T. Ost, J. Collins, and D. Turner. 2010. FRT-seq: Amplification-free, strand-specific, transcriptome sequencing. Nat. Methods 7: 130-132.
17. McCormack, J. E., S. M. Hird, A. J. Zellmer, B. C. Carstens, and R. T. Brumfield. 2013. Applications of next-generation sequencing to phylogeography and phylogenetics. Mol. Phylogenet. Evol. 66: 526-538.
18. Miller, M., J. Dunham, A. Amores, W. Cresko, and E. Johnson. 2007. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res. 17: 240-248.
19. Narum, S. R., C. A. Buerkle, J. W. Davey, M. R. Miller, and P. A. Hohenlohe. 2013. Genotyping-by-sequencing in ecological and conservation genomics. Mol. Ecol. 22: 2841-2847.
20. Peterson, B., J. Weber, E. Kay, H. Fisher, and H. Hoekstra. 2012. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 7: e37135.
21. R Core Team. 2013. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
22. Shannon, C. 1948. A mathematical theory of communication. Bell Syst. Tech. J. 27: 379-423, 623-656.
23. Skelly, D., M. Johansson, J. Madeoy, J. Wakefield, and J. Akey. 2011. A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data. Genome Res. 21: 1728-1737.
24. Sunnucks, P., and D. Hales. 1996. Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae). Mol. Biol. Evol. 13: 510-524.
25. Toonen, R., J. Puritz, Z. Forsman, J. Whitney, I. Fernandez-Silva, K. Andrews, and C. Bird. 2013. ezRAD: a simplified method for genomic genotyping in non-model organisms. PeerJ 1: e203.
26. Wang, S., E. Meyer, J. McKay, and M. Matz. 2012. 2b-RAD: a simple and flexible method for genome-wide genotyping. Nat. Methods 9: 808-810.
27. Watkins, N., and J. SantaLucia. 2005. Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes. Nucleic Acids Res. 33: 6258-6267.