RAD/Paired-end RAD-Seq/ddRAD-Seq
RAD/Paired-end RAD-Seq/ddRAD-Seq
Restriction-site associated DNA (RAD/Paired-end RAD-Seq or ddRADseq) sequencing is a protocol used for SNP discovery and genotyping. In this method, genomic DNA is first digested with restriction enzymes, next barcoded adapters are added, DNA sheared, amplified and sequenced. Deep sequencing allows accurate SNP discovery and genotyping.
- RAD-Seq:Baird N. A., Etter P. D., Atwood T. S., Currey M. C., Shiver A. L., et al. (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3: e3376
- Paired end RAD-Seq: Willing E. M., Hoffmann M., Klein J. D., Weigel D. and Dreyer C. (2011) Paired-end RAD-seq for de novo assembly and marker design without available reference. Bioinformatics 27: 2187-2193
- Combosch D. J. and Vollmer S. V. (2015) Trans-Pacific RAD-Seq population genomics confirms introgressive hybridization in Eastern Pacific Pocillopora corals. Mol Phylogenet Evol 88: 154-162
- DaCosta J. M. and Sorenson M. D. (2015) ddRAD-seq phylogenetics based on nucleotide, indel, and presence-absence polymorphisms: Analyses of two avian genera with contrasting histories. Mol Phylogenet Evol 94: 122-135
- Demos T. C., Kerbis Peterhans J. C., Joseph T. A., Robinson J. D., Agwanda B., et al. (2015) Comparative Population Genomics of African Montane Forest Mammals Support Population Persistence across a Climatic Gradient and Quaternary Climatic Cycles. PLoS One 10: e0131800
- Guo B., DeFaveri J., Sotelo G., Nair A. and Merila J. (2015) Population genomic evidence for adaptive differentiation in Baltic Sea three-spined sticklebacks. BMC Biol 13: 19
- Liu S., Clark L. V., Swaminathan K., Gifford J. M., Juvik J. A., et al. (2015) High-density genetic map of Miscanthus sinensis reveals inheritance of zebra stripe. GCB Bioenergy n/a-n/a
- Longo G. and Bernardi G. (2015) The evolutionary history of the embiotocid surfperch radiation based on genome-wide RAD sequence data. Mol Phylogenet Evol 88: 55-63
- Mathers T. C., Hammond R. L., Jenner R. A., Hanfling B., Atkins J., et al. (2015) Transition in sexual system and sex chromosome evolution in the tadpole shrimp Triops cancriformis. Heredity (Edinb) 115: 37-46
- Marubodee R., Ogiso-Tanaka E., Isemura T., Chankaew S., Kaga A., et al. (2015) Construction of an SSR and RAD-Marker Based Molecular Linkage Map of Vigna vexillata (L.) A. Rich. PLoS One 10: e0138942
- Shao C., Niu Y., Rastas P., Liu Y., Xie Z., et al. (2015) Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis. DNA Res 22: 161-170
- Takahashi T. and Moreno E. (2015) A RAD-based phylogenetics for Orestias fishes from Lake Titicaca. Mol Phylogenet Evol 93: 307-317
- Tennessen J. A., Bonner K. M., Bollmann S. R., Johnstun J. A., Yeh J. Y., et al. (2015) Genome-Wide Scan and Test of Candidate Genes in the Snail Biomphalaria glabrata Reveal New Locus Influencing Resistance to Schistosoma mansoni. PLoS Negl Trop Dis 9: e0004077
- Yu S., Chu W., Zhang L., Han H., Zhao R., et al. (2015) Identification of Laying-Related SNP Markers in Geese Using RAD Sequencing. PLoS One 10: e0131572
- Zhou Z., Liu S., Dong Y., Gao S., Chen Z., et al. (2015) High-Density Genetic Mapping with Interspecific Hybrids of Two Sea Urchins, Strongylocentrotus nudus and S. intermedius, by RAD Sequencing. PLoS One 10: e0138585