ddRADseq
Double Digest Restriction-Site Associated DNA Marker Generation
ddRADseq (Peterson et al., 2012), also called ddRAD, is a variation on the RAD sequencing protocol (Baird et al., 2008), which is used for SNP discovery and genotyping (Baird et al., 2008) (Willing et al., 2011). In this variation, the fragment shearing is replaced with a second restriction digestion to improve the tunability and accuracy of the size-selection step. The protocol also includes a second index to allow combinatorial indexing. Several RAD variations, such as 2b-RAD (Wang et al., 2012), SLAF-seq (Sun et al., 2013), and hyRAD (Suchan et al., 2016), have been developed to address specific applications, and multiple software packages are available to analyze RAD data (Fan et al., 2016) (Catchen et al., 2013).
In this method, gDNA is first digested with a restriction enzyme, and a barcoded P1 adapter is ligated to the fragments. The adapter-ligated fragments from different samples are combined, if samples are multiplexed, and the DNA is digested by a second restriction enzyme. The fragments are size-selected and purified. The P2 adapter-primers are ligated, and the fragments are amplified to produce the sequencing library.
Advantages:
- No reference genome required (Reitzel et al., 2013)
- Relatively inexpensive, compared to whole-genome sequencing
- The degree of genome coverage can be adjusted by selecting various restriction enzymes
Disadvantages:
- There can be gaps in the genome coverage
- Requires high-quality DNA (see hyRAD for low-quality DNA) (Suchan et al., 2016)
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
Andrews K. R., Good J. M., Miller M. R., Luikart G. and Hohenlohe P. A. Harnessing the power of RADseq for ecological and evolutionary genomics. Nat Rev Genet. 2016;17:81-92
Kagale S., Koh C., Clarke W. E., Bollina V., Parkin I. A., et al. Analysis of Genotyping-by-Sequencing (GBS) Data. Methods Mol Biol. 2016;1374:269-284
References:
DaCosta J. M. and Sorenson M. D. ddRAD-seq phylogenetics based on nucleotide, indel, and presence-absence polymorphisms: Analyses of two avian genera with contrasting histories. Mol Phylogenet Evol. 2016;94:122-135
Lal M. M., Southgate P. C., Jerry D. R. and Zenger K. R. Fishing for divergence in a sea of connectivity: The utility of ddRADseq genotyping in a marine invertebrate, the black-lip pearl oyster Pinctada margaritifera. Mar Genomics. 2016;25:57-68
Brown J. K., Taggart J. B., Bekaert M., et al. Mapping the sex determination locus in the hapuku (Polyprion oxygeneios) using ddRAD sequencing. BMC Genomics. 2016;17:448
Clark L. V. and Sacks E. J. TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data. Source Code Biol Med. 2016;11:11
Hou Y., Nowak M. D., Mirre V., Bjora C. S., Brochmann C. and Popp M. RAD-seq data point to a northern origin of the arctic-alpine genus Cassiope (Ericaceae). Mol Phylogenet Evol. 2016;95:152-160
Shirasawa K., Hirakawa H. and Isobe S. Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical and in silico optimization in tomato. DNA Res. 2016;23:145-153
Wu Z., Wang B., Chen X., et al. Evaluation of Linkage Disequilibrium Pattern and Association Study on Seed Oil Content in Brassica napus Using ddRAD Sequencing. PLoS One. 2016;11:e0146383
Yang G. Q., Chen Y. M., Wang J. P., et al. Development of a universal and simplified ddRAD library preparation approach for SNP discovery and genotyping in angiosperm plants. Plant Methods. 2016;12:39
Cai G., Yang Q., Yi B., et al. A bi-filtering method for processing single nucleotide polymorphism array data improves the quality of genetic map and accuracy of quantitative trait locus mapping in doubled haploid populations of polyploid Brassica napus. BMC Genomics. 2015;16:409
Davik J., Sargent D. J., Brurberg M. B., Lien S., Kent M. and Alsheikh M. A ddRAD Based Linkage Map of the Cultivated Strawberry, Fragaria xananassa. PLoS One. 2015;10:e0137746
Leache A. D., Banbury B. L., Felsenstein J., de Oca A. N. and Stamatakis A. Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies. Syst Biol. 2015;64:1032-1047
Leache A. D., Chavez A. S., Jones L. N., Grummer J. A., Gottscho A. D. and Linkem C. W. Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing. Genome Biol Evol. 2015;7:706-719
Meik J. M., Streicher J. W., Lawing A. M., Flores-Villela O. and Fujita M. K. Limitations of climatic data for inferring species boundaries: insights from speckled rattlesnakes. PLoS One. 2015;10:e0131435
Related
History: ddRADseq
Revision by sbrumpton on 2017-06-21 07:50:21 - Show/Hide
Double Digest Restriction-Site Associated DNA Marker Generation
ddRADseq (Peterson et al., 2012), also called ddRAD, is a variation on the RAD sequencing protocol (Baird et al., 2008), which is used for SNP discovery and genotyping (Baird et al., 2008) (Willing et al., 2011). In this variation, the fragment shearing is replaced with a second restriction digestion to improve the tunability and accuracy of the size-selection step. The protocol also includes a second index to allow combinatorial indexing. Several RAD variations, such as 2b-RAD (Wang et al., 2012), SLAF-seq (Sun et al., 2013), and hyRAD (Suchan et al., 2016), have been developed to address specific applications, and multiple software packages are available to analyze RAD data (Fan et al., 2016) (Catchen et al., 2013).
