Tag Archives: ddRADseq

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

Posted on February 1, 2023 by Alex

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 »

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Optimising ddRAD sequencing for population genomic studies with ddgRADer

Posted on November 14, 2022 by Alex

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 »

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Decimated little brown bats show potential for adaptive change

Posted on April 9, 2020 by Alex

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 »

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Museum epigenomics: characterizing cytosine methylation in historic museum specimens

Posted on May 15, 2019 by Alex

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 »

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

Posted on November 27, 2017 by Alex

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 »

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ddRAD-seq Study Explores Behavioral Roles in Speciation

Posted on July 25, 2017 by Alex

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 »

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

Posted on May 25, 2017 by Alex

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 »

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

Posted on March 25, 2017 by Alex

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 »

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

Posted on March 25, 2017 by Alex

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 »

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

Posted on February 25, 2017 by Alex

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 »

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