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Evaluation of ddRADseq for reduced representation metagenome sequencing
Michael Y Liu1, Paul Worden1, Leigh G Monahan1
1The ithree institute, University of Technology Sydney, Sydney, New South Wales, Australia.
Peerj
|September 27, 2017
Summary
This study introduces a metagenomic adaptation of double digest restriction site associated DNA sequencing (ddRADseq) for microbial community profiling. The method provides a feasible alternative to shotgun sequencing, with minimal bias for metagenome-wide association studies.
Area of Science:
- Microbiology
- Genomics
- Bioinformatics
Background:
- Metagenomic shotgun sequencing offers deep insights into microbial community structure and function.
- Reduced representation metagenome profiling is an emerging area of study.
Purpose of the Study:
- To describe a novel method for reduced representation metagenome profiling using a metagenomic adaptation of the double digest restriction site associated DNA sequencing (ddRADseq) protocol.
- To assess the performance and potential biases of this metagenomic ddRADseq approach.
Main Methods:
- Developed a ddRADseq library preparation method utilizing restriction endonuclease specificity for targeted DNA fragment selection.
- Applied the metagenomic ddRADseq protocol to human stool samples and generated sequencing data.
- Compared taxonomic profiles derived from ddRADseq with those from shotgun metagenomic sequencing.
Main Results:
- Metagenomic ddRADseq yielded taxonomic profiles comparable to shotgun metagenomic sequencing.
- No significant bias was detected concerning genomic G+C content or estimated relative species abundance.
- The ddRADseq method demonstrated feasibility in profiling microbial communities.
Conclusions:
- Metagenomic ddRADseq is a viable tool for reduced representation metagenome profiling.
- While some bias exists, it is likely less significant than DNA extraction bias.
- The approach holds potential for application in metagenome-wide association studies.