In this method, gDNA is first digested with a restriction enzyme, and a barcoded P1 adapter is ligated to the fragments. The adapter-ligated fragments from different samples are combined, if samples are multiplexed, and the DNA is digested by a second restriction enzyme. The fragments are size-selected and purified. The P2 adapter-primers are ligated, and the fragments are amplified to produce the sequencing library.
Advantages:- No reference genome required (Reitzel et al., 2013)
- Relatively inexpensive, compared to whole-genome sequencing
- The degree of genome coverage can be adjusted by selecting various restriction enzymes
Disadvantages:- There can be gaps in the genome coverage
- Requires high-quality DNA (see hyRAD for low-quality DNA) (Suchan et al., 2016)
Reagents:Illumina Library prep and Array Kit SelectorReviews:Andrews K. R., Good J. M., Miller M. R., Luikart G. and Hohenlohe P. A. Harnessing the power of RADseq for ecological and evolutionary genomics. Nat Rev Genet. 2016;17:81-92Kagale S., Koh C., Clarke W. E., Bollina V., Parkin I. A., et al. Analysis of Genotyping-by-Sequencing (GBS) Data. Methods Mol Biol. 2016;1374:269-284References:DaCosta J. M. and Sorenson M. D. ddRAD-seq phylogenetics based on nucleotide, indel, and presence-absence polymorphisms: Analyses of two avian genera with contrasting histories. Mol Phylogenet Evol. 2016;94:122-135Lal M. M., Southgate P. C., Jerry D. R. and Zenger K. R. Fishing for divergence in a sea of connectivity: The utility of ddRADseq genotyping in a marine invertebrate, the black-lip pearl oyster Pinctada margaritifera. Mar Genomics. 2016;25:57-68Brown J. K., Taggart J. B., Bekaert M., et al. Mapping the sex determination locus in the hapuku (Polyprion oxygeneios) using ddRAD sequencing. BMC Genomics. 2016;17:448Clark L. V. and Sacks E. J. TagDigger: user-friendly extraction of read counts from GBS and RAD-seq data. Source Code Biol Med. 2016;11:11Hou Y., Nowak M. D., Mirre V., Bjora C. S., Brochmann C. and Popp M. RAD-seq data point to a northern origin of the arctic-alpine genus Cassiope (Ericaceae). Mol Phylogenet Evol. 2016;95:152-160Shirasawa K., Hirakawa H. and Isobe S. Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical and in silico optimization in tomato. DNA Res. 2016;23:145-153Wu Z., Wang B., Chen X., et al. Evaluation of Linkage Disequilibrium Pattern and Association Study on Seed Oil Content in Brassica napus Using ddRAD Sequencing. PLoS One. 2016;11:e0146383Yang G. Q., Chen Y. M., Wang J. P., et al. Development of a universal and simplified ddRAD library preparation approach for SNP discovery and genotyping in angiosperm plants. Plant Methods. 2016;12:39Cai G., Yang Q., Yi B., et al. A bi-filtering method for processing single nucleotide polymorphism array data improves the quality of genetic map and accuracy of quantitative trait locus mapping in doubled haploid populations of polyploid Brassica napus. BMC Genomics. 2015;16:409Davik J., Sargent D. J., Brurberg M. B., Lien S., Kent M. and Alsheikh M. A ddRAD Based Linkage Map of the Cultivated Strawberry, Fragaria xananassa. PLoS One. 2015;10:e0137746Leache A. D., Banbury B. L., Felsenstein J., de Oca A. N. and Stamatakis A. Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies. Syst Biol. 2015;64:1032-1047Leache A. D., Chavez A. S., Jones L. N., Grummer J. A., Gottscho A. D. and Linkem C. W. Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing. Genome Biol Evol. 2015;7:706-719Meik J. M., Streicher J. W., Lawing A. M., Flores-Villela O. and Fujita M. K. Limitations of climatic data for inferring species boundaries: insights from speckled rattlesnakes. PLoS One. 2015;10:e0131435