Evaluation of ddRADseq for reduced representation metagenome sequencing

Michael Y. Liu, Paul Worden, Leigh G. Monahan, Matthew Z. DeMaere, Catherine M. Burke, Steven P. Djordjevic, Ian G. Charles, Aaron E. Darling

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)
9 Downloads (Pure)


Background. Profiling of microbial communities via metagenomic shotgun sequenc- ing has enabled researches to gain unprecedented insight into microbial community structure and the functional roles of community members. This study describes a method and basic analysis for a metagenomic adaptation of the double digest restriction site associated DNA sequencing (ddRADseq) protocol for reduced representation metagenome profiling. Methods. This technique takes advantage of the sequence specificity of restriction endonucleases to construct an Illumina-compatible sequencing library containingDNA fragments that are between a pair of restriction sites located within close proximity. This results in a reduced sequencing library with coverage breadth that can be tuned by size selection. We assessed the performance of the metagenomic ddRADseq approach by applying the full method to human stool samples and generating sequence data. Results. The ddRADseq data yields a similar estimate of community taxonomic profile as obtained from shotgun metagenome sequencing of the same human stool samples. No obvious bias with respect to genomic G + C content and the estimated relative species abundance was detected. Discussion. Although ddRADseq does introduce some bias in taxonomic representa- tion, the bias is likely to be small relative to DNA extraction bias. ddRADseq appears feasible and could have value as a tool for metagenome-wide association studies.

Original languageEnglish
Article number3837
Issue number9
Publication statusPublished - 19 Sep 2017
Externally publishedYes


  • ddRADseq
  • Double digest restriction site associated DNA sequencing
  • Human gut microbial communities
  • Metagenome-wide association studies

Cite this