Natural history bycatch: a pipeline for identifying metagenomic sequences in RADseq data

Area of Science:

• Genomics
• Bioinformatics
• Ecology

Background:

• Reduced representation genomic datasets, like RADseq, are increasingly common.
• These datasets may contain unintended sequences from parasites and microbes.
• Tissue collections can house diverse metagenomic communities.

Purpose of the Study:

• To demonstrate RADseq datasets are suitable for exploratory metagenomic analysis.
• To show tissue collections preserve complete metagenomic communities.

Main Methods:

• Utilized the pyRAD assembly pipeline, NCBI's blastn, and R scripts.
• Developed an exploratory method for mining metagenomic "bycatch" from RADseq data.
• Analyzed sequences from host tissue and hind-gut samples.

Main Results:

• 3-5% of identifiable double-digest restriction site associated DNA (ddRAD) sequences from host tissues were from parasite phyla.
• Sequences from snake and lizard hind-gut samples matched expected bacterial and eukaryotic microbiome phyla.
• Demonstrated RADseq's utility in identifying metagenomic communities.

Conclusions:

• Museum tissue banks preserve valuable parasite and microbiome data.
• Publicly available RADseq datasets offer opportunities for metagenomic exploration.
• Restriction site approaches are effective for identifying microbiome lineages, complementing primer-based methods.