Double Digest Restriction-Site Associated DNA Sequencing (ddRAD-Seq).

Zenaida V Magbanua, Chuan-Yu Hsu, Olga Pechanova, Mark Arick, Daniel G Peterson

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it

0cells of the map it votes in

0citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Zenaida V MagbanuaInstitute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS, USA. zvm2@msstate.edu.

Chuan-Yu HsuInstitute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS, USA.

Olga PechanovaInstitute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS, USA.

Mark ArickInstitute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS, USA.

Daniel G PetersonInstitute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

ddRAD-Seq is a reduced representation sequencing technique that results in sequence datasets that can be compared and used to identify SNPs. We present an improved ddRAD-Seq protocol that increases efficiency and decreases the time to complete a ddRAD-Seq experiment. It utilizes selected restriction enzyme digestion fragments, quick acting ligases that are neutral with the restriction enzyme buffer eliminating buffer exchange steps, and adapters designed to be compatible with Illumina index primers. Enzyme deactivation steps are eliminated, library amplification and barcoding are completed in one PCR step, highly-efficient and precise size selection with BluePippin system and cleanup steps using magnetic beads are consolidated at the end of the library generation step. The SNPs that we identified using this streamlined protocol were validated in population and evolutionary studies of cotton (plant) (Magbanua et al., Anal Biochem 662:115001, https://doi.org/10.1016/j.ab.2022.115001 , 2023) and rohu carp (animal) (Arick et al., G3 (Bethesda) 13, https://doi.org/10.1093/g3journal/jkad009 , 2023).

Indexed as

High-Throughput Nucleotide SequencingSequence Analysis, DNAAnimalsDNA Restriction EnzymesGene LibraryGossypiumPolymerase Chain ReactionPolymorphism, Single NucleotideDNA Restriction EnzymesNext-generation sequencingReduced genome representationRestriction enzyme digestionSNP identification

Identifiers

PMID40580296

DOI10.1038/nrg.2015.28

What OpenQuestion holds

Textmetadata

Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.