Tag Archives: ddRADseq

Innovations in double digest restriction-site associated DNA sequencing (ddRAD-Seq) method for more efficient SNP identification

February 2023 Authors: Zenaida V.Magbanua, Chuan-YuHsu, OlgaPechanova, Mark Arick II, Corrinne E.Grover, Daniel G.Peterson Abstract: “We present an improved ddRAD-Seq protocol for identifying single nucleotide polymorphisms (SNPs). It utilizes selected restriction enzyme digestion fragments, quick acting ligases that are neutral … more »

Posted in Citation | Tagged , | Comments Off on Innovations in double digest restriction-site associated DNA sequencing (ddRAD-Seq) method for more efficient SNP identification

Optimising ddRAD sequencing for population genomic studies with ddgRADer

October 2022 Authors: Aparna Lajmi, Felix Glinka, Eyal Privman Info: In this preprint, the authors describe an online webtool that they have developed for designing ddRAD-seq experiments. This webtool assists in the recommendation of restriction enzyme pairs and size-selection criteria. … more »

Posted in Citation | Tagged , , | Comments Off on Optimising ddRAD sequencing for population genomic studies with ddgRADer

Decimated little brown bats show potential for adaptive change

April 2020 Authors: Giorgia G. Auteri & L. Lacey Knowles Info: Little brown bats have experienced a 90% population decline due to fungal pathogen that causes a disease, white-nose syndrome. The authors used ddRADseq to compare surviving and non-surviving individuals. … more »

Posted in Citation | Tagged , | Comments Off on Decimated little brown bats show potential for adaptive change

Museum epigenomics: characterizing cytosine methylation in historic museum specimens

April 2019 Authors: Tricia L. Rubi, L. Lacey Knowles, Ben Dantzer Info: In this preprint, researchers developed method the study epigenetic markers on historically preserved deer mouse specimens using ddRAD-seq and bisulfite sequencing. The oldest group of specimens was 76 … more »

Posted in Citation | Tagged , | Comments Off on Museum epigenomics: characterizing cytosine methylation in historic museum specimens

Preprint Roundup: Long-Read Sequencing, ddRAD-seq, and a New Look at Viruses

We always keep our eyes peeled for interesting new research from scientists using Sage Science automated DNA size selection instruments, and several recent preprints caught our attention. Here’s a look: Nanopore Sequencing Reveals High-Resolution Structural Variation in the Cancer Genome … more »

Posted in Blog | Tagged , , , | Comments Off on Preprint Roundup: Long-Read Sequencing, ddRAD-seq, and a New Look at Viruses

ddRAD-seq Study Explores Behavioral Roles in Speciation

A new preprint from the Hoekstra lab at Harvard makes great use of the double digest RAD-seq protocol to better understand reproductive barriers and speciation in closely related species of mice. Since it was the Hoekstra lab that gave us … more »

Posted in Blog | Tagged , | Comments Off on ddRAD-seq Study Explores Behavioral Roles in Speciation

quaddRAD: a new high-multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage

May 2017 Authors: Franchini P, Monné Parera D, Kautt AF, Meyer A Info: Scientists from the University of Konstanz modified the original ddRAD-seq protocol to make it faster, more cost-effective, and higher-capacity. They report results from validating the new method … more »

Posted in Citation | Tagged , , | Comments Off on quaddRAD: a new high-multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage

Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species

February 2017 Authors: Alison G. Nazareno, Jordan B. Bemmels, Christopher W. Dick, Lúcia G. Lohmann Info: Scientists in Michigan and São Paulo, Brazil, performed ddRAD-seq on two separate populations of Amphirrhox longifolia to determine how many SNPs and organisms have … more »

Posted in Citation | Tagged , | Comments Off on Minimum sample sizes for population genomics: an empirical study from an Amazonian plant species

Genetic diversity of Atlantic Bluefin tuna in the Mediterranean Sea: insights from genome-wide SNPs and microsatellites

February 2017 Authors: Aglaia Antoniou, Panagiotis Kasapidis, Georgios Kotoulas, Constantinos C. Mylonas and Antonios Magoulas Info: Scientists from the Hellenic Centre for Marine Research used ddRAD-seq to analyze genome-wide SNPs in the Atlantic Bluefin tuna, with the goal of understanding … more »

Posted in Citation | Tagged , | Comments Off on Genetic diversity of Atlantic Bluefin tuna in the Mediterranean Sea: insights from genome-wide SNPs and microsatellites

Whole Genome Amplification and Reduced-Representation Genome Sequencing of Schistosoma japonicum Miracidia

January 2017 Authors: Jonathan A. Shortt, Daren C. Card, Drew R. Schield, Yang Liu, Bo Zhong, Todd A. Castoe, Elizabeth J. Carlton, and David D. Pollock Info: Researchers used ddRAD-seq to study the schistosome species S. japonicum miracidia, finding that … more »

Posted in Citation | Tagged , , | Comments Off on Whole Genome Amplification and Reduced-Representation Genome Sequencing of Schistosoma japonicum Miracidia